Sender: LSF System <lsf@node1528>
Subject: Job 1120392: <iteration_181708> Done

Job <iteration_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1528>, 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/181708> was used as the working directory.
Started at Wed Oct 10 14:21:30 2012
Results reported at Wed Oct 10 14:21:32 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 ${return_code} > exited;
exit 1;
fi
/xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 181708 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/
return_code=$?
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/181708
rmdir iteration*
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :      0.76 sec.
    Max Memory :         3 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 181708 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/
Finished in 1 iterations
*** Scatter Gather stdandard out:
Sender: LSF System <lsf@node1725>
Subject: Job 1120388: <gather_181708> Done

Job <gather_181708> was submitted from host <node439> 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/181708/iteration1> was used as the working directory.
Started at Wed Oct 10 14:11:04 2012
Results reported at Wed Oct 10 14:21:28 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.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 0  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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   :    471.75 sec.
    Max Memory :      2159 MB
    Max Swap   :      3137 MB

    Max Processes  :         9
    Max Threads    :        72

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.165.3896/
-whichjob
0
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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 ./BLCA.mutation_filtering_report.txt
Writing coverage to ./BLCA.per_exon.coverage.txt
  [save_struct] 15/38 16/38 17/38 18/38 19/38 20/38 21/38 22/38 23/38 24/38 25/38 26/38 27/38 28/38 29/38 30/38 31/38 32/38 33/38 34/38 35/38 36/38 37/38 38/38  [collapse] [write]
Outputting gene_sample_coverage_table: ./BLCA.per_gene.coverage.txt
Outputting gene_sample_mutation_counts_table: ./BLCA.per_gene.mutation_counts.txt
Mutation breakdown by type

           Frame_Shift_Del: [98]
           Frame_Shift_Ins: [45]
              In_Frame_Del: [29]
              In_Frame_Ins: [5]
         Missense_Mutation: [4694]
         Nonsense_Mutation: [413]
          Nonstop_Mutation: [9]
                    Silent: [1816]
               Splice_Site: [116]
    Translation_Start_Site: [8]
                 ----TOTAL: [7233]
Finding number of unique sites, unique patients: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 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: ./BLCA.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.
29	ARFPATHWAY	2.228816e-05
127	FBW7PATHWAY	7.551736e-06
140	G1PATHWAY	2.835829e-05
448	P53PATHWAY	6.580105e-06
468	PLK3PATHWAY	1.505399e-06
469	PMLPATHWAY	2.981756e-09
493	RBPATHWAY	9.478987e-08
503	RNAPATHWAY	2.958992e-07
510	SA_G1_AND_S_PHASES	1.066774e-06
587	TERTPATHWAY	6.313173e-09
591	TIDPATHWAY	2.443301e-08
Done
Outputting significance table: ./BLCA.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.
Done
Outputting significance table: ./BLCA.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 1000/4520 2000/4520 3000/4520 4000/4520 
Loading refseq database...

Mutation coordinate error (line 193): Length of alternate bases must equal length of refence bases.
132527208	132527209	GG	GG	T
Mutation coordinate error (line 261): Length of alternate bases must equal length of refence bases.
139428760	139428761	GT	GT	A
Mutation coordinate error (line 362): Length of alternate bases must equal length of refence bases.
143159109	143159110	CC	CC	T
Mutation coordinate error (line 558): Length of alternate bases must equal length of refence bases.
168807914	168807915	TC	TC	A
Mutation coordinate error (line 958): Length of alternate bases must equal length of refence bases.
27003913	27003914	CC	CC	A
Mutation coordinate error (line 1130): Length of alternate bases must equal length of refence bases.
51524156	51524157	TC	TC	C
Mutation coordinate error (line 1405): Length of alternate bases must equal length of refence bases.
49030735	49030736	CC	CC	T
Mutation coordinate error (line 1429): Length of alternate bases must equal length of refence bases.
113161719	113161720	CC	CC	A
Mutation coordinate error (line 1434): Length of alternate bases must equal length of refence bases.
152285219	152285220	GG	GG	C
Mutation coordinate error (line 1440): Length of alternate bases must equal length of refence bases.
156845891	156845892	CC	CC	A
Mutation coordinate error (line 1501): Length of alternate bases must equal length of refence bases.
155505643	155505644	CC	CC	A
Mutation coordinate error (line 1515): Length of alternate bases must equal length of refence bases.
29640795	29640796	GG	GG	C
Mutation coordinate error (line 1518): Length of alternate bases must equal length of refence bases.
36291124	36291125	TG	TG	C
Mutation coordinate error (line 1540): Length of alternate bases must equal length of refence bases.
107718630	107718631	GA	GA	T
Mutation coordinate error (line 1547): Length of alternate bases must equal length of refence bases.
7608067	7608068	GG	GG	T
Mutation coordinate error (line 1696): Length of alternate bases must equal length of refence bases.
205902176	205902177	CC	CC	A
Mutation coordinate error (line 1786): Length of alternate bases must equal length of refence bases.
68937670	68937671	GG	GG	A
Mutation coordinate error (line 1822): Length of alternate bases must equal length of refence bases.
44352248	44352249	GG	GG	T
Mutation coordinate error (line 1827): Length of alternate bases must equal length of refence bases.
54632680	54632681	GG	GG	C
Mutation coordinate error (line 2066): Length of alternate bases must equal length of refence bases.
176903363	176903364	CC	CC	T
Mutation coordinate error (line 2351): Length of alternate bases must equal length of refence bases.
62393546	62393547	GG	GG	A
Mutation coordinate error (line 2769): Length of alternate bases must equal length of refence bases.
36889754	36889755	GG	GG	A
Mutation coordinate error (line 2910): Length of alternate bases must equal length of refence bases.
48698816	48698817	TC	TC	A
Mutation coordinate error (line 3782): Length of alternate bases must equal length of refence bases.
77242312	77242313	GC	GC	A
Mutation coordinate error (line 3804): Length of alternate bases must equal length of refence bases.
7577121	7577122	GC	GC	T
Mutation coordinate error (line 3874): Length of alternate bases must equal length of refence bases.
101704696	101704697	CA	CA	A
Mutation coordinate error (line 3878): Length of alternate bases must equal length of refence bases.
158670235	158670236	CC	CC	A
Mutation coordinate error (line 3969): Length of alternate bases must equal length of refence bases.
28421740	28421741	CC	CC	A
Mutation coordinate error (line 3981): Length of alternate bases must equal length of refence bases.
61935121	61935122	CC	CC	A
Mutation coordinate error (line 4149): Length of alternate bases must equal length of refence bases.
100868687	100868688	GG	GG	T
Mutation coordinate error (line 4166): Length of alternate bases must equal length of refence bases.
6554303	6554304	CC	CC	A
Mutation coordinate error (line 4176): Length of alternate bases must equal length of refence bases.
37838794	37838795	CT	CT	G
Mutation coordinate error (line 4190): Length of alternate bases must equal length of refence bases.
9271246	9271247	GA	GA	T
Mutation coordinate error (line 4242): Length of alternate bases must equal length of refence bases.
67411832	67411833	GG	GG	T
Mutation coordinate error (line 4319): Length of alternate bases must equal length of refence bases.
113417182	113417183	GT	GT	T
Mutation coordinate error (line 4356): Length of alternate bases must equal length of refence bases.
73004392	73004393	GA	GA	C
Mutation coordinate error (line 4530): Length of alternate bases must equal length of refence bases.
4928820	4928821	CC	CC	T
Mutation coordinate error (line 4680): Length of alternate bases must equal length of refence bases.
47428979	47428980	CC	CC	A

Error in maflite format!  The faulty lines displayed above will not be included in output.
Ignoring the mutations listed above.
Analyzing clustered mutations
Problem with re-annotating mutations in gene A2M: skipping.
Problem with re-annotating mutations in gene ABCA10: skipping.
Problem with re-annotating mutations in gene ABCA13: skipping.
Problem with re-annotating mutations in gene ABCA8: skipping.
Problem with re-annotating mutations in gene ABCC11: skipping.
Problem with re-annotating mutations in gene ABCC9: skipping.
Problem with re-annotating mutations in gene ACE: skipping.
Problem with re-annotating mutations in gene ACHE: skipping.
Problem with re-annotating mutations in gene ACN9: skipping.
Problem with re-annotating mutations in gene ACTA2: skipping.
Problem with re-annotating mutations in gene ACTN4: skipping.
Problem with re-annotating mutations in gene ADAMTS12: skipping.
Problem with re-annotating mutations in gene ADAMTS14: skipping.
Problem with re-annotating mutations in gene ADCY2: skipping.
Problem with re-annotating mutations in gene ADHFE1: skipping.
Problem with re-annotating mutations in gene AFF1: skipping.
Problem with re-annotating mutations in gene AFF3: skipping.
Problem with re-annotating mutations in gene AGFG2: skipping.
Problem with re-annotating mutations in gene AHCTF1: skipping.
Problem with re-annotating mutations in gene AHNAK: skipping.
Problem with re-annotating mutations in gene AHNAK2: skipping.
Problem with re-annotating mutations in gene AHR: skipping.
100/4047 Problem with re-annotating mutations in gene AIFM2: skipping.
Problem with re-annotating mutations in gene AKAP6: skipping.
Problem with re-annotating mutations in gene AKAP9: skipping.
Problem with re-annotating mutations in gene AKD1: skipping.
Problem with re-annotating mutations in gene ALMS1: skipping.
Problem with re-annotating mutations in gene AMACR: skipping.
Problem with re-annotating mutations in gene AMOTL1: skipping.
Problem with re-annotating mutations in gene ANK1: skipping.
Problem with re-annotating mutations in gene ANK2: skipping.
Problem with re-annotating mutations in gene ANKAR: skipping.
Problem with re-annotating mutations in gene ANKHD1-EIF4EBP3: skipping.
Problem with re-annotating mutations in gene ANKLE2: skipping.
Problem with re-annotating mutations in gene ANKRD12: skipping.
Problem with re-annotating mutations in gene ANKRD26: skipping.
Problem with re-annotating mutations in gene ANKRD27: skipping.
Problem with re-annotating mutations in gene ANKRD30A: skipping.
Problem with re-annotating mutations in gene ANPEP: skipping.
Problem with re-annotating mutations in gene APH1A: skipping.
Problem with re-annotating mutations in gene APOB: skipping.
Problem with re-annotating mutations in gene APPL2: skipping.
Problem with re-annotating mutations in gene ARHGAP30: skipping.
200/4047 Problem with re-annotating mutations in gene ARHGAP32: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene ARHGAP36: skipping.
Problem with re-annotating mutations in gene ARHGAP39: skipping.
Problem with re-annotating mutations in gene ARHGAP5: skipping.
Problem with re-annotating mutations in gene ARHGEF11: skipping.
Problem with re-annotating mutations in gene ARID1A: skipping.
Problem with re-annotating mutations in gene ARID1B: skipping.
Problem with re-annotating mutations in gene ARID5A: skipping.
Problem with re-annotating mutations in gene ARID5B: skipping.
Problem with re-annotating mutations in gene ARL13B: skipping.
Problem with re-annotating mutations in gene ARMC3: skipping.
Problem with re-annotating mutations in gene ARMC4: skipping.
Problem with re-annotating mutations in gene ARMC9: skipping.
Problem with re-annotating mutations in gene ARVCF: skipping.
Problem with re-annotating mutations in gene ASCC3: skipping.
Problem with re-annotating mutations in gene ASH1L: skipping.
Problem with re-annotating mutations in gene ASPM: skipping.
Problem with re-annotating mutations in gene ASXL2: skipping.
Problem with re-annotating mutations in gene ATAD2: skipping.
Problem with re-annotating mutations in gene ATG2A: skipping.
Problem with re-annotating mutations in gene ATG4D: skipping.
Problem with re-annotating mutations in gene ATM: skipping.
Problem with re-annotating mutations in gene ATP10A: skipping.
Problem with re-annotating mutations in gene ATP2A1: skipping.
Problem with re-annotating mutations in gene ATP2B2: skipping.
Problem with re-annotating mutations in gene ATP2B4: skipping.
Problem with re-annotating mutations in gene ATP6V0A1: skipping.
Problem with re-annotating mutations in gene ATP8B3: skipping.
Problem with re-annotating mutations in gene ATR: skipping.
Problem with re-annotating mutations in gene ATRNL1: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene ATRX: skipping.
Problem with re-annotating mutations in gene ATXN7: skipping.
Problem with re-annotating mutations in gene AXIN1: skipping.
Problem with re-annotating mutations in gene AZI1: skipping.
Problem with re-annotating mutations in gene B3GALT4: skipping.
300/4047 Problem with re-annotating mutations in gene BAG5: skipping.
Problem with re-annotating mutations in gene BAIAP3: skipping.
Problem with re-annotating mutations in gene BAP1: skipping.
Problem with re-annotating mutations in gene BAT1: skipping.
Problem with re-annotating mutations in gene BAZ2A: skipping.
Problem with re-annotating mutations in gene BCLAF1: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene BCORL1: skipping.
Problem with re-annotating mutations in gene BEST1: skipping.
Problem with re-annotating mutations in gene BIRC6: skipping.
Problem with re-annotating mutations in gene BMPER: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene BMX: skipping.
Problem with re-annotating mutations in gene BNC2: skipping.
Problem with re-annotating mutations in gene BRCA2: skipping.
Problem with re-annotating mutations in gene BRDT: skipping.
Problem with re-annotating mutations in gene BRF1: skipping.
Problem with re-annotating mutations in gene BRIP1: skipping.
Problem with re-annotating mutations in gene BRWD1: skipping.
Problem with re-annotating mutations in gene BTN2A1: skipping.
Problem with re-annotating mutations in gene BUB1B: skipping.
Problem with re-annotating mutations in gene C10orf79: skipping.
400/4047 Problem with re-annotating mutations in gene C11orf85: skipping.
Problem with re-annotating mutations in gene C12orf11: skipping.
Problem with re-annotating mutations in gene C12orf35: skipping.
Problem with re-annotating mutations in gene C12orf51: skipping.
Problem with re-annotating mutations in gene C12orf74: skipping.
Problem with re-annotating mutations in gene C14orf43: skipping.
Problem with re-annotating mutations in gene C15orf42: skipping.
Problem with re-annotating mutations in gene C15orf44: skipping.
Problem with re-annotating mutations in gene C16orf62: skipping.
Problem with re-annotating mutations in gene C17orf62: skipping.
Problem with re-annotating mutations in gene C17orf81: skipping.
Problem with re-annotating mutations in gene C19orf28: skipping.
Problem with re-annotating mutations in gene C19orf44: skipping.
Problem with re-annotating mutations in gene C1orf107: skipping.
Problem with re-annotating mutations in gene C1orf158: skipping.
Problem with re-annotating mutations in gene C1orf168: skipping.
Problem with re-annotating mutations in gene C1orf51: skipping.
Problem with re-annotating mutations in gene C20orf20: skipping.
Problem with re-annotating mutations in gene C3orf26: skipping.
Problem with re-annotating mutations in gene C3orf37: skipping.
500/4047 Problem with re-annotating mutations in gene C5orf42: skipping.
Problem with re-annotating mutations in gene C6orf174: skipping.
Problem with re-annotating mutations in gene C6orf223: skipping.
Problem with re-annotating mutations in gene C7orf36: skipping.
Problem with re-annotating mutations in gene C8orf42: skipping.
Problem with re-annotating mutations in gene C9orf41: skipping.
Problem with re-annotating mutations in gene CABC1: skipping.
Problem with re-annotating mutations in gene CACNA1B: skipping.
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene CACNA1F: skipping.
Problem with re-annotating mutations in gene CACNA2D3: skipping.
Problem with re-annotating mutations in gene CADPS: skipping.
Problem with re-annotating mutations in gene CAMK2G: skipping.
Problem with re-annotating mutations in gene CAMKK2: skipping.
Problem with re-annotating mutations in gene CAMTA1: skipping.
Problem with re-annotating mutations in gene CAMTA2: skipping.
Problem with re-annotating mutations in gene CASC4: skipping.
Problem with re-annotating mutations in gene CASKIN2: skipping.
Problem with re-annotating mutations in gene CASP8: skipping.
Problem with re-annotating mutations in gene CASP8AP2: skipping.
Problem with re-annotating mutations in gene CAT: skipping.
Problem with re-annotating mutations in gene CATSPERB: skipping.
Problem with re-annotating mutations in gene CCDC135: skipping.
Problem with re-annotating mutations in gene CCDC18: skipping.
Problem with re-annotating mutations in gene CCDC30: skipping.
Problem with re-annotating mutations in gene CCDC33: skipping.
Problem with re-annotating mutations in gene CCDC36: skipping.
600/4047 Problem with re-annotating mutations in gene CCDC86: skipping.
Problem with re-annotating mutations in gene CCR3: skipping.
Problem with re-annotating mutations in gene CD163: skipping.
Problem with re-annotating mutations in gene CD1D: skipping.
Problem with re-annotating mutations in gene CD200: skipping.
Problem with re-annotating mutations in gene CDAN1: skipping.
Problem with re-annotating mutations in gene CDH11: skipping.
Problem with re-annotating mutations in gene CDH22: skipping.
Problem with re-annotating mutations in gene CDK12: skipping.
Problem with re-annotating mutations in gene CDK13: skipping.
Problem with re-annotating mutations in gene CDKN1A: skipping.
Problem with re-annotating mutations in gene CELSR2: skipping.
Problem with re-annotating mutations in gene CEP350: skipping.
700/4047 Problem with re-annotating mutations in gene CEP72: skipping.
Problem with re-annotating mutations in gene CFH: skipping.
Problem with re-annotating mutations in gene CHD2: skipping.
Problem with re-annotating mutations in gene CHD4: skipping.
Problem with re-annotating mutations in gene CHD7: skipping.
Problem with re-annotating mutations in gene CHD8: skipping.
Problem with re-annotating mutations in gene CHERP: skipping.
Problem with re-annotating mutations in gene CHN2: skipping.
Problem with re-annotating mutations in gene CHRNB2: skipping.
Problem with re-annotating mutations in gene CHRNB3: skipping.
Problem with re-annotating mutations in gene CIZ1: skipping.
Problem with re-annotating mutations in gene CLCA1: skipping.
Problem with re-annotating mutations in gene CLUAP1: skipping.
Problem with re-annotating mutations in gene CNGB1: skipping.
Problem with re-annotating mutations in gene CNN3: skipping.
Problem with re-annotating mutations in gene CNNM3: skipping.
Problem with re-annotating mutations in gene CNOT3: skipping.
Problem with re-annotating mutations in gene CNST: skipping.
Problem with re-annotating mutations in gene CNTN1: skipping.
Problem with re-annotating mutations in gene CNTN6: skipping.
Problem with re-annotating mutations in gene COG2: skipping.
Problem with re-annotating mutations in gene COL12A1: skipping.
Problem with re-annotating mutations in gene COL19A1: skipping.
Problem with re-annotating mutations in gene COL24A1: skipping.
Problem with re-annotating mutations in gene COL27A1: skipping.
800/4047 Problem with re-annotating mutations in gene COL2A1: skipping.
Problem with re-annotating mutations in gene COL4A4: skipping.
Problem with re-annotating mutations in gene COL5A1: skipping.
Problem with re-annotating mutations in gene COL5A2: skipping.
Problem with re-annotating mutations in gene COL6A3: skipping.
Problem with re-annotating mutations in gene COL6A6: skipping.
Problem with re-annotating mutations in gene COL7A1: skipping.
Problem with re-annotating mutations in gene COL9A2: skipping.
Problem with re-annotating mutations in gene COMP: skipping.
Problem with re-annotating mutations in gene COPS4: skipping.
Problem with re-annotating mutations in gene CORO6: skipping.
Problem with re-annotating mutations in gene CPNE1: skipping.
Problem with re-annotating mutations in gene CRAT: skipping.
Problem with re-annotating mutations in gene CRB1: skipping.
Problem with re-annotating mutations in gene CREB3L3: skipping.
Problem with re-annotating mutations in gene CREBBP: skipping.
Problem with re-annotating mutations in gene CRIM1: skipping.
Problem with re-annotating mutations in gene CRNKL1: skipping.
Problem with re-annotating mutations in gene CSF1R: skipping.
Problem with re-annotating mutations in gene CSMD1: skipping.
Problem with re-annotating mutations in gene CSMD3: skipping.
Problem with re-annotating mutations in gene CSNK1E: skipping.
Problem with re-annotating mutations in gene CTAGE5: skipping.
Problem with re-annotating mutations in gene CTNNA2: skipping.
Problem with re-annotating mutations in gene CTNND2: skipping.
Problem with re-annotating mutations in gene CUBN: skipping.
Problem with re-annotating mutations in gene CUL1: skipping.
Problem with re-annotating mutations in gene CUL2: skipping.
Problem with re-annotating mutations in gene CUL9: skipping.
Problem with re-annotating mutations in gene CUX1: skipping.
900/4047 Problem with re-annotating mutations in gene CYP26A1: skipping.
Problem with re-annotating mutations in gene DAB1: skipping.
Problem with re-annotating mutations in gene DAGLB: skipping.
Problem with re-annotating mutations in gene DARS: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene DCAF12L1: skipping.
Problem with re-annotating mutations in gene DCC: skipping.
Problem with re-annotating mutations in gene DCHS1: skipping.
Problem with re-annotating mutations in gene DDHD2: skipping.
Problem with re-annotating mutations in gene DDX23: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene DDX53: skipping.
Problem with re-annotating mutations in gene DDX60: skipping.
Problem with re-annotating mutations in gene DEM1: skipping.
Problem with re-annotating mutations in gene DENND4A: skipping.
Problem with re-annotating mutations in gene DENND5B: skipping.
Problem with re-annotating mutations in gene DHX29: skipping.
Problem with re-annotating mutations in gene DHX9: skipping.
Problem with re-annotating mutations in gene DIP2B: skipping.
Problem with re-annotating mutations in gene DISP1: skipping.
Problem with re-annotating mutations in gene DLX3: skipping.
Problem with re-annotating mutations in gene DMBT1: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene DMD: skipping.
Problem with re-annotating mutations in gene DMXL2: skipping.
Problem with re-annotating mutations in gene DNAH11: skipping.
Problem with re-annotating mutations in gene DNAH3: skipping.
1000/4047 Problem with re-annotating mutations in gene DNAH5: skipping.
Problem with re-annotating mutations in gene DNAH8: skipping.
Problem with re-annotating mutations in gene DNAH9: skipping.
Problem with re-annotating mutations in gene DNAI2: skipping.
Problem with re-annotating mutations in gene DNAJC14: skipping.
Problem with re-annotating mutations in gene DNER: skipping.
Problem with re-annotating mutations in gene DNM1: skipping.
Problem with re-annotating mutations in gene DNM3: skipping.
Problem with re-annotating mutations in gene DOCK4: skipping.
Problem with re-annotating mutations in gene DOT1L: skipping.
Problem with re-annotating mutations in gene DRG2: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene DRP2: skipping.
Problem with re-annotating mutations in gene DSCAM: skipping.
Problem with re-annotating mutations in gene DSP: skipping.
Problem with re-annotating mutations in gene EAPP: skipping.
Problem with re-annotating mutations in gene ECE2: skipping.
Problem with re-annotating mutations in gene EDC4: skipping.
Problem with re-annotating mutations in gene EDEM1: skipping.
Problem with re-annotating mutations in gene EFCAB5: skipping.
Problem with re-annotating mutations in gene EIF3A: skipping.
Problem with re-annotating mutations in gene EIF3I: skipping.
Problem with re-annotating mutations in gene EIF4A3: skipping.
1100/4047 Problem with re-annotating mutations in gene EIF4G2: skipping.
Problem with re-annotating mutations in gene EIF4G3: skipping.
Problem with re-annotating mutations in gene ELF1: skipping.
Problem with re-annotating mutations in gene ELF3: skipping.
Problem with re-annotating mutations in gene EMILIN3: skipping.
Problem with re-annotating mutations in gene EP300: skipping.
Problem with re-annotating mutations in gene EPB41L1: skipping.
Problem with re-annotating mutations in gene EPHA1: skipping.
Problem with re-annotating mutations in gene EPRS: skipping.
Problem with re-annotating mutations in gene ERBB2: skipping.
Problem with re-annotating mutations in gene ERCC2: skipping.
Problem with re-annotating mutations in gene ERG: skipping.
Problem with re-annotating mutations in gene ESPL1: skipping.
Problem with re-annotating mutations in gene EVC2: skipping.
Problem with re-annotating mutations in gene EVL: skipping.
Problem with re-annotating mutations in gene EXT1: skipping.
Problem with re-annotating mutations in gene EZH1: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene F8: skipping.
1200/4047 Problem with re-annotating mutations in gene FAM166A: skipping.
Problem with re-annotating mutations in gene FAM171B: skipping.
Problem with re-annotating mutations in gene FAM178A: skipping.
Problem with re-annotating mutations in gene FAM179B: skipping.
Problem with re-annotating mutations in gene FAM193A: skipping.
Problem with re-annotating mutations in gene FAM21C: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene FAM47A: skipping.
Problem with re-annotating mutations in gene FAM57A: skipping.
Problem with re-annotating mutations in gene FAM5C: skipping.
Problem with re-annotating mutations in gene FAM63A: skipping.
Problem with re-annotating mutations in gene FAM83E: skipping.
Problem with re-annotating mutations in gene FANCA: skipping.
Problem with re-annotating mutations in gene FANCD2: skipping.
Problem with re-annotating mutations in gene FAT1: skipping.
Problem with re-annotating mutations in gene FAT3: skipping.
Problem with re-annotating mutations in gene FAT4: skipping.
Problem with re-annotating mutations in gene FBXL19: skipping.
Problem with re-annotating mutations in gene FBXO21: skipping.
Problem with re-annotating mutations in gene FBXO4: skipping.
Problem with re-annotating mutations in gene FBXO40: skipping.
Problem with re-annotating mutations in gene FBXO42: skipping.
Problem with re-annotating mutations in gene FBXW7: skipping.
Problem with re-annotating mutations in gene FER1L5: skipping.
Problem with re-annotating mutations in gene FEZ2: skipping.
Problem with re-annotating mutations in gene FGA: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene FGD1: skipping.
1300/4047 Problem with re-annotating mutations in gene FGF8: skipping.
Problem with re-annotating mutations in gene FGFR3: skipping.
Problem with re-annotating mutations in gene FHOD1: skipping.
Problem with re-annotating mutations in gene FIGN: skipping.
Problem with re-annotating mutations in gene FKBP5: skipping.
Problem with re-annotating mutations in gene FLG: skipping.
Problem with re-annotating mutations in gene FLG2: skipping.
Problem with re-annotating mutations in gene FMO3: skipping.
Problem with re-annotating mutations in gene FNBP4: skipping.
Problem with re-annotating mutations in gene FOLH1: skipping.
Problem with re-annotating mutations in gene FOXM1: skipping.
Problem with re-annotating mutations in gene FOXP2: skipping.
Problem with re-annotating mutations in gene FRAS1: skipping.
Problem with re-annotating mutations in gene FREM2: skipping.
Problem with re-annotating mutations in gene FRS2: skipping.
Problem with re-annotating mutations in gene G3BP2: skipping.
Problem with re-annotating mutations in gene GABRA6: skipping.
Problem with re-annotating mutations in gene GABRB2: skipping.
Problem with re-annotating mutations in gene GAD1: skipping.
Problem with re-annotating mutations in gene GALNT5: skipping.
1400/4047 Problem with re-annotating mutations in gene GARNL3: skipping.
Problem with re-annotating mutations in gene GATAD2B: skipping.
Problem with re-annotating mutations in gene GBF1: skipping.
Problem with re-annotating mutations in gene GCC2: skipping.
Problem with re-annotating mutations in gene GCN1L1: skipping.
Problem with re-annotating mutations in gene GFM1: skipping.
Problem with re-annotating mutations in gene GHDC: skipping.
Problem with re-annotating mutations in gene GIMAP5: skipping.
Problem with re-annotating mutations in gene GLIS1: skipping.
Problem with re-annotating mutations in gene GOLGB1: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene GPR112: skipping.
Problem with re-annotating mutations in gene GPR126: skipping.
Problem with re-annotating mutations in gene GPR155: skipping.
Problem with re-annotating mutations in gene GPR17: skipping.
Problem with re-annotating mutations in gene GPR180: skipping.
Problem with re-annotating mutations in gene GPR98: skipping.
1500/4047 Problem with re-annotating mutations in gene GPS2: skipping.
Problem with re-annotating mutations in gene GRIA4: skipping.
Problem with re-annotating mutations in gene GRM4: skipping.
Problem with re-annotating mutations in gene GRM7: skipping.
Problem with re-annotating mutations in gene GRN: skipping.
Problem with re-annotating mutations in gene GTF3C3: skipping.
Problem with re-annotating mutations in gene GUCY1A2: skipping.
Problem with re-annotating mutations in gene H1FX: skipping.
Problem with re-annotating mutations in gene HAS3: skipping.
Problem with re-annotating mutations in gene HAUS3: skipping.
Problem with re-annotating mutations in gene HCN1: skipping.
Problem with re-annotating mutations in gene HDAC4: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene HDAC6: skipping.
Problem with re-annotating mutations in gene HEATR5B: skipping.
Problem with re-annotating mutations in gene HECTD1: skipping.
Problem with re-annotating mutations in gene HEG1: skipping.
Problem with re-annotating mutations in gene HEPHL1: skipping.
Problem with re-annotating mutations in gene HERC1: skipping.
Problem with re-annotating mutations in gene HIP1R: skipping.
1600/4047 Problem with re-annotating mutations in gene HIVEP1: skipping.
Problem with re-annotating mutations in gene HJURP: skipping.
Problem with re-annotating mutations in gene HK1: skipping.
Problem with re-annotating mutations in gene HK3: skipping.
WARNING: unknown chromosome(s):
    'chr6_dbb_hap3'

Problem with re-annotating mutations in gene HLA-A: skipping.
Problem with re-annotating mutations in gene HMCN1: skipping.
Problem with re-annotating mutations in gene HMGB2: skipping.
Problem with re-annotating mutations in gene HNF4G: skipping.
Problem with re-annotating mutations in gene HOXB4: skipping.
Problem with re-annotating mutations in gene HPSE: skipping.
Problem with re-annotating mutations in gene HRH1: skipping.
Problem with re-annotating mutations in gene HRNR: skipping.
Problem with re-annotating mutations in gene HSD17B8: skipping.
Problem with re-annotating mutations in gene HSF1: skipping.
Problem with re-annotating mutations in gene HSP90AB1: skipping.
Problem with re-annotating mutations in gene HSP90B1: skipping.
Problem with re-annotating mutations in gene HYI: skipping.
Problem with re-annotating mutations in gene IDE: skipping.
Problem with re-annotating mutations in gene IFIH1: skipping.
Problem with re-annotating mutations in gene IGSF10: skipping.
Problem with re-annotating mutations in gene IKBKAP: skipping.
Problem with re-annotating mutations in gene IL17RC: skipping.
Problem with re-annotating mutations in gene IL18RAP: skipping.
Problem with re-annotating mutations in gene IL34: skipping.
1700/4047 Problem with re-annotating mutations in gene IMPG2: skipping.
Problem with re-annotating mutations in gene INF2: skipping.
Problem with re-annotating mutations in gene INO80: skipping.
Problem with re-annotating mutations in gene INO80D: skipping.
Problem with re-annotating mutations in gene INPP5F: skipping.
Problem with re-annotating mutations in gene INSR: skipping.
Problem with re-annotating mutations in gene INTS1: skipping.
Problem with re-annotating mutations in gene INTS9: skipping.
Problem with re-annotating mutations in gene IPO8: skipping.
Problem with re-annotating mutations in gene IQGAP3: skipping.
Problem with re-annotating mutations in gene ITGA11: skipping.
Problem with re-annotating mutations in gene ITGA4: skipping.
Problem with re-annotating mutations in gene ITGA8: skipping.
Problem with re-annotating mutations in gene ITGA9: skipping.
Problem with re-annotating mutations in gene ITSN1: skipping.
Problem with re-annotating mutations in gene KALRN: skipping.
Problem with re-annotating mutations in gene KAT2A: skipping.
Problem with re-annotating mutations in gene KBTBD6: skipping.
Problem with re-annotating mutations in gene KCNH7: skipping.
Problem with re-annotating mutations in gene KCNH8: skipping.
Problem with re-annotating mutations in gene KCNJ16: skipping.
Problem with re-annotating mutations in gene KCNK2: skipping.
1800/4047 Problem with re-annotating mutations in gene KDM2A: skipping.
Problem with re-annotating mutations in gene KDM3B: skipping.
Problem with re-annotating mutations in gene KDM5A: skipping.
Problem with re-annotating mutations in gene KDM5B: skipping.
convert_chr: assuming human for chrX/chrY
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene KDM6A: skipping.
Problem with re-annotating mutations in gene KEAP1: skipping.
Problem with re-annotating mutations in gene KIAA0100: skipping.
Problem with re-annotating mutations in gene KIAA0146: skipping.
Problem with re-annotating mutations in gene KIAA0182: skipping.
Problem with re-annotating mutations in gene KIAA0368: skipping.
Problem with re-annotating mutations in gene KIAA0564: skipping.
Problem with re-annotating mutations in gene KIAA0664: skipping.
Problem with re-annotating mutations in gene KIAA1033: skipping.
Problem with re-annotating mutations in gene KIAA1109: skipping.
Problem with re-annotating mutations in gene KIAA1468: skipping.
Problem with re-annotating mutations in gene KIAA1543: skipping.
Problem with re-annotating mutations in gene KIAA1632: skipping.
Problem with re-annotating mutations in gene KIAA1826: skipping.
Problem with re-annotating mutations in gene KIAA2018: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene KIAA2022: skipping.
Problem with re-annotating mutations in gene KIF13A: skipping.
Problem with re-annotating mutations in gene KIF15: skipping.
Problem with re-annotating mutations in gene KIF18A: skipping.
Problem with re-annotating mutations in gene KIF21A: skipping.
Problem with re-annotating mutations in gene KIRREL2: skipping.
Problem with re-annotating mutations in gene KLF5: skipping.
Problem with re-annotating mutations in gene KNTC1: skipping.
Problem with re-annotating mutations in gene KPNA1: skipping.
Problem with re-annotating mutations in gene KPNA2: skipping.
1900/4047 Problem with re-annotating mutations in gene KPNA3: skipping.
Problem with re-annotating mutations in gene KRTAP24-1: skipping.
Problem with re-annotating mutations in gene KRTAP4-9: skipping.
Problem with re-annotating mutations in gene LAMA2: skipping.
Problem with re-annotating mutations in gene LAMA3: skipping.
Problem with re-annotating mutations in gene LAMA5: skipping.
Problem with re-annotating mutations in gene LAMB2: skipping.
Problem with re-annotating mutations in gene LASP1: skipping.
Problem with re-annotating mutations in gene LATS1: skipping.
Problem with re-annotating mutations in gene LATS2: skipping.
Problem with re-annotating mutations in gene LAX1: skipping.
Problem with re-annotating mutations in gene LCT: skipping.
Problem with re-annotating mutations in gene LETMD1: skipping.
Problem with re-annotating mutations in gene LILRA2: skipping.
Problem with re-annotating mutations in gene LLGL2: skipping.
Problem with re-annotating mutations in gene LMOD2: skipping.
Problem with re-annotating mutations in gene LPHN2: skipping.
2000/4047 Problem with re-annotating mutations in gene LRIG3: skipping.
Problem with re-annotating mutations in gene LRP1: skipping.
Problem with re-annotating mutations in gene LRP1B: skipping.
Problem with re-annotating mutations in gene LRP2: skipping.
Problem with re-annotating mutations in gene LRRC6: skipping.
Problem with re-annotating mutations in gene LRRC7: skipping.
Problem with re-annotating mutations in gene LTBP2: skipping.
Problem with re-annotating mutations in gene MACF1: skipping.
Problem with re-annotating mutations in gene MAGI2: skipping.
Problem with re-annotating mutations in gene MALT1: skipping.
Problem with re-annotating mutations in gene MAP3K1: skipping.
Problem with re-annotating mutations in gene MAP3K5: skipping.
Problem with re-annotating mutations in gene MAP4K2: skipping.
Problem with re-annotating mutations in gene MAPK8: skipping.
Problem with re-annotating mutations in gene MAPK8IP3: skipping.
Problem with re-annotating mutations in gene MARCH6: skipping.
Problem with re-annotating mutations in gene MBD6: skipping.
Problem with re-annotating mutations in gene MBTPS1: skipping.
2100/4047 Problem with re-annotating mutations in gene MCM4: skipping.
Problem with re-annotating mutations in gene MCPH1: skipping.
Problem with re-annotating mutations in gene MDN1: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene MED12: skipping.
Problem with re-annotating mutations in gene MED13L: skipping.
Problem with re-annotating mutations in gene MEP1A: skipping.
Problem with re-annotating mutations in gene MERTK: skipping.
Problem with re-annotating mutations in gene MET: skipping.
Problem with re-annotating mutations in gene MGA: skipping.
Problem with re-annotating mutations in gene MICAL1: skipping.
Problem with re-annotating mutations in gene MICAL2: skipping.
Problem with re-annotating mutations in gene MKI67: skipping.
Problem with re-annotating mutations in gene MLL: skipping.
Problem with re-annotating mutations in gene MLL2: skipping.
Problem with re-annotating mutations in gene MLL3: skipping.
Problem with re-annotating mutations in gene MLL4: skipping.
Problem with re-annotating mutations in gene MMP16: skipping.
Problem with re-annotating mutations in gene MMP9: skipping.
Problem with re-annotating mutations in gene MOGS: skipping.
Problem with re-annotating mutations in gene MORC3: skipping.
Problem with re-annotating mutations in gene MPDZ: skipping.
2200/4047 Problem with re-annotating mutations in gene MSLNL: skipping.
Problem with re-annotating mutations in gene MST1R: skipping.
Problem with re-annotating mutations in gene MTERFD2: skipping.
Problem with re-annotating mutations in gene MTMR11: skipping.
Problem with re-annotating mutations in gene MUC16: skipping.
Problem with re-annotating mutations in gene MUC4: skipping.
Problem with re-annotating mutations in gene MUC5B: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene MXRA5: skipping.
Problem with re-annotating mutations in gene MYBPC1: skipping.
Problem with re-annotating mutations in gene MYCBP2: skipping.
Problem with re-annotating mutations in gene MYH1: skipping.
Problem with re-annotating mutations in gene MYH13: skipping.
Problem with re-annotating mutations in gene MYH15: skipping.
Problem with re-annotating mutations in gene MYH2: skipping.
Problem with re-annotating mutations in gene MYH4: skipping.
Problem with re-annotating mutations in gene MYH7: skipping.
Problem with re-annotating mutations in gene MYH7B: skipping.
Problem with re-annotating mutations in gene MYH9: skipping.
Problem with re-annotating mutations in gene MYLK: skipping.
Problem with re-annotating mutations in gene MYO15A: skipping.
Problem with re-annotating mutations in gene MYO18B: skipping.
Problem with re-annotating mutations in gene MYO1C: skipping.
Problem with re-annotating mutations in gene MYO3A: skipping.
Problem with re-annotating mutations in gene MYO6: skipping.
Problem with re-annotating mutations in gene MYO9B: skipping.
Problem with re-annotating mutations in gene MYOF: skipping.
Problem with re-annotating mutations in gene MYOM3: skipping.
Problem with re-annotating mutations in gene MYOT: skipping.
Problem with re-annotating mutations in gene MYST4: skipping.
Problem with re-annotating mutations in gene NAA15: skipping.
Problem with re-annotating mutations in gene NAA25: skipping.
Problem with re-annotating mutations in gene NARF: skipping.
2300/4047 Problem with re-annotating mutations in gene NBEA: skipping.
Problem with re-annotating mutations in gene NBN: skipping.
Problem with re-annotating mutations in gene NBPF1: skipping.
Problem with re-annotating mutations in gene NBPF10: skipping.
Problem with re-annotating mutations in gene NBPF9: skipping.
Problem with re-annotating mutations in gene NBR1: skipping.
Problem with re-annotating mutations in gene NCAPD2: skipping.
Problem with re-annotating mutations in gene NCF2: skipping.
Problem with re-annotating mutations in gene NCOR1: skipping.
Problem with re-annotating mutations in gene NCOR2: skipping.
Problem with re-annotating mutations in gene NDC80: skipping.
Problem with re-annotating mutations in gene NEB: skipping.
Problem with re-annotating mutations in gene NEK11: skipping.
Problem with re-annotating mutations in gene NEK5: skipping.
Problem with re-annotating mutations in gene NELL2: skipping.
Problem with re-annotating mutations in gene NES: skipping.
Problem with re-annotating mutations in gene NEU2: skipping.
Problem with re-annotating mutations in gene NF1: skipping.
Problem with re-annotating mutations in gene NFE2L2: skipping.
Problem with re-annotating mutations in gene NHLRC1: skipping.
Problem with re-annotating mutations in gene NID2: skipping.
Problem with re-annotating mutations in gene NIN: skipping.
Problem with re-annotating mutations in gene NIPBL: skipping.
Problem with re-annotating mutations in gene NISCH: skipping.
Problem with re-annotating mutations in gene NKTR: skipping.
Problem with re-annotating mutations in gene NLRP10: skipping.
Problem with re-annotating mutations in gene NLRP14: skipping.
Problem with re-annotating mutations in gene NLRP4: skipping.
Problem with re-annotating mutations in gene NLRP7: skipping.
Problem with re-annotating mutations in gene NLRP8: skipping.
Problem with re-annotating mutations in gene NLRP9: skipping.
Problem with re-annotating mutations in gene NMD3: skipping.
Problem with re-annotating mutations in gene NOS2: skipping.
Problem with re-annotating mutations in gene NOTCH1: skipping.
Problem with re-annotating mutations in gene NOTCH2: skipping.
Problem with re-annotating mutations in gene NR3C2: skipping.
2400/4047 Problem with re-annotating mutations in gene NRBP1: skipping.
Problem with re-annotating mutations in gene NRG3: skipping.
Problem with re-annotating mutations in gene NRIP1: skipping.
Problem with re-annotating mutations in gene NRXN1: skipping.
Problem with re-annotating mutations in gene NSD1: skipping.
Problem with re-annotating mutations in gene NSMCE2: skipping.
Problem with re-annotating mutations in gene NUMA1: skipping.
Problem with re-annotating mutations in gene NUP107: skipping.
Problem with re-annotating mutations in gene NUP153: skipping.
Problem with re-annotating mutations in gene NUP155: skipping.
Problem with re-annotating mutations in gene NUP188: skipping.
Problem with re-annotating mutations in gene NUP214: skipping.
Problem with re-annotating mutations in gene OBSCN: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene ODZ1: skipping.
Problem with re-annotating mutations in gene ODZ2: skipping.
Problem with re-annotating mutations in gene OPA1: skipping.
Problem with re-annotating mutations in gene OPCML: skipping.
Problem with re-annotating mutations in gene OR10A5: skipping.
Problem with re-annotating mutations in gene OR2T6: skipping.
Problem with re-annotating mutations in gene OR4A47: skipping.
2500/4047 Problem with re-annotating mutations in gene OR5K2: skipping.
Problem with re-annotating mutations in gene OR5M10: skipping.
Problem with re-annotating mutations in gene OR6N1: skipping.
Problem with re-annotating mutations in gene OR6S1: skipping.
Problem with re-annotating mutations in gene OR7A5: skipping.
Problem with re-annotating mutations in gene ORC3L: skipping.
Problem with re-annotating mutations in gene OSBPL3: skipping.
Problem with re-annotating mutations in gene OTUD7A: skipping.
Problem with re-annotating mutations in gene PAF1: skipping.
Problem with re-annotating mutations in gene PAIP1: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene PAK3: skipping.
Problem with re-annotating mutations in gene PALB2: skipping.
Problem with re-annotating mutations in gene PARP9: skipping.
Problem with re-annotating mutations in gene PCDH17: skipping.
Problem with re-annotating mutations in gene PCDH9: skipping.
Problem with re-annotating mutations in gene PCDHA7: skipping.
Problem with re-annotating mutations in gene PCDHAC1: skipping.
Problem with re-annotating mutations in gene PCDHB5: skipping.
2600/4047 Problem with re-annotating mutations in gene PCDHGB4: skipping.
Problem with re-annotating mutations in gene PCDHGC5: skipping.
Problem with re-annotating mutations in gene PCLO: skipping.
Problem with re-annotating mutations in gene PCNT: skipping.
Problem with re-annotating mutations in gene PDE1A: skipping.
Problem with re-annotating mutations in gene PDE1C: skipping.
Problem with re-annotating mutations in gene PDE4C: skipping.
Problem with re-annotating mutations in gene PDE4DIP: skipping.
Problem with re-annotating mutations in gene PDIA5: skipping.
Problem with re-annotating mutations in gene PDLIM3: skipping.
Problem with re-annotating mutations in gene PDZRN3: skipping.
Problem with re-annotating mutations in gene PHIP: skipping.
Problem with re-annotating mutations in gene PIK3CA: skipping.
Problem with re-annotating mutations in gene PIK3CB: skipping.
Problem with re-annotating mutations in gene PITRM1: skipping.
Problem with re-annotating mutations in gene PIWIL4: skipping.
Problem with re-annotating mutations in gene PKD1: skipping.
Problem with re-annotating mutations in gene PKD1L2: skipping.
Problem with re-annotating mutations in gene PKHD1L1: skipping.
Problem with re-annotating mutations in gene PKNOX2: skipping.
Problem with re-annotating mutations in gene PLAUR: skipping.
Problem with re-annotating mutations in gene PLCD4: skipping.
Problem with re-annotating mutations in gene PLCG1: skipping.
Problem with re-annotating mutations in gene PLCH1: skipping.
Problem with re-annotating mutations in gene PLEKHA4: skipping.
Problem with re-annotating mutations in gene PLEKHG1: skipping.
2700/4047 Problem with re-annotating mutations in gene PMFBP1: skipping.
Problem with re-annotating mutations in gene PML: skipping.
Problem with re-annotating mutations in gene PNMA1: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene POLA1: skipping.
Problem with re-annotating mutations in gene POLN: skipping.
Problem with re-annotating mutations in gene POLQ: skipping.
Problem with re-annotating mutations in gene POTEC: skipping.
Problem with re-annotating mutations in gene PPBP: skipping.
Problem with re-annotating mutations in gene PPEF2: skipping.
Problem with re-annotating mutations in gene PPP1CA: skipping.
Problem with re-annotating mutations in gene PPP1R15B: skipping.
Problem with re-annotating mutations in gene PPP1R9A: skipping.
Problem with re-annotating mutations in gene PPP2R1B: skipping.
Problem with re-annotating mutations in gene PRDM16: skipping.
Problem with re-annotating mutations in gene PREX2: skipping.
Problem with re-annotating mutations in gene PRF1: skipping.
Problem with re-annotating mutations in gene PRKD1: skipping.
2800/4047 Problem with re-annotating mutations in gene PRX: skipping.
Problem with re-annotating mutations in gene PSMG1: skipping.
Problem with re-annotating mutations in gene PSPC1: skipping.
Problem with re-annotating mutations in gene PTCH1: skipping.
Problem with re-annotating mutations in gene PTGER4: skipping.
Problem with re-annotating mutations in gene PTH1R: skipping.
Problem with re-annotating mutations in gene PTPRC: skipping.
Problem with re-annotating mutations in gene PTPRT: skipping.
Problem with re-annotating mutations in gene PTPRU: skipping.
Problem with re-annotating mutations in gene PXDN: skipping.
Problem with re-annotating mutations in gene PYGO1: skipping.
Problem with re-annotating mutations in gene R3HDM1: skipping.
Problem with re-annotating mutations in gene RAB11FIP1: skipping.
Problem with re-annotating mutations in gene RAB40B: skipping.
Problem with re-annotating mutations in gene RAD50: skipping.
Problem with re-annotating mutations in gene RAD51AP2: skipping.
Problem with re-annotating mutations in gene RAD52: skipping.
Problem with re-annotating mutations in gene RAD54B: skipping.
2900/4047 Problem with re-annotating mutations in gene RAI1: skipping.
Problem with re-annotating mutations in gene RALY: skipping.
Problem with re-annotating mutations in gene RAP1B: skipping.
Problem with re-annotating mutations in gene RAPGEF2: skipping.
Problem with re-annotating mutations in gene RARA: skipping.
Problem with re-annotating mutations in gene RB1: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene RBM10: skipping.
Problem with re-annotating mutations in gene RBM15: skipping.
Problem with re-annotating mutations in gene RBM44: skipping.
Problem with re-annotating mutations in gene RBM4B: skipping.
Problem with re-annotating mutations in gene RECQL5: skipping.
Problem with re-annotating mutations in gene RELN: skipping.
Problem with re-annotating mutations in gene RERE: skipping.
Problem with re-annotating mutations in gene RFC1: skipping.
Problem with re-annotating mutations in gene RFC4: skipping.
Problem with re-annotating mutations in gene RFTN2: skipping.
Problem with re-annotating mutations in gene RGPD3: skipping.
Problem with re-annotating mutations in gene RGPD4: skipping.
Problem with re-annotating mutations in gene RIMKLB: skipping.
Problem with re-annotating mutations in gene RIMS3: skipping.
Problem with re-annotating mutations in gene RINL: skipping.
Problem with re-annotating mutations in gene RIOK2: skipping.
Problem with re-annotating mutations in gene RLF: skipping.
Problem with re-annotating mutations in gene RLTPR: skipping.
3000/4047 Problem with re-annotating mutations in gene RNF113B: skipping.
Problem with re-annotating mutations in gene RNF123: skipping.
Problem with re-annotating mutations in gene RNF216: skipping.
Problem with re-annotating mutations in gene ROBO4: skipping.
Problem with re-annotating mutations in gene ROCK2: skipping.
Problem with re-annotating mutations in gene ROS1: skipping.
Problem with re-annotating mutations in gene RP1: skipping.
Problem with re-annotating mutations in gene RP1L1: skipping.
Problem with re-annotating mutations in gene RPAP1: skipping.
Problem with re-annotating mutations in gene RPGRIP1: skipping.
Problem with re-annotating mutations in gene RPL31: skipping.
Problem with re-annotating mutations in gene RPRD2: skipping.
Problem with re-annotating mutations in gene RPS6KC1: skipping.
Problem with re-annotating mutations in gene RSPRY1: skipping.
Problem with re-annotating mutations in gene RUSC1: skipping.
Problem with re-annotating mutations in gene RXRG: skipping.
Problem with re-annotating mutations in gene RYR1: skipping.
Problem with re-annotating mutations in gene RYR2: skipping.
Problem with re-annotating mutations in gene RYR3: skipping.
Problem with re-annotating mutations in gene SACS: skipping.
Problem with re-annotating mutations in gene SALL2: skipping.
Problem with re-annotating mutations in gene SAP130: skipping.
Problem with re-annotating mutations in gene SAPS3: skipping.
3100/4047 Problem with re-annotating mutations in gene SCN11A: skipping.
Problem with re-annotating mutations in gene SCN2A: skipping.
Problem with re-annotating mutations in gene SCN3A: skipping.
Problem with re-annotating mutations in gene SCNM1: skipping.
Problem with re-annotating mutations in gene SCYL3: skipping.
Problem with re-annotating mutations in gene SDK1: skipping.
Problem with re-annotating mutations in gene SDK2: skipping.
Problem with re-annotating mutations in gene SDPR: skipping.
Problem with re-annotating mutations in gene SEL1L: skipping.
Problem with re-annotating mutations in gene SETBP1: skipping.
Problem with re-annotating mutations in gene SETD2: skipping.
Problem with re-annotating mutations in gene SETX: skipping.
Problem with re-annotating mutations in gene SF3B3: skipping.
Problem with re-annotating mutations in gene SFRS15: skipping.
Problem with re-annotating mutations in gene SFRS2IP: skipping.
Problem with re-annotating mutations in gene SGOL1: skipping.
Problem with re-annotating mutations in gene SGOL2: skipping.
Problem with re-annotating mutations in gene SKIL: skipping.
3200/4047 Problem with re-annotating mutations in gene SLC12A4: skipping.
Problem with re-annotating mutations in gene SLC34A1: skipping.
Problem with re-annotating mutations in gene SLC39A3: skipping.
Problem with re-annotating mutations in gene SLC4A8: skipping.
Problem with re-annotating mutations in gene SLC5A7: skipping.
Problem with re-annotating mutations in gene SLCO1B3: skipping.
Problem with re-annotating mutations in gene SLCO4C1: skipping.
Problem with re-annotating mutations in gene SLMAP: skipping.
Problem with re-annotating mutations in gene SMAP1: skipping.
Problem with re-annotating mutations in gene SMARCA2: skipping.
Problem with re-annotating mutations in gene SMARCC1: skipping.
Problem with re-annotating mutations in gene SMOC2: skipping.
Problem with re-annotating mutations in gene SMPD1: skipping.
Problem with re-annotating mutations in gene SMYD1: skipping.
Problem with re-annotating mutations in gene SND1: skipping.
3300/4047 Problem with re-annotating mutations in gene SNX25: skipping.
Problem with re-annotating mutations in gene SORCS3: skipping.
Problem with re-annotating mutations in gene SOS1: skipping.
Problem with re-annotating mutations in gene SP3: skipping.
Problem with re-annotating mutations in gene SPATA21: skipping.
Problem with re-annotating mutations in gene SPATS2: skipping.
Problem with re-annotating mutations in gene SPEG: skipping.
Problem with re-annotating mutations in gene SPG11: skipping.
Problem with re-annotating mutations in gene SPHK2: skipping.
Problem with re-annotating mutations in gene SPRYD3: skipping.
Problem with re-annotating mutations in gene SPTA1: skipping.
Problem with re-annotating mutations in gene SRPRB: skipping.
Problem with re-annotating mutations in gene SRRM1: skipping.
Problem with re-annotating mutations in gene SSPO: skipping.
Problem with re-annotating mutations in gene ST18: skipping.
Problem with re-annotating mutations in gene STAB1: skipping.
Problem with re-annotating mutations in gene STUB1: skipping.
Problem with re-annotating mutations in gene STXBP5: skipping.
Problem with re-annotating mutations in gene SUV420H1: skipping.
3400/4047 Problem with re-annotating mutations in gene SVEP1: skipping.
Problem with re-annotating mutations in gene SYNE1: skipping.
Problem with re-annotating mutations in gene SYNE2: skipping.
Problem with re-annotating mutations in gene SYNJ1: skipping.
Problem with re-annotating mutations in gene SYNPO: skipping.
Problem with re-annotating mutations in gene SYT10: skipping.
Problem with re-annotating mutations in gene SYT3: skipping.
Problem with re-annotating mutations in gene SYTL2: skipping.
Problem with re-annotating mutations in gene TACC3: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene TAF1: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene TAF7L: skipping.
Problem with re-annotating mutations in gene TAOK2: skipping.
Problem with re-annotating mutations in gene TASP1: skipping.
Problem with re-annotating mutations in gene TBC1D5: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene TBC1D8B: skipping.
Problem with re-annotating mutations in gene TBCC: skipping.
Problem with re-annotating mutations in gene TBX5: skipping.
Problem with re-annotating mutations in gene TCF20: skipping.
Problem with re-annotating mutations in gene TCHH: skipping.
Problem with re-annotating mutations in gene TCP11L2: skipping.
Problem with re-annotating mutations in gene TET2: skipping.
Problem with re-annotating mutations in gene TFEC: skipping.
Problem with re-annotating mutations in gene TGFBR3: skipping.
3500/4047 Problem with re-annotating mutations in gene TGS1: skipping.
Problem with re-annotating mutations in gene THADA: skipping.
Problem with re-annotating mutations in gene THEMIS: skipping.
Problem with re-annotating mutations in gene TICAM1: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene TKTL1: skipping.
Problem with re-annotating mutations in gene TLR10: skipping.
Problem with re-annotating mutations in gene TLR5: skipping.
Problem with re-annotating mutations in gene TMC3: skipping.
Problem with re-annotating mutations in gene TMCO2: skipping.
Problem with re-annotating mutations in gene TMEM132D: skipping.
Problem with re-annotating mutations in gene TMEM41B: skipping.
Problem with re-annotating mutations in gene TMEM62: skipping.
Problem with re-annotating mutations in gene TMPRSS11F: skipping.
Problem with re-annotating mutations in gene TNC: skipping.
Problem with re-annotating mutations in gene TOPORS: skipping.
Problem with re-annotating mutations in gene TP53: skipping.
Problem with re-annotating mutations in gene TP53BP1: skipping.
3600/4047 Problem with re-annotating mutations in gene TP53I3: skipping.
Problem with re-annotating mutations in gene TPK1: skipping.
Problem with re-annotating mutations in gene TPO: skipping.
Problem with re-annotating mutations in gene TPR: skipping.
Problem with re-annotating mutations in gene TRAPPC10: skipping.
Problem with re-annotating mutations in gene TRERF1: skipping.
Problem with re-annotating mutations in gene TRHDE: skipping.
Problem with re-annotating mutations in gene TRIM10: skipping.
Problem with re-annotating mutations in gene TRIM36: skipping.
Problem with re-annotating mutations in gene TRIM37: skipping.
Problem with re-annotating mutations in gene TRIM42: skipping.
Problem with re-annotating mutations in gene TRIM59: skipping.
Problem with re-annotating mutations in gene TRIO: skipping.
Problem with re-annotating mutations in gene TROAP: skipping.
Problem with re-annotating mutations in gene TRPC4: skipping.
Problem with re-annotating mutations in gene TRPV5: skipping.
Problem with re-annotating mutations in gene TRRAP: skipping.
Problem with re-annotating mutations in gene TRUB1: skipping.
Problem with re-annotating mutations in gene TSC1: skipping.
Problem with re-annotating mutations in gene TSHZ2: skipping.
Problem with re-annotating mutations in gene TSKU: skipping.
Problem with re-annotating mutations in gene TTC23: skipping.
Problem with re-annotating mutations in gene TTC3: skipping.
Problem with re-annotating mutations in gene TTF2: skipping.
Problem with re-annotating mutations in gene TTN: skipping.
3700/4047 Problem with re-annotating mutations in gene U2AF2: skipping.
Problem with re-annotating mutations in gene UBAP2L: skipping.
Problem with re-annotating mutations in gene UBE4A: skipping.
Problem with re-annotating mutations in gene UBR4: skipping.
Problem with re-annotating mutations in gene UGDH: skipping.
Problem with re-annotating mutations in gene UGT1A1: skipping.
Problem with re-annotating mutations in gene UNC13C: skipping.
Problem with re-annotating mutations in gene UNC45B: skipping.
Problem with re-annotating mutations in gene URB2: skipping.
Problem with re-annotating mutations in gene USH2A: skipping.
Problem with re-annotating mutations in gene USP13: skipping.
Problem with re-annotating mutations in gene USP34: skipping.
Problem with re-annotating mutations in gene USP38: skipping.
Problem with re-annotating mutations in gene USP43: skipping.
Problem with re-annotating mutations in gene USP47: skipping.
Problem with re-annotating mutations in gene UTP18: skipping.
Problem with re-annotating mutations in gene UTP20: skipping.
Problem with re-annotating mutations in gene VCAN: skipping.
Problem with re-annotating mutations in gene VPS13B: skipping.
Problem with re-annotating mutations in gene VPS13D: skipping.
3800/4047 Problem with re-annotating mutations in gene VPS8: skipping.
Problem with re-annotating mutations in gene VWA3B: skipping.
Problem with re-annotating mutations in gene WDFY3: skipping.
Problem with re-annotating mutations in gene WDHD1: skipping.
Problem with re-annotating mutations in gene WDR49: skipping.
Problem with re-annotating mutations in gene WDR62: skipping.
Problem with re-annotating mutations in gene WHSC1: skipping.
Problem with re-annotating mutations in gene WNK1: skipping.
Problem with re-annotating mutations in gene WWC2: skipping.
Problem with re-annotating mutations in gene XIRP2: skipping.
Problem with re-annotating mutations in gene XPR1: skipping.
Problem with re-annotating mutations in gene ZBTB37: skipping.
Problem with re-annotating mutations in gene ZBTB40: skipping.
Problem with re-annotating mutations in gene ZCCHC11: skipping.
Problem with re-annotating mutations in gene ZCCHC14: skipping.
Problem with re-annotating mutations in gene ZFC3H1: skipping.
Problem with re-annotating mutations in gene ZFHX4: skipping.
Problem with re-annotating mutations in gene ZFP37: skipping.
WARNING: unknown chromosome(s):
    'chr6_cox_hap2'

Problem with re-annotating mutations in gene ZFP57: skipping.
Problem with re-annotating mutations in gene ZFYVE9: skipping.
3900/4047 convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene ZMAT1: skipping.
Problem with re-annotating mutations in gene ZMYM2: skipping.
Problem with re-annotating mutations in gene ZNF160: skipping.
Problem with re-annotating mutations in gene ZNF200: skipping.
Problem with re-annotating mutations in gene ZNF205: skipping.
Problem with re-annotating mutations in gene ZNF207: skipping.
Problem with re-annotating mutations in gene ZNF263: skipping.
Problem with re-annotating mutations in gene ZNF335: skipping.
Problem with re-annotating mutations in gene ZNF354C: skipping.
Problem with re-annotating mutations in gene ZNF418: skipping.
Problem with re-annotating mutations in gene ZNF461: skipping.
Problem with re-annotating mutations in gene ZNF518A: skipping.
Problem with re-annotating mutations in gene ZNF536: skipping.
Problem with re-annotating mutations in gene ZNF555: skipping.
Problem with re-annotating mutations in gene ZNF594: skipping.
4000/4047 Problem with re-annotating mutations in gene ZNF644: skipping.
Problem with re-annotating mutations in gene ZNF655: skipping.
Problem with re-annotating mutations in gene ZNF671: skipping.
Problem with re-annotating mutations in gene ZNF681: skipping.
Problem with re-annotating mutations in gene ZNF710: skipping.
convert_chr: assuming human for chrX/chrY
Problem with re-annotating mutations in gene ZNF75D: skipping.
Problem with re-annotating mutations in gene ZNF814: skipping.
Problem with re-annotating mutations in gene ZNF816A: skipping.
Problem with re-annotating mutations in gene ZNF829: skipping.
Problem with re-annotating mutations in gene ZNF831: skipping.
Problem with re-annotating mutations in gene ZNF845: skipping.
Problem with re-annotating mutations in gene ZNF99: skipping.
Problem with re-annotating mutations in gene ZSCAN1: skipping.
Problem with re-annotating mutations in gene ZSCAN5A: skipping.
Problem with re-annotating mutations in gene ZZEF1: skipping.
Problem with re-annotating mutations in gene ZZZ3: skipping.

Analyzing gene-gene correlations and anti-correlations
Performing permutations:
0.01	2/1000000	0.00	0.005	206.4	6/6 pairs	4/4 genes done

Top gene-gene pairs:
FBXW7	NFE2L2	0.135043	0.664225	none
FBXW7	TP53	0.329345	0.664225	none
FBXW7	ZNF814	0.459402	0.664225	none
NFE2L2	TP53	0.481563	0.664225	none
NFE2L2	ZNF814	0.617827	0.664225	none
TP53	ZNF814	0.664225	0.664225	none
Analyzing power per gene...
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
Generating gene coverage plots...
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/1.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/2.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/3.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/4.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/5.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/6.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/7.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/8.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/9.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/10.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/11.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/12.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/13.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/14.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/15.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/16.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/17.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/18.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/19.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/20.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/21.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/22.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/23.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/24.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/25.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/26.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/27.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/28.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/29.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/30.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/31.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/32.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/33.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/34.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/35.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/36.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/37.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/38.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/39.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/40.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/41.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/42.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/43.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/44.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/45.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/46.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/47.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/48.png
Superimposing mutations
Outputting figure to ./BLCA.gene_coverage_plots/49.png
Superimposing mutations
Outputting figure to ./BLCA.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.165.3896/
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/181708/iteration1
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 0 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1646>
Subject: Job 1119475: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000001> was used as the working directory.
Started at Wed Oct 10 10:41:32 2012
Results reported at Wed Oct 10 10:43:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000001.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000001.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 1  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    140.23 sec.
    Max Memory :      1421 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.165.3896/
-whichjob
1
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 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	1
2	A1CF	1
3	A2BP1	1
4	A2M	2.595574e-02
5	A2ML1	1
6	A4GALT	1
7	A4GNT	1
8	AAAS	1
9	AACS	1
10	AADAC	1
11	AADACL2	1
12	AADACL3	1
13	AADACL4	1
14	AADAT	1
15	AAGAB	1
16	AAK1	1
17	AAMP	1
18	AANAT	1
19	AARS	1
20	AARS2	1
21	AARSD1	1
22	AASDH	1.797069e-01
23	AASDHPPT	1
24	AASS	1
25	AATF	1
26	AATK	1
27	ABAT	1
28	ABCA1	6.038299e-01
29	ABCA10	3.331200e-03
30	ABCA12	4.415553e-01
31	ABCA13	5.632604e-01
32	ABCA2	5.163467e-01
33	ABCA3	1
34	ABCA4	1
35	ABCA5	3.384007e-01
36	ABCA6	5.483951e-01
37	ABCA7	1
38	ABCA8	4.674314e-02
39	ABCA9	4.458603e-01
40	ABCB1	1
41	ABCB10	1
42	ABCB11	1
43	ABCB4	3.975529e-01
44	ABCB5	1
45	ABCB6	1
46	ABCB7	1
47	ABCB8	1
48	ABCB9	1
49	ABCC1	1
50	ABCC10	3.598691e-01
51	ABCC11	1.257283e-01
52	ABCC12	1
53	ABCC2	1
54	ABCC3	3.736812e-01
55	ABCC4	2.726772e-01
56	ABCC5	5.363090e-01
57	ABCC6	1
58	ABCC8	1
59	ABCC9	2.196160e-01
60	ABCD1	1.805981e-01
61	ABCD2	1
62	ABCD3	1
63	ABCD4	1
64	ABCE1	1
65	ABCF1	1
66	ABCF2	1
67	ABCF3	1
68	ABCG1	1
69	ABCG2	1
70	ABCG4	1
71	ABCG5	1
72	ABCG8	1
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	1.502270e-01
89	ABI2	2.261080e-01
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...
ABCA10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.878481e-02	ci left: 2.986610e-01	ci right 3.168511e-01	k: 3077	n:10000
Cons ci ratio: 6.597726e-02	ci left: 2.522150e-01	ci right 2.695245e-01	k: 2608	n:10000
KS ci ratio: 5.146020e-02	ci left: 3.576425e-01	ci right 3.766349e-01	k: 3671	n:10000
ABCA10   10000 perm   3 sec   (2966 perm/sec)   p_kst 3.671000e-01   p_cons 2.608000e-01   p_joint 3.077000e-01

Outputting figure to mutsig2_images.part000000000001/ABCA10.5_4780_10000_0.3671_0.2608_0.3077.png
                gene_name: ABCA10
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.31 
     ci_joint_bounds_left: 0.30 
    ci_joint_bounds_right: 0.32 

Current progress: 17 percent done.
A2M
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: 4.392995e-02	ci left: 4.334314e-01	ci right 4.530017e-01	k: 4432	n:10000
KS ci ratio: 1.251182e-02	ci left: 9.017548e-01	ci right 9.132066e-01	k: 9076	n:10000
A2M   10000 perm   2 sec   (4888 perm/sec)   p_kst 9.076000e-01   p_cons 4.432000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000001/A2M.3_4569_10000_0.9076_0.4432_1.png
                gene_name: A2M
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.91 
        ci_ks_bounds_left: 0.90 
       ci_ks_bounds_right: 0.91 
                   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.
ABCA13
Processing conservation and coverage...
65% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.605704e-02	ci left: 4.103009e-01	ci right 4.297457e-01	k: 4200	n:10000
Cons ci ratio: 3.010923e-02	ci left: 6.193450e-01	ci right 6.383799e-01	k: 6289	n:10000
KS ci ratio: 6.939426e-02	ci left: 2.334341e-01	ci right 2.503165e-01	k: 2418	n:10000
ABCA13   10000 perm   4 sec   (2785 perm/sec)   p_kst 2.418000e-01   p_cons 6.289000e-01   p_joint 4.200000e-01

Outputting figure to mutsig2_images.part000000000001/ABCA13.3_15254_10000_0.2418_0.6289_0.42.png
                gene_name: ABCA13
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.64 
                  p_joint: 0.42 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.43 

Current progress: 50 percent done.
ABCA8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.830889e-02	ci left: 6.478024e-01	ci right 6.665060e-01	k: 6572	n:10000
Cons ci ratio: 5.061829e-02	ci left: 3.653000e-01	ci right 3.843730e-01	k: 3748	n:10000
KS ci ratio: 7.296213e-03	ci left: 9.628897e-01	ci right 9.700352e-01	k: 9666	n:10000
ABCA8   10000 perm   2 sec   (4886 perm/sec)   p_kst 9.666000e-01   p_cons 3.748000e-01   p_joint 6.572000e-01

Outputting figure to mutsig2_images.part000000000001/ABCA8.3_4894_10000_0.9666_0.3748_0.6572.png
                gene_name: ABCA8
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.66 
     ci_joint_bounds_left: 0.65 
    ci_joint_bounds_right: 0.67 

Current progress: 67 percent done.
ABCC11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.094610e-02	ci left: 7.696229e-01	ci right 7.860149e-01	k: 7779	n:10000
Cons ci ratio: 3.288380e-02	ci left: 5.771752e-01	ci right 5.965742e-01	k: 5869	n:10000
KS ci ratio: 6.210389e-02	ci left: 2.759680e-01	ci right 2.937575e-01	k: 2848	n:10000
ABCC11   10000 perm   2 sec   (5411 perm/sec)   p_kst 2.848000e-01   p_cons 5.869000e-01   p_joint 7.779000e-01

Outputting figure to mutsig2_images.part000000000001/ABCC11.2_4265_10000_0.2848_0.5869_0.7779.png
                gene_name: ABCC11
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.60 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.79 

Current progress: 83 percent done.
ABCC9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.469983e-02	ci left: 1.688761e-01	ci right 1.839129e-01	k: 1763	n:10000
Cons ci ratio: 4.473089e-02	ci left: 4.245555e-01	ci right 4.440828e-01	k: 4343	n:10000
KS ci ratio: 1.036624e-01	ci left: 1.185779e-01	ci right 1.316413e-01	k: 1250	n:10000
ABCC9   10000 perm   2 sec   (4995 perm/sec)   p_kst 1.250000e-01   p_cons 4.343000e-01   p_joint 1.763000e-01

Joint ci ratio: 5.684346e-02	ci left: 1.866108e-01	ci right 1.975789e-01	k: 3841	n:20000
Cons ci ratio: 3.151030e-02	ci left: 4.293118e-01	ci right 4.431067e-01	k: 8724	n:20000
KS ci ratio: 7.176879e-02	ci left: 1.251220e-01	ci right 1.344859e-01	k: 2595	n:20000
ABCC9   20000 perm   4 sec   (4504 perm/sec)   p_kst 1.297500e-01   p_cons 4.362000e-01   p_joint 1.920500e-01

Outputting figure to mutsig2_images.part000000000001/ABCC9.2_4944_20000_0.12975_0.4362_0.19205.png
                gene_name: ABCC9
               theta_stop: 0.072 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.20 

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.165.3896/
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/181708/iteration1/scatter.0000000001
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 1 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119479: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000002> was used as the working directory.
Started at Wed Oct 10 10:41:32 2012
Results reported at Wed Oct 10 10:43:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000002.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000002.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 2  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    109.67 sec.
    Max Memory :      1213 MB
    Max Swap   :      3902 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.165.3896/
-whichjob
2
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 2: processing genes 91 - 181
Calculating significance of each gene.
Using projection method.
91	ABI3BP	1
92	ABL1	4.440951e-01
93	ABL2	1
94	ABLIM1	3.309422e-01
95	ABLIM2	1
96	ABLIM3	2.044374e-01
97	ABO	1
98	ABP1	1
99	ABR	1
100	ABRA	1
101	ABT1	1
102	ABTB1	1
103	ABTB2	1
104	ACAA1	1
105	ACAA2	1
106	ACACA	5.689360e-01
107	ACACB	6.400253e-01
108	ACAD10	4.012705e-01
109	ACAD11	9.213544e-02
110	ACAD8	1.680568e-01
111	ACAD9	1
112	ACADL	1
113	ACADM	1
114	ACADS	1
115	ACADSB	1
116	ACADVL	1
117	ACAN	5.454974e-01
118	ACAP1	1
119	ACAP2	1
120	ACAP3	1
121	ACAT1	1
122	ACAT2	1
123	ACBD3	3.471908e-02
124	ACBD4	1
125	ACBD5	1
126	ACBD6	1
127	ACBD7	2.603807e-02
128	ACCN1	2.435957e-01
129	ACCN2	1.595495e-01
130	ACCN3	1
131	ACCN4	1
132	ACCN5	1
133	ACCS	1
134	ACCSL	1
135	ACD	1.825142e-01
136	ACE	8.109696e-02
137	ACE2	1.604022e-01
138	ACER1	1
139	ACER2	1
140	ACER3	1
141	ACHE	1.667601e-02
142	ACIN1	1
143	ACLY	4.037291e-01
144	ACMSD	1
145	ACN9	1.279553e-03
146	ACO1	1
147	ACO2	1
148	ACOT1	1
149	ACOT11	1
150	ACOT12	1
151	ACOT13	1
152	ACOT2	1
153	ACOT4	1
154	ACOT6	1.030815e-01
155	ACOT7	1
156	ACOT8	1
157	ACOT9	1
158	ACOX1	1
159	ACOX2	2.653487e-01
160	ACOX3	1
161	ACOXL	2.244666e-01
162	ACP1	1
163	ACP2	1
164	ACP5	1
165	ACP6	1
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	1.942057e-01
175	ACSF2	1
176	ACSF3	2.124833e-01
177	ACSL1	1
178	ACSL3	1
179	ACSL4	1
180	ACSL5	1
181	ACSL6	1
Done

Running MutSig 2:
Scatter job 2: processing genes 91 - 181
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ACE
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.994475e-02	ci left: 3.715671e-01	ci right 3.907022e-01	k: 3811	n:10000
Cons ci ratio: 2.906652e-02	ci left: 6.357313e-01	ci right 6.545841e-01	k: 6452	n:10000
KS ci ratio: 1.098228e-01	ci left: 1.067607e-01	ci right 1.192658e-01	k: 1129	n:10000
ACE   10000 perm   3 sec   (3230 perm/sec)   p_kst 1.129000e-01   p_cons 6.452000e-01   p_joint 3.811000e-01

Joint ci ratio: 3.265727e-02	ci left: 4.118499e-01	ci right 4.255737e-01	k: 8374	n:20000
Cons ci ratio: 2.045761e-02	ci left: 6.406822e-01	ci right 6.539750e-01	k: 12947	n:20000
KS ci ratio: 7.814601e-02	ci left: 1.073661e-01	ci right 1.161471e-01	k: 2234	n:20000
ACE   20000 perm   8 sec   (2482 perm/sec)   p_kst 1.117000e-01   p_cons 6.473500e-01   p_joint 4.187000e-01

Outputting figure to mutsig2_images.part000000000002/ACE.2_4224_20000_0.1117_0.64735_0.4187.png
                gene_name: ACE
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.42 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.43 

Current progress: 33 percent done.
ACHE
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: 3.574771e-02	ci left: 5.360794e-01	ci right 5.556939e-01	k: 5459	n:10000
KS ci ratio: 1.473093e-02	ci left: 8.696873e-01	ci right 8.826927e-01	k: 8763	n:10000
ACHE   10000 perm   2 sec   (5353 perm/sec)   p_kst 8.763000e-01   p_cons 5.459000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000002/ACHE.2_1996_10000_0.8763_0.5459_1.png
                gene_name: ACHE
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.88 
        ci_ks_bounds_left: 0.87 
       ci_ks_bounds_right: 0.88 
                   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: 67 percent done.
ACN9
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: 5.753719e-03	ci left: 9.759962e-01	ci right 9.817201e-01	k: 9790	n:10000
KS ci ratio: 4.037172e-02	ci left: 4.753600e-01	ci right 4.950486e-01	k: 4852	n:10000
ACN9   10000 perm   1 sec   (7038 perm/sec)   p_kst 4.852000e-01   p_cons 9.790000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000002/ACN9.2_386_10000_0.4852_0.979_1.png
                gene_name: ACN9
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     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.165.3896/
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/181708/iteration1/scatter.0000000002
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 2 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119482: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000003> was used as the working directory.
Started at Wed Oct 10 10:41:32 2012
Results reported at Wed Oct 10 10:43:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000003.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000003.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 3  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    145.98 sec.
    Max Memory :      1218 MB
    Max Swap   :      3811 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.165.3896/
-whichjob
3
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 3: processing genes 182 - 271
Calculating significance of each gene.
Using projection method.
182	ACSM1	1
183	ACSM2A	1
184	ACSM2B	1
185	ACSM3	1
186	ACSM4	1
187	ACSM5	8.137588e-02
188	ACSS1	1
189	ACSS2	1
190	ACSS3	1
191	ACTA1	1.721655e-01
192	ACTA2	5.636022e-03
193	ACTB	1
194	ACTBL2	1
195	ACTC1	1
196	ACTG1	7.039195e-02
197	ACTG2	1
198	ACTL6A	1.426533e-01
199	ACTL6B	1
200	ACTL7A	1
201	ACTL7B	1
202	ACTL8	1
203	ACTL9	1
204	ACTN1	2.017212e-01
205	ACTN2	1
206	ACTN3	1
207	ACTN4	5.002513e-03
208	ACTR10	8.056711e-02
209	ACTR1A	1
210	ACTR1B	1
211	ACTR2	1
212	ACTR3	1
213	ACTR3B	1
214	ACTR3C	1
215	ACTR5	1
216	ACTR6	1
217	ACTR8	1
218	ACTRT1	1
219	ACTRT2	1
220	ACVR1	1
221	ACVR1B	1
222	ACVR1C	1
223	ACVR2A	1
224	ACVR2B	1
225	ACVRL1	9.461846e-02
226	ACY1	1
227	ACY3	1
228	ACYP1	1
229	ACYP2	1
230	ADA	1
231	ADAD1	1
232	ADAD2	1
233	ADAL	1
234	ADAM10	1
235	ADAM11	1
236	ADAM12	2.548003e-01
237	ADAM15	2.681092e-01
238	ADAM17	1
239	ADAM18	1
240	ADAM19	1
241	ADAM2	1.378419e-01
242	ADAM20	1
243	ADAM21	1
244	ADAM22	1
245	ADAM23	1
246	ADAM28	1
247	ADAM29	2.810174e-01
248	ADAM30	1
249	ADAM32	1
250	ADAM33	1
251	ADAM7	1
252	ADAM8	1
253	ADAM9	2.386491e-01
254	ADAMDEC1	1
255	ADAMTS1	1
256	ADAMTS10	9.767270e-02
257	ADAMTS12	6.171878e-03
258	ADAMTS13	1
259	ADAMTS14	5.930490e-02
260	ADAMTS15	1
261	ADAMTS16	4.089512e-01
262	ADAMTS17	1
263	ADAMTS18	1.579918e-01
264	ADAMTS19	1
265	ADAMTS2	1
266	ADAMTS20	3.484866e-01
267	ADAMTS3	2.818591e-01
268	ADAMTS4	1
269	ADAMTS5	1
270	ADAMTS6	3.053582e-01
271	ADAMTS7	1
Done

Running MutSig 2:
Scatter job 3: processing genes 182 - 271
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ADAMTS12
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: 3.799760e-02	ci left: 5.056516e-01	ci right 5.253394e-01	k: 5155	n:10000
KS ci ratio: 1.762899e-02	ci left: 8.243225e-01	ci right 8.390837e-01	k: 8318	n:10000
ADAMTS12   10000 perm   2 sec   (4422 perm/sec)   p_kst 8.318000e-01   p_cons 5.155000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000003/ADAMTS12.4_4881_10000_0.8318_0.5155_1.png
                gene_name: ADAMTS12
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.83 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.84 
                   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: 25 percent done.
ACTN4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.928515e-02	ci left: 2.950918e-01	ci right 3.132224e-01	k: 3041	n:10000
Cons ci ratio: 3.760404e-02	ci left: 5.108537e-01	ci right 5.305342e-01	k: 5207	n:10000
KS ci ratio: 7.415534e-02	ci left: 2.102365e-01	ci right 2.265279e-01	k: 2183	n:10000
ACTN4   10000 perm   2 sec   (5203 perm/sec)   p_kst 2.183000e-01   p_cons 5.207000e-01   p_joint 3.041000e-01

Outputting figure to mutsig2_images.part000000000003/ACTN4.3_2820_10000_0.2183_0.5207_0.3041.png
                gene_name: ACTN4
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.30 
     ci_joint_bounds_left: 0.30 
    ci_joint_bounds_right: 0.31 

Current progress: 50 percent done.
ACTA2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.538916e-02	ci left: 8.596771e-01	ci right 8.731087e-01	k: 8665	n:10000
Cons ci ratio: 9.187494e-02	ci left: 1.468790e-01	ci right 1.611232e-01	k: 1539	n:10000
KS ci ratio: 3.563252e-02	ci left: 5.376819e-01	ci right 5.572905e-01	k: 5475	n:10000
ACTA2   10000 perm   2 sec   (6532 perm/sec)   p_kst 5.475000e-01   p_cons 1.539000e-01   p_joint 8.665000e-01

Outputting figure to mutsig2_images.part000000000003/ACTA2.2_1166_10000_0.5475_0.1539_0.8665.png
                gene_name: ACTA2
               theta_stop: 0.092 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.16 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

Current progress: 75 percent done.
ADAMTS14
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.624928e-02	ci left: 8.463146e-01	ci right 8.602789e-01	k: 8534	n:10000
Cons ci ratio: 8.649139e-02	ci left: 1.629794e-01	ci right 1.778132e-01	k: 1703	n:10000
KS ci ratio: 1.208232e-02	ci left: 9.076136e-01	ci right 9.187443e-01	k: 9133	n:10000
ADAMTS14   10000 perm   2 sec   (4860 perm/sec)   p_kst 9.133000e-01   p_cons 1.703000e-01   p_joint 8.534000e-01

Outputting figure to mutsig2_images.part000000000003/ADAMTS14.2_3769_10000_0.9133_0.1703_0.8534.png
                gene_name: ADAMTS14
               theta_stop: 0.086 
                    nperm: 10000 
                     p_ks: 0.91 
        ci_ks_bounds_left: 0.91 
       ci_ks_bounds_right: 0.92 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.18 
                  p_joint: 0.85 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.86 

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.165.3896/
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/181708/iteration1/scatter.0000000003
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 3 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119486: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000004> was used as the working directory.
Started at Wed Oct 10 10:41:37 2012
Results reported at Wed Oct 10 10:45:28 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000004.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000004.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 4  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    252.60 sec.
    Max Memory :      1363 MB
    Max Swap   :      3874 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.165.3896/
-whichjob
4
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 4: processing genes 272 - 362
Calculating significance of each gene.
Using projection method.
272	ADAMTS8	1
273	ADAMTS9	2.830332e-01
274	ADAMTSL1	4.356332e-01
275	ADAMTSL2	3.672242e-02
276	ADAMTSL3	4.407721e-01
277	ADAMTSL4	1
278	ADAMTSL5	1
279	ADAP1	1
280	ADAP2	1
281	ADAR	1
282	ADARB1	1
283	ADARB2	1.872613e-01
284	ADAT1	1
285	ADAT2	1
286	ADAT3	1
287	ADC	1
288	ADCK1	1
289	ADCK2	1
290	ADCK4	1.639851e-01
291	ADCK5	1
292	ADCY1	1
293	ADCY10	5.596469e-01
294	ADCY2	1.064814e-01
295	ADCY3	1
296	ADCY4	8.949511e-02
297	ADCY5	4.551261e-01
298	ADCY6	4.444572e-01
299	ADCY7	1
300	ADCY8	2.277400e-01
301	ADCY9	4.507593e-01
302	ADCYAP1	1
303	ADCYAP1R1	1
304	ADD1	1
305	ADD2	1
306	ADD3	1
307	ADH1A	1
308	ADH1B	1.427710e-01
309	ADH1C	1
310	ADH4	1
311	ADH5	1
312	ADH6	1
313	ADH7	1
314	ADHFE1	7.439780e-03
315	ADI1	1
316	ADIG	1
317	ADIPOQ	1
318	ADIPOR1	1
319	ADIPOR2	1
320	ADK	8.675857e-02
321	ADM	1
322	ADM2	1
323	ADNP	1
324	ADNP2	1
325	ADO	1
326	ADORA1	1
327	ADORA2A	1
328	ADORA2B	1
329	ADORA3	1
330	ADPGK	1
331	ADPRH	1
332	ADPRHL1	1
333	ADPRHL2	1
334	ADRA1A	1
335	ADRA1B	1.282974e-01
336	ADRA1D	1
337	ADRA2A	1
338	ADRA2B	1
339	ADRA2C	1
340	ADRB1	1
341	ADRB2	1
342	ADRB3	1
343	ADRBK1	1
344	ADRBK2	1
345	ADRM1	1
346	ADSL	1
347	ADSS	1.935061e-01
348	ADSSL1	1
349	AEBP1	1
350	AEBP2	1
351	AEN	1
352	AES	1
353	AFAP1	1
354	AFAP1L1	1
355	AFAP1L2	1
356	AFF1	8.082354e-02
357	AFF2	1
358	AFF3	1.364080e-01
359	AFF4	1
360	AFG3L2	1
361	AFM	1.355448e-01
362	AFMID	1
Done

Running MutSig 2:
Scatter job 4: processing genes 272 - 362
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ADCY2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.479208e-01	ci left: 5.903663e-03	ci right 9.392367e-03	k: 75	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: 3.787022e-01	ci left: 8.595766e-03	ci right 1.269681e-02	k: 105	n:10000
ADCY2   10000 perm   2 sec   (4607 perm/sec)   p_kst 1.050000e-02   p_cons 5.730000e-02   p_joint 7.500000e-03

Joint ci ratio: 3.301307e-01	ci left: 5.845775e-03	ci right 8.200977e-03	k: 139	n:20000
Cons ci ratio: 1.131622e-01	ci left: 5.338848e-02	ci right 5.984119e-02	k: 1131	n:20000
KS ci ratio: 2.646529e-01	ci left: 9.413987e-03	ci right 1.233084e-02	k: 216	n:20000
ADCY2   20000 perm   9 sec   (2285 perm/sec)   p_kst 1.080000e-02   p_cons 5.655000e-02   p_joint 6.950000e-03

Joint ci ratio: 2.954537e-01	ci left: 4.972185e-03	ci right 6.725594e-03	k: 174	n:30000
Cons ci ratio: 9.120750e-02	ci left: 5.534861e-02	ci right 6.067072e-02	k: 1739	n:30000
KS ci ratio: 2.152558e-01	ci left: 9.755930e-03	ci right 1.214020e-02	k: 327	n:30000
ADCY2   30000 perm   11 sec   (2618 perm/sec)   p_kst 1.090000e-02   p_cons 5.796667e-02   p_joint 5.800000e-03

Joint ci ratio: 9.488183e-02	ci left: 3.897995e-02	ci right 4.288705e-02	k: 1636	n:40000
Cons ci ratio: 1.117373e-01	ci left: 2.817971e-02	ci right 3.153900e-02	k: 1193	n:40000
KS ci ratio: 1.882394e-01	ci left: 9.714880e-03	ci right 1.175708e-02	k: 428	n:40000
ADCY2   40000 perm   14 sec   (2855 perm/sec)   p_kst 1.070000e-02   p_cons 2.982500e-02   p_joint 4.090000e-02

Joint ci ratio: 1.206380e-01	ci left: 1.943109e-02	ci right 2.194499e-02	k: 1033	n:50000
Cons ci ratio: 9.982055e-02	ci left: 2.842452e-02	ci right 3.143038e-02	k: 1495	n:50000
KS ci ratio: 1.696913e-01	ci left: 9.663382e-03	ci right 1.147412e-02	k: 527	n:50000
ADCY2   50000 perm   17 sec   (2921 perm/sec)   p_kst 1.054000e-02   p_cons 2.990000e-02   p_joint 2.066000e-02

Joint ci ratio: 2.276676e-01	ci left: 4.356993e-03	ci right 5.491709e-03	k: 294	n:60000
Cons ci ratio: 9.060961e-02	ci left: 2.887767e-02	ci right 3.163468e-02	k: 1814	n:60000
KS ci ratio: 1.540002e-01	ci left: 9.860094e-03	ci right 1.152108e-02	k: 640	n:60000
ADCY2   60000 perm   21 sec   (2921 perm/sec)   p_kst 1.066667e-02   p_cons 3.023333e-02   p_joint 4.900000e-03

Joint ci ratio: 2.120734e-01	ci left: 4.342053e-03	ci right 5.385356e-03	k: 339	n:70000
Cons ci ratio: 8.367460e-02	ci left: 2.912652e-02	ci right 3.168403e-02	k: 2127	n:70000
KS ci ratio: 1.414183e-01	ci left: 1.008885e-02	ci right 1.163781e-02	k: 759	n:70000
ADCY2   70000 perm   24 sec   (2919 perm/sec)   p_kst 1.084286e-02   p_cons 3.038571e-02   p_joint 4.842857e-03

Joint ci ratio: 2.011449e-01	ci left: 4.249713e-03	ci right 5.211746e-03	k: 377	n:80000
Cons ci ratio: 7.860445e-02	ci left: 2.896360e-02	ci right 3.134563e-02	k: 2411	n:80000
KS ci ratio: 1.320217e-01	ci left: 1.017993e-02	ci right 1.163087e-02	k: 871	n:80000
ADCY2   80000 perm   27 sec   (2912 perm/sec)   p_kst 1.088750e-02   p_cons 3.013750e-02   p_joint 4.712500e-03

Joint ci ratio: 1.917481e-01	ci left: 4.178971e-03	ci right 5.075640e-03	k: 415	n:90000
Cons ci ratio: 7.431401e-02	ci left: 2.887331e-02	ci right 3.111268e-02	k: 2698	n:90000
KS ci ratio: 1.255760e-01	ci left: 1.003808e-02	ci right 1.139374e-02	k: 963	n:90000
ADCY2   90000 perm   31 sec   (2949 perm/sec)   p_kst 1.070000e-02   p_cons 2.997778e-02   p_joint 4.611111e-03

Joint ci ratio: 1.803898e-01	ci left: 4.275958e-03	ci right 5.133159e-03	k: 469	n:100000
Cons ci ratio: 7.027000e-02	ci left: 2.911845e-02	ci right 3.124891e-02	k: 3017	n:100000
KS ci ratio: 1.194769e-01	ci left: 1.001331e-02	ci right 1.129531e-02	k: 1064	n:100000
ADCY2   100000 perm   34 sec   (2975 perm/sec)   p_kst 1.064000e-02   p_cons 3.017000e-02   p_joint 4.690000e-03

Joint ci ratio: 1.710009e-01	ci left: 4.347889e-03	ci right 5.169466e-03	k: 522	n:110000
Cons ci ratio: 6.687325e-02	ci left: 2.927701e-02	ci right 3.131149e-02	k: 3331	n:110000
KS ci ratio: 1.138432e-01	ci left: 1.005620e-02	ci right 1.127890e-02	k: 1172	n:110000
ADCY2   110000 perm   37 sec   (2988 perm/sec)   p_kst 1.065455e-02   p_cons 3.028182e-02   p_joint 4.745455e-03

Joint ci ratio: 1.646727e-01	ci left: 4.312876e-03	ci right 5.094689e-03	k: 563	n:120000
Cons ci ratio: 6.406182e-02	ci left: 2.928814e-02	ci right 3.123465e-02	k: 3630	n:120000
KS ci ratio: 1.095883e-01	ci left: 9.971508e-03	ci right 1.113566e-02	k: 1265	n:120000
ADCY2   120000 perm   40 sec   (2992 perm/sec)   p_kst 1.054167e-02   p_cons 3.025000e-02   p_joint 4.691667e-03

Joint ci ratio: 1.588669e-01	ci left: 4.291113e-03	ci right 5.038939e-03	k: 605	n:130000
Cons ci ratio: 6.140056e-02	ci left: 2.946579e-02	ci right 3.133985e-02	k: 3951	n:130000
KS ci ratio: 1.052697e-01	ci left: 9.997954e-03	ci right 1.111635e-02	k: 1371	n:130000
ADCY2   130000 perm   43 sec   (2991 perm/sec)   p_kst 1.054615e-02   p_cons 3.039231e-02   p_joint 4.653846e-03

Joint ci ratio: 1.537540e-01	ci left: 4.266004e-03	ci right 4.983322e-03	k: 646	n:140000
Cons ci ratio: 5.941228e-02	ci left: 2.926043e-02	ci right 3.105910e-02	k: 4221	n:140000
KS ci ratio: 1.016681e-01	ci left: 9.972652e-03	ci right 1.104777e-02	k: 1470	n:140000
ADCY2   140000 perm   47 sec   (2981 perm/sec)   p_kst 1.050000e-02   p_cons 3.015000e-02   p_joint 4.614286e-03

Joint ci ratio: 1.482416e-01	ci left: 4.295935e-03	ci right 4.990093e-03	k: 695	n:150000
Cons ci ratio: 5.752616e-02	ci left: 2.916221e-02	ci right 3.089602e-02	k: 4503	n:150000
KS ci ratio: 9.812861e-02	ci left: 1.000983e-02	ci right 1.104922e-02	k: 1578	n:150000
ADCY2   150000 perm   51 sec   (2970 perm/sec)   p_kst 1.052000e-02   p_cons 3.002000e-02   p_joint 4.633333e-03

Joint ci ratio: 1.433792e-01	ci left: 4.316499e-03	ci right 4.989144e-03	k: 743	n:160000
Cons ci ratio: 5.568315e-02	ci left: 2.920653e-02	ci right 3.088556e-02	k: 4806	n:160000
KS ci ratio: 9.473637e-02	ci left: 1.008565e-02	ci right 1.109470e-02	k: 1693	n:160000
ADCY2   160000 perm   54 sec   (2957 perm/sec)   p_kst 1.058125e-02   p_cons 3.003750e-02   p_joint 4.643750e-03

Joint ci ratio: 6.450965e-02	ci left: 2.057258e-02	ci right 2.194970e-02	k: 3613	n:170000
Cons ci ratio: 5.386552e-02	ci left: 2.939736e-02	ci right 3.103047e-02	k: 5135	n:170000
KS ci ratio: 9.208571e-02	ci left: 1.006112e-02	ci right 1.103803e-02	k: 1792	n:170000
ADCY2   170000 perm   58 sec   (2935 perm/sec)   p_kst 1.054118e-02   p_cons 3.020588e-02   p_joint 2.125294e-02

Outputting figure to mutsig2_images.part000000000004/ADCY2.2_3376_170000_0.010541_0.030206_0.021253.png
                gene_name: ADCY2
               theta_stop: 0.092 
                    nperm: 170000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.010 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.030 
      ci_cons_bounds_left: 0.029 
     ci_cons_bounds_right: 0.031 
                  p_joint: 0.021 
     ci_joint_bounds_left: 0.021 
    ci_joint_bounds_right: 0.022 

Current progress: 25 percent done.
ADHFE1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.198857e-01	ci left: 2.740624e-02	ci right 3.427066e-02	k: 307	n:10000
Cons ci ratio: 4.730797e-02	ci left: 3.973494e-01	ci right 4.167048e-01	k: 4070	n:10000
KS ci ratio: 4.002490e-01	ci left: 7.602648e-03	ci right 1.149110e-02	k: 94	n:10000
ADHFE1   10000 perm   2 sec   (5843 perm/sec)   p_kst 9.400000e-03   p_cons 4.070000e-01   p_joint 3.070000e-02

Joint ci ratio: 1.178714e-01	ci left: 4.930341e-02	ci right 5.552753e-02	k: 1047	n:20000
Cons ci ratio: 3.336847e-02	ci left: 4.014269e-01	ci right 4.150998e-01	k: 8165	n:20000
KS ci ratio: 2.717025e-01	ci left: 8.900643e-03	ci right 1.174443e-02	k: 205	n:20000
ADHFE1   20000 perm   4 sec   (4997 perm/sec)   p_kst 1.025000e-02   p_cons 4.082500e-01   p_joint 5.235000e-02

Joint ci ratio: 7.390625e-02	ci left: 8.255602e-02	ci right 8.892448e-02	k: 2571	n:30000
Cons ci ratio: 2.635015e-02	ci left: 4.188978e-01	ci right 4.301168e-01	k: 12735	n:30000
KS ci ratio: 2.236817e-01	ci left: 8.999499e-03	ci right 1.129686e-02	k: 303	n:30000
ADHFE1   30000 perm   6 sec   (4852 perm/sec)   p_kst 1.010000e-02   p_cons 4.245000e-01   p_joint 8.570000e-02

Joint ci ratio: 6.438901e-02	ci left: 8.206300e-02	ci right 8.754745e-02	k: 3391	n:40000
Cons ci ratio: 2.290451e-02	ci left: 4.178523e-01	ci right 4.275590e-01	k: 16908	n:40000
KS ci ratio: 1.904966e-01	ci left: 9.476622e-03	ci right 1.149539e-02	k: 418	n:40000
ADHFE1   40000 perm   8 sec   (4725 perm/sec)   p_kst 1.045000e-02   p_cons 4.227000e-01   p_joint 8.477500e-02

Joint ci ratio: 5.755432e-02	ci left: 8.245125e-02	ci right 8.735706e-02	k: 4244	n:50000
Cons ci ratio: 2.100296e-02	ci left: 4.062833e-01	ci right 4.149271e-01	k: 20530	n:50000
KS ci ratio: 1.751363e-01	ci left: 9.050745e-03	ci right 1.080686e-02	k: 495	n:50000
ADHFE1   50000 perm   11 sec   (4637 perm/sec)   p_kst 9.900000e-03   p_cons 4.106000e-01   p_joint 8.488000e-02

Joint ci ratio: 6.915191e-02	ci left: 4.907277e-02	ci right 5.260417e-02	k: 3049	n:60000
Cons ci ratio: 1.913092e-02	ci left: 4.077249e-01	ci right 4.156170e-01	k: 24700	n:60000
KS ci ratio: 1.608627e-01	ci left: 9.011227e-03	ci right 1.060339e-02	k: 587	n:60000
ADHFE1   60000 perm   13 sec   (4545 perm/sec)   p_kst 9.783333e-03   p_cons 4.116667e-01   p_joint 5.081667e-02

Joint ci ratio: 6.396865e-02	ci left: 4.928328e-02	ci right 5.255408e-02	k: 3563	n:70000
Cons ci ratio: 1.772162e-02	ci left: 4.077512e-01	ci right 4.150561e-01	k: 28798	n:70000
KS ci ratio: 1.501506e-01	ci left: 8.918411e-03	ci right 1.037981e-02	k: 674	n:70000
ADHFE1   70000 perm   16 sec   (4452 perm/sec)   p_kst 9.628571e-03   p_cons 4.114000e-01   p_joint 5.090000e-02

Joint ci ratio: 5.989259e-02	ci left: 4.930074e-02	ci right 5.235694e-02	k: 4065	n:80000
Cons ci ratio: 1.660281e-02	ci left: 4.072381e-01	ci right 4.140684e-01	k: 32852	n:80000
KS ci ratio: 1.409548e-01	ci left: 8.899705e-03	ci right 1.026122e-02	k: 765	n:80000
ADHFE1   80000 perm   18 sec   (4332 perm/sec)   p_kst 9.562500e-03   p_cons 4.106500e-01   p_joint 5.081250e-02

Joint ci ratio: 5.647544e-02	ci left: 4.937432e-02	ci right 5.225472e-02	k: 4572	n:90000
Cons ci ratio: 1.563232e-02	ci left: 4.080826e-01	ci right 4.145232e-01	k: 37017	n:90000
KS ci ratio: 1.323326e-01	ci left: 9.016232e-03	ci right 1.030456e-02	k: 868	n:90000
ADHFE1   90000 perm   21 sec   (4195 perm/sec)   p_kst 9.644444e-03   p_cons 4.113000e-01   p_joint 5.080000e-02

Joint ci ratio: 5.343407e-02	ci left: 4.970374e-02	ci right 5.244237e-02	k: 5106	n:100000
Cons ci ratio: 1.449628e-02	ci left: 4.193059e-01	ci right 4.254386e-01	k: 42237	n:100000
KS ci ratio: 1.251209e-01	ci left: 9.111484e-03	ci right 1.033721e-02	k: 971	n:100000
ADHFE1   100000 perm   24 sec   (4132 perm/sec)   p_kst 9.710000e-03   p_cons 4.223700e-01   p_joint 5.106000e-02

Joint ci ratio: 5.086017e-02	ci left: 4.993176e-02	ci right 5.254652e-02	k: 5635	n:110000
Cons ci ratio: 1.381671e-02	ci left: 4.196239e-01	ci right 4.254711e-01	k: 46480	n:110000
KS ci ratio: 1.186943e-01	ci left: 9.235092e-03	ci right 1.040915e-02	k: 1079	n:110000
ADHFE1   110000 perm   27 sec   (4070 perm/sec)   p_kst 9.809091e-03   p_cons 4.225455e-01   p_joint 5.122727e-02

Joint ci ratio: 4.857166e-02	ci left: 5.023148e-02	ci right 5.274025e-02	k: 6177	n:120000
Cons ci ratio: 1.319884e-02	ci left: 4.208436e-01	ci right 4.264434e-01	k: 50837	n:120000
KS ci ratio: 1.127830e-01	ci left: 9.404239e-03	ci right 1.053630e-02	k: 1195	n:120000
ADHFE1   120000 perm   30 sec   (4006 perm/sec)   p_kst 9.958333e-03   p_cons 4.236417e-01   p_joint 5.147500e-02

Joint ci ratio: 4.665452e-02	ci left: 5.030474e-02	ci right 5.271532e-02	k: 6695	n:130000
Cons ci ratio: 1.266876e-02	ci left: 4.214268e-01	ci right 4.268074e-01	k: 55135	n:130000
KS ci ratio: 1.091986e-01	ci left: 9.279105e-03	ci right 1.035831e-02	k: 1275	n:130000
ADHFE1   130000 perm   33 sec   (3943 perm/sec)   p_kst 9.807692e-03   p_cons 4.241154e-01   p_joint 5.150000e-02

Joint ci ratio: 4.494455e-02	ci left: 5.037627e-02	ci right 5.269950e-02	k: 7214	n:140000
Cons ci ratio: 1.220564e-02	ci left: 4.216163e-01	ci right 4.268011e-01	k: 59389	n:140000
KS ci ratio: 1.049244e-01	ci left: 9.353202e-03	ci right 1.039582e-02	k: 1381	n:140000
ADHFE1   140000 perm   36 sec   (3883 perm/sec)   p_kst 9.864286e-03   p_cons 4.242071e-01   p_joint 5.152857e-02

Joint ci ratio: 4.339204e-02	ci left: 5.047925e-02	ci right 5.272479e-02	k: 7739	n:150000
Cons ci ratio: 1.179308e-02	ci left: 4.216505e-01	ci right 4.266591e-01	k: 63623	n:150000
KS ci ratio: 1.014259e-01	ci left: 9.359637e-03	ci right 1.036611e-02	k: 1478	n:150000
ADHFE1   150000 perm   39 sec   (3823 perm/sec)   p_kst 9.853333e-03   p_cons 4.241533e-01   p_joint 5.159333e-02

Joint ci ratio: 4.198469e-02	ci left: 5.058294e-02	ci right 5.275835e-02	k: 8266	n:160000
Cons ci ratio: 1.140803e-02	ci left: 4.221826e-01	ci right 4.270327e-01	k: 67937	n:160000
KS ci ratio: 9.791105e-02	ci left: 9.432853e-03	ci right 1.041003e-02	k: 1586	n:160000
ADHFE1   160000 perm   43 sec   (3763 perm/sec)   p_kst 9.912500e-03   p_cons 4.246063e-01   p_joint 5.166250e-02

Outputting figure to mutsig2_images.part000000000004/ADHFE1.2_1460_160000_0.0099125_0.42461_0.051663.png
                gene_name: ADHFE1
               theta_stop: 0.098 
                    nperm: 160000 
                     p_ks: 0.0099 
        ci_ks_bounds_left: 0.0094 
       ci_ks_bounds_right: 0.010 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.052 
     ci_joint_bounds_left: 0.051 
    ci_joint_bounds_right: 0.053 

Current progress: 50 percent done.
AFF1
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: 1.663683e-02	ci left: 8.402009e-01	ci right 8.543961e-01	k: 8474	n:10000
KS ci ratio: 4.153682e-02	ci left: 4.611763e-01	ci right 4.808406e-01	k: 4710	n:10000
AFF1   10000 perm   2 sec   (4701 perm/sec)   p_kst 4.710000e-01   p_cons 8.474000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000004/AFF1.2_3758_10000_0.471_0.8474_1.png
                gene_name: AFF1
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.85 
      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: 75 percent done.
AFF3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.517048e-02	ci left: 4.197698e-01	ci right 4.392713e-01	k: 4295	n:10000
Cons ci ratio: 5.100929e-02	ci left: 3.617196e-01	ci right 3.807555e-01	k: 3712	n:10000
KS ci ratio: 5.545381e-02	ci left: 3.238620e-01	ci right 3.424353e-01	k: 3331	n:10000
AFF3   10000 perm   2 sec   (5095 perm/sec)   p_kst 3.331000e-01   p_cons 3.712000e-01   p_joint 4.295000e-01

Outputting figure to mutsig2_images.part000000000004/AFF3.2_3848_10000_0.3331_0.3712_0.4295.png
                gene_name: AFF3
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    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.165.3896/
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/181708/iteration1/scatter.0000000004
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 4 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119489: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000005> was used as the working directory.
Started at Wed Oct 10 10:41:37 2012
Results reported at Wed Oct 10 14:10:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000005.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000005.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 5  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :  13227.94 sec.
    Max Memory :      1555 MB
    Max Swap   :      3960 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.165.3896/
-whichjob
5
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 5: processing genes 363 - 452
Calculating significance of each gene.
Using projection method.
363	AFP	5.745948e-02
364	AFTPH	2.811677e-01
365	AGA	1
366	AGAP1	1
367	AGAP11	1
368	AGAP2	1
369	AGAP3	3.327753e-01
370	AGAP5	1
371	AGAP6	1
372	AGAP7	1
373	AGAP8	1
374	AGBL1	1.628307e-01
375	AGBL2	1
376	AGBL4	1
377	AGBL5	1
378	AGER	1
379	AGFG1	1
380	AGFG2	2.354919e-03
381	AGGF1	1
382	AGK	1
383	AGL	2.810950e-01
384	AGMAT	1
385	AGPAT1	1
386	AGPAT2	1
387	AGPAT3	1
388	AGPAT4	1
389	AGPAT5	1
390	AGPAT6	1
391	AGPAT9	1
392	AGPHD1	1
393	AGPS	1
394	AGR2	1
395	AGR3	1
396	AGRN	1
397	AGRP	1
398	AGT	1
399	AGTPBP1	1
400	AGTR1	1
401	AGTR2	1
402	AGTRAP	1
403	AGXT	1
404	AGXT2	1
405	AGXT2L1	1
406	AGXT2L2	1
407	AHCTF1	2.527701e-01
408	AHCY	1
409	AHCYL1	1
410	AHCYL2	1
411	AHDC1	1
412	AHI1	1
413	AHNAK	1
414	AHNAK2	2.273899e-01
415	AHR	6.497312e-03
416	AHRR	1
417	AHSA1	1
418	AHSA2	1
419	AHSG	1
420	AHSP	1
421	AICDA	1
422	AIDA	1
423	AIF1	1
424	AIF1L	1
425	AIFM1	1
426	AIFM2	1.641401e-03
427	AIFM3	1
428	AIG1	1
429	AIM1	1
430	AIM1L	1
431	AIM2	1
432	AIMP1	1
433	AIMP2	1
434	AIP	1
435	AIPL1	1
436	AIRE	2.474837e-01
437	AJAP1	1
438	AK1	1
439	AK2	1
440	AK3	1
441	AK3L1	1
442	AK5	1
443	AK7	1
444	AKAP1	1
445	AKAP10	1.673484e-01
446	AKAP11	1
447	AKAP12	1
448	AKAP13	1
449	AKAP14	1
450	AKAP2	1
451	AKAP3	1
452	AKAP4	1
Done

Running MutSig 2:
Scatter job 5: processing genes 363 - 452
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: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 4.444821e-03	ci left: 9.850162e-01	ci right 9.894933e-01	k: 9874	n:10000
KS ci ratio: 3.143295e-02	ci left: 5.989536e-01	ci right 6.181831e-01	k: 6086	n:10000
AHNAK2   10000 perm   5 sec   (1888 perm/sec)   p_kst 6.086000e-01   p_cons 9.874000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000005/AHNAK2.4_17416_10000_0.6086_0.9874_1.png
                gene_name: AHNAK2
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.99 
      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: 17 percent done.
AHNAK
Processing conservation and coverage...
56% 
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: 2.147262e-02	ci left: 7.608141e-01	ci right 7.774289e-01	k: 7692	n:10000
KS ci ratio: 2.126095e-02	ci left: 7.643573e-01	ci right 7.808836e-01	k: 7727	n:10000
AHNAK   10000 perm   5 sec   (2018 perm/sec)   p_kst 7.727000e-01   p_cons 7.692000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000005/AHNAK.3_17801_10000_0.7727_0.7692_1.png
                gene_name: AHNAK
               theta_stop: 0.021 
                    nperm: 10000 
                     p_ks: 0.77 
        ci_ks_bounds_left: 0.76 
       ci_ks_bounds_right: 0.78 
                   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.
AGFG2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.476731e-02	ci left: 4.241566e-01	ci right 4.436819e-01	k: 4339	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: 6.304674e-02	ci left: 2.699278e-01	ci right 2.876013e-01	k: 2787	n:10000
AGFG2   10000 perm   2 sec   (5533 perm/sec)   p_kst 2.787000e-01   p_cons 4.726000e-01   p_joint 4.339000e-01

Outputting figure to mutsig2_images.part000000000005/AGFG2.2_1494_10000_0.2787_0.4726_0.4339.png
                gene_name: AGFG2
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.48 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 50 percent done.
AHCTF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.959510e+00	ci left: 6.187149e-05	ci right 8.764745e-04	k: 3	n:10000
Cons ci ratio: 2.331969e-02	ci left: 7.298693e-01	ci right 7.471916e-01	k: 7386	n:10000
KS ci ratio: 2.771443e+00	ci left: 2.531778e-06	ci right 5.570370e-04	k: 1	n:10000
AHCTF1   10000 perm   3 sec   (3840 perm/sec)   p_kst 1.000000e-04   p_cons 7.386000e-01   p_joint 3.000000e-04

Joint ci ratio: 1.239272e+00	ci left: 2.057886e-04	ci right 8.540675e-04	k: 9	n:20000
Cons ci ratio: 1.650894e-02	ci left: 7.319977e-01	ci right 7.442330e-01	k: 14763	n:20000
KS ci ratio: 2.262987e+00	ci left: 1.211069e-05	ci right 3.611872e-04	k: 2	n:20000
AHCTF1   20000 perm   6 sec   (3483 perm/sec)   p_kst 1.000000e-04   p_cons 7.381500e-01   p_joint 4.500000e-04

Joint ci ratio: 1.752902e+00	ci left: 3.633000e-05	ci right 3.413508e-04	k: 4	n:30000
Cons ci ratio: 1.348130e-02	ci left: 7.330852e-01	ci right 7.430686e-01	k: 22143	n:30000
KS ci ratio: 2.263062e+00	ci left: 8.073745e-06	ci right 2.408020e-04	k: 2	n:30000
AHCTF1   30000 perm   9 sec   (3351 perm/sec)   p_kst 6.666667e-05   p_cons 7.381000e-01   p_joint 1.333333e-04

Joint ci ratio: 1.385773e+00	ci left: 7.036188e-05	ci right 3.605334e-04	k: 7	n:40000
Cons ci ratio: 1.164573e-02	ci left: 7.347418e-01	ci right 7.433735e-01	k: 29563	n:40000
KS ci ratio: 1.600193e+00	ci left: 4.058837e-05	ci right 2.916840e-04	k: 5	n:40000
AHCTF1   40000 perm   12 sec   (3264 perm/sec)   p_kst 1.250000e-04   p_cons 7.390750e-01   p_joint 1.750000e-04

Joint ci ratio: 1.181783e+00	ci left: 9.591181e-05	ci right 3.677763e-04	k: 10	n:50000
Cons ci ratio: 1.043396e-02	ci left: 7.345440e-01	ci right 7.422683e-01	k: 36921	n:50000
KS ci ratio: 1.481502e+00	ci left: 4.403912e-05	ci right 2.611710e-04	k: 6	n:50000
AHCTF1   50000 perm   16 sec   (3204 perm/sec)   p_kst 1.200000e-04   p_cons 7.384200e-01   p_joint 2.000000e-04

Joint ci ratio: 1.481522e+00	ci left: 3.669909e-05	ci right 2.176451e-04	k: 6	n:60000
Cons ci ratio: 9.490849e-03	ci left: 7.362695e-01	ci right 7.433073e-01	k: 44388	n:60000
KS ci ratio: 1.481522e+00	ci left: 3.669909e-05	ci right 2.176451e-04	k: 6	n:60000
AHCTF1   60000 perm   19 sec   (3144 perm/sec)   p_kst 1.000000e-04   p_cons 7.398000e-01   p_joint 1.000000e-04

Joint ci ratio: 1.306573e+00	ci left: 4.934171e-05	ci right 2.251759e-04	k: 8	n:70000
Cons ci ratio: 8.786498e-03	ci left: 7.365471e-01	ci right 7.430616e-01	k: 51787	n:70000
KS ci ratio: 1.306573e+00	ci left: 4.934171e-05	ci right 2.251759e-04	k: 8	n:70000
AHCTF1   70000 perm   23 sec   (3097 perm/sec)   p_kst 1.142857e-04   p_cons 7.398143e-01   p_joint 1.142857e-04

Joint ci ratio: 1.239528e+00	ci left: 5.144341e-05	ci right 2.135493e-04	k: 9	n:80000
Cons ci ratio: 8.233469e-03	ci left: 7.360798e-01	ci right 7.421778e-01	k: 59131	n:80000
KS ci ratio: 1.239528e+00	ci left: 5.144341e-05	ci right 2.135493e-04	k: 9	n:80000
AHCTF1   80000 perm   26 sec   (3049 perm/sec)   p_kst 1.125000e-04   p_cons 7.391375e-01   p_joint 1.125000e-04

Joint ci ratio: 1.131525e+00	ci left: 6.101442e-05	ci right 2.186788e-04	k: 11	n:90000
Cons ci ratio: 7.771175e-03	ci left: 7.358276e-01	ci right 7.415792e-01	k: 66484	n:90000
KS ci ratio: 1.131525e+00	ci left: 6.101442e-05	ci right 2.186788e-04	k: 11	n:90000
AHCTF1   90000 perm   30 sec   (3007 perm/sec)   p_kst 1.222222e-04   p_cons 7.387111e-01   p_joint 1.222222e-04

Joint ci ratio: 1.012059e+00	ci left: 7.654135e-05	ci right 2.348851e-04	k: 14	n:100000
Cons ci ratio: 7.385967e-03	ci left: 7.352627e-01	ci right 7.407234e-01	k: 73800	n:100000
KS ci ratio: 1.012059e+00	ci left: 7.654135e-05	ci right 2.348851e-04	k: 14	n:100000
AHCTF1   100000 perm   34 sec   (2967 perm/sec)   p_kst 1.400000e-04   p_cons 7.380000e-01   p_joint 1.400000e-04

Joint ci ratio: 9.506619e-01	ci left: 8.314205e-05	ci right 2.361984e-04	k: 16	n:110000
Cons ci ratio: 7.033140e-03	ci left: 7.358922e-01	ci right 7.410952e-01	k: 81235	n:110000
KS ci ratio: 9.506619e-01	ci left: 8.314205e-05	ci right 2.361984e-04	k: 16	n:110000
AHCTF1   110000 perm   38 sec   (2924 perm/sec)   p_kst 1.454545e-04   p_cons 7.385000e-01   p_joint 1.454545e-04

Joint ci ratio: 8.992347e-01	ci left: 8.890185e-05	ci right 2.370543e-04	k: 18	n:120000
Cons ci ratio: 6.731251e-03	ci left: 7.361458e-01	ci right 7.411260e-01	k: 88637	n:120000
KS ci ratio: 8.992347e-01	ci left: 8.890185e-05	ci right 2.370543e-04	k: 18	n:120000
AHCTF1   120000 perm   42 sec   (2885 perm/sec)   p_kst 1.500000e-04   p_cons 7.386417e-01   p_joint 1.500000e-04

Joint ci ratio: 8.764678e-01	ci left: 8.799638e-05	ci right 2.282280e-04	k: 19	n:130000
Cons ci ratio: 6.243796e-03	ci left: 7.496276e-01	ci right 7.543304e-01	k: 97758	n:130000
KS ci ratio: 8.764678e-01	ci left: 8.799638e-05	ci right 2.282280e-04	k: 19	n:130000
AHCTF1   130000 perm   46 sec   (2840 perm/sec)   p_kst 1.461538e-04   p_cons 7.519846e-01   p_joint 1.461538e-04

Joint ci ratio: 8.764729e-01	ci left: 8.171078e-05	ci right 2.119266e-04	k: 19	n:140000
Cons ci ratio: 6.018614e-03	ci left: 7.495930e-01	ci right 7.541252e-01	k: 105261	n:140000
KS ci ratio: 8.764729e-01	ci left: 8.171078e-05	ci right 2.119266e-04	k: 19	n:140000
AHCTF1   140000 perm   50 sec   (2805 perm/sec)   p_kst 1.357143e-04   p_cons 7.518643e-01   p_joint 1.357143e-04

Joint ci ratio: 8.553514e-01	ci left: 8.144531e-05	ci right 2.059150e-04	k: 20	n:150000
Cons ci ratio: 5.808887e-03	ci left: 7.500337e-01	ci right 7.544099e-01	k: 112834	n:150000
KS ci ratio: 8.553514e-01	ci left: 8.144531e-05	ci right 2.059150e-04	k: 20	n:150000
AHCTF1   150000 perm   54 sec   (2772 perm/sec)   p_kst 1.333333e-04   p_cons 7.522267e-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: 5.617761e-03	ci left: 7.505469e-01	ci right 7.547814e-01	k: 120427	n:160000
KS ci ratio: 8.356867e-01	ci left: 8.124760e-05	ci right 2.006226e-04	k: 21	n:160000
AHCTF1   160000 perm   58 sec   (2739 perm/sec)   p_kst 1.312500e-04   p_cons 7.526687e-01   p_joint 1.312500e-04

Joint ci ratio: 8.173188e-01	ci left: 8.110338e-05	ci right 1.959245e-04	k: 22	n:170000
Cons ci ratio: 5.455513e-03	ci left: 7.502348e-01	ci right 7.543448e-01	k: 127890	n:170000
KS ci ratio: 8.173188e-01	ci left: 8.110338e-05	ci right 1.959245e-04	k: 22	n:170000
AHCTF1   170000 perm   63 sec   (2701 perm/sec)   p_kst 1.294118e-04   p_cons 7.522941e-01   p_joint 1.294118e-04

Joint ci ratio: 8.173220e-01	ci left: 7.659755e-05	ci right 1.850401e-04	k: 22	n:180000
Cons ci ratio: 5.299825e-03	ci left: 7.504327e-01	ci right 7.544259e-01	k: 135438	n:180000
KS ci ratio: 8.173220e-01	ci left: 7.659755e-05	ci right 1.850401e-04	k: 22	n:180000
AHCTF1   180000 perm   68 sec   (2658 perm/sec)   p_kst 1.222222e-04   p_cons 7.524333e-01   p_joint 1.222222e-04

Joint ci ratio: 8.001140e-01	ci left: 7.673848e-05	ci right 1.816329e-04	k: 23	n:190000
Cons ci ratio: 5.156674e-03	ci left: 7.506164e-01	ci right 7.545023e-01	k: 142987	n:190000
KS ci ratio: 8.001140e-01	ci left: 7.673848e-05	ci right 1.816329e-04	k: 23	n:190000
AHCTF1   190000 perm   72 sec   (2630 perm/sec)   p_kst 1.210526e-04   p_cons 7.525632e-01   p_joint 1.210526e-04

Joint ci ratio: 7.839490e-01	ci left: 7.688773e-05	ci right 1.785453e-04	k: 24	n:200000
Cons ci ratio: 5.033636e-03	ci left: 7.501062e-01	ci right 7.538965e-01	k: 150401	n:200000
KS ci ratio: 7.839490e-01	ci left: 7.688773e-05	ci right 1.785453e-04	k: 24	n:200000
AHCTF1   200000 perm   77 sec   (2603 perm/sec)   p_kst 1.200000e-04   p_cons 7.520050e-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: 4.910260e-03	ci left: 7.503094e-01	ci right 7.540074e-01	k: 157954	n:210000
KS ci ratio: 7.839515e-01	ci left: 7.322634e-05	ci right 1.700433e-04	k: 24	n:210000
AHCTF1   210000 perm   82 sec   (2575 perm/sec)   p_kst 1.142857e-04   p_cons 7.521619e-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: 4.797168e-03	ci left: 7.503676e-01	ci right 7.539803e-01	k: 165479	n:220000
KS ci ratio: 7.543563e-01	ci left: 7.720169e-05	ci right 1.731590e-04	k: 26	n:220000
AHCTF1   220000 perm   86 sec   (2549 perm/sec)   p_kst 1.181818e-04   p_cons 7.521773e-01   p_joint 1.181818e-04

Joint ci ratio: 7.543584e-01	ci left: 7.384504e-05	ci right 1.656305e-04	k: 26	n:230000
Cons ci ratio: 4.694172e-03	ci left: 7.502123e-01	ci right 7.537465e-01	k: 172956	n:230000
KS ci ratio: 7.543584e-01	ci left: 7.384504e-05	ci right 1.656305e-04	k: 26	n:230000
AHCTF1   230000 perm   91 sec   (2517 perm/sec)   p_kst 1.130435e-04   p_cons 7.519826e-01   p_joint 1.130435e-04

Joint ci ratio: 7.407656e-01	ci left: 7.413948e-05	ci right 1.636774e-04	k: 27	n:240000
Cons ci ratio: 4.598408e-03	ci left: 7.499999e-01	ci right 7.534607e-01	k: 180416	n:240000
KS ci ratio: 7.407656e-01	ci left: 7.413948e-05	ci right 1.636774e-04	k: 27	n:240000
AHCTF1   240000 perm   97 sec   (2485 perm/sec)   p_kst 1.125000e-04   p_cons 7.517333e-01   p_joint 1.125000e-04

Joint ci ratio: 7.278820e-01	ci left: 7.442444e-05	ci right 1.618671e-04	k: 28	n:250000
Cons ci ratio: 4.502572e-03	ci left: 7.502782e-01	ci right 7.536680e-01	k: 187994	n:250000
KS ci ratio: 7.278820e-01	ci left: 7.442444e-05	ci right 1.618671e-04	k: 28	n:250000
AHCTF1   250000 perm   102 sec   (2456 perm/sec)   p_kst 1.120000e-04   p_cons 7.519760e-01   p_joint 1.120000e-04

Joint ci ratio: 7.278837e-01	ci left: 7.156191e-05	ci right 1.556416e-04	k: 28	n:260000
Cons ci ratio: 4.416536e-03	ci left: 7.501927e-01	ci right 7.535171e-01	k: 195483	n:260000
KS ci ratio: 7.278837e-01	ci left: 7.156191e-05	ci right 1.556416e-04	k: 28	n:260000
AHCTF1   260000 perm   107 sec   (2422 perm/sec)   p_kst 1.076923e-04   p_cons 7.518577e-01   p_joint 1.076923e-04

Joint ci ratio: 7.278853e-01	ci left: 6.891143e-05	ci right 1.498773e-04	k: 28	n:270000
Cons ci ratio: 4.334646e-03	ci left: 7.501661e-01	ci right 7.534285e-01	k: 202986	n:270000
KS ci ratio: 7.278853e-01	ci left: 6.891143e-05	ci right 1.498773e-04	k: 28	n:270000
AHCTF1   270000 perm   113 sec   (2380 perm/sec)   p_kst 1.037037e-04   p_cons 7.518000e-01   p_joint 1.037037e-04

Joint ci ratio: 6.929238e-01	ci left: 7.522619e-05	ci right 1.571464e-04	k: 31	n:280000
Cons ci ratio: 4.255438e-03	ci left: 7.502922e-01	ci right 7.534954e-01	k: 210531	n:280000
KS ci ratio: 6.929238e-01	ci left: 7.522619e-05	ci right 1.571464e-04	k: 31	n:280000
AHCTF1   280000 perm   119 sec   (2346 perm/sec)   p_kst 1.107143e-04   p_cons 7.518964e-01   p_joint 1.107143e-04

Joint ci ratio: 6.722339e-01	ci left: 7.833119e-05	ci right 1.598041e-04	k: 33	n:290000
Cons ci ratio: 4.183936e-03	ci left: 7.500957e-01	ci right 7.532441e-01	k: 217985	n:290000
KS ci ratio: 6.722339e-01	ci left: 7.833119e-05	ci right 1.598041e-04	k: 33	n:290000
AHCTF1   290000 perm   126 sec   (2305 perm/sec)   p_kst 1.137931e-04   p_cons 7.516724e-01   p_joint 1.137931e-04

Joint ci ratio: 6.444032e-01	ci left: 8.404790e-05	ci right 1.661267e-04	k: 36	n:300000
Cons ci ratio: 4.115072e-03	ci left: 7.499896e-01	ci right 7.530855e-01	k: 225462	n:300000
KS ci ratio: 6.444032e-01	ci left: 8.404790e-05	ci right 1.661267e-04	k: 36	n:300000
AHCTF1   300000 perm   132 sec   (2270 perm/sec)   p_kst 1.200000e-04   p_cons 7.515400e-01   p_joint 1.200000e-04

Joint ci ratio: 6.358680e-01	ci left: 8.403817e-05	ci right 1.645112e-04	k: 37	n:310000
Cons ci ratio: 4.045162e-03	ci left: 7.502916e-01	ci right 7.533360e-01	k: 233063	n:310000
KS ci ratio: 6.358680e-01	ci left: 8.403817e-05	ci right 1.645112e-04	k: 37	n:310000
AHCTF1   310000 perm   139 sec   (2237 perm/sec)   p_kst 1.193548e-04   p_cons 7.518161e-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: 3.983528e-03	ci left: 7.501210e-01	ci right 7.531182e-01	k: 240519	n:320000
KS ci ratio: 6.276631e-01	ci left: 8.403590e-05	ci right 1.629900e-04	k: 38	n:320000
AHCTF1   320000 perm   144 sec   (2219 perm/sec)   p_kst 1.187500e-04   p_cons 7.516219e-01   p_joint 1.187500e-04

Joint ci ratio: 6.197679e-01	ci left: 8.404013e-05	ci right 1.615549e-04	k: 39	n:330000
Cons ci ratio: 3.921345e-03	ci left: 7.502739e-01	ci right 7.532247e-01	k: 248078	n:330000
KS ci ratio: 6.197679e-01	ci left: 8.404013e-05	ci right 1.615549e-04	k: 39	n:330000
AHCTF1   330000 perm   150 sec   (2194 perm/sec)   p_kst 1.181818e-04   p_cons 7.517515e-01   p_joint 1.181818e-04

Joint ci ratio: 6.121633e-01	ci left: 8.405007e-05	ci right 1.601985e-04	k: 40	n:340000
Cons ci ratio: 3.866429e-03	ci left: 7.499878e-01	ci right 7.528961e-01	k: 255491	n:340000
KS ci ratio: 6.121633e-01	ci left: 8.405007e-05	ci right 1.601985e-04	k: 40	n:340000
AHCTF1   340000 perm   156 sec   (2174 perm/sec)   p_kst 1.176471e-04   p_cons 7.514441e-01   p_joint 1.176471e-04

Joint ci ratio: 5.779337e-01	ci left: 9.378238e-05	ci right 1.720349e-04	k: 45	n:350000
Cons ci ratio: 3.811478e-03	ci left: 7.499417e-01	ci right 7.528084e-01	k: 262982	n:350000
KS ci ratio: 5.779337e-01	ci left: 9.378238e-05	ci right 1.720349e-04	k: 45	n:350000
AHCTF1   350000 perm   163 sec   (2151 perm/sec)   p_kst 1.285714e-04   p_cons 7.513771e-01   p_joint 1.285714e-04

Joint ci ratio: 5.779347e-01	ci left: 9.117727e-05	ci right 1.672563e-04	k: 45	n:360000
Cons ci ratio: 3.758469e-03	ci left: 7.499319e-01	ci right 7.527585e-01	k: 270485	n:360000
KS ci ratio: 5.779347e-01	ci left: 9.117727e-05	ci right 1.672563e-04	k: 45	n:360000
AHCTF1   360000 perm   169 sec   (2130 perm/sec)   p_kst 1.250000e-04   p_cons 7.513472e-01   p_joint 1.250000e-04

Joint ci ratio: 5.657658e-01	ci left: 9.333613e-05	ci right 1.689155e-04	k: 47	n:370000
Cons ci ratio: 3.708818e-03	ci left: 7.498010e-01	ci right 7.525897e-01	k: 277943	n:370000
KS ci ratio: 5.657658e-01	ci left: 9.333613e-05	ci right 1.689155e-04	k: 47	n:370000
AHCTF1   370000 perm   175 sec   (2111 perm/sec)   p_kst 1.270270e-04   p_cons 7.511973e-01   p_joint 1.270270e-04

Joint ci ratio: 5.599632e-01	ci left: 9.313671e-05	ci right 1.674730e-04	k: 48	n:380000
Cons ci ratio: 3.658481e-03	ci left: 7.499435e-01	ci right 7.526948e-01	k: 285502	n:380000
KS ci ratio: 5.599632e-01	ci left: 9.313671e-05	ci right 1.674730e-04	k: 48	n:380000
AHCTF1   380000 perm   182 sec   (2093 perm/sec)   p_kst 1.263158e-04   p_cons 7.513211e-01   p_joint 1.263158e-04

Joint ci ratio: 5.435693e-01	ci left: 9.736778e-05	ci right 1.719338e-04	k: 51	n:390000
Cons ci ratio: 3.612443e-03	ci left: 7.498400e-01	ci right 7.525562e-01	k: 292968	n:390000
KS ci ratio: 5.435693e-01	ci left: 9.736778e-05	ci right 1.719338e-04	k: 51	n:390000
AHCTF1   390000 perm   188 sec   (2077 perm/sec)   p_kst 1.307692e-04   p_cons 7.512000e-01   p_joint 1.307692e-04

Joint ci ratio: 5.334078e-01	ci left: 9.925312e-05	ci right 1.733097e-04	k: 53	n:400000
Cons ci ratio: 3.566739e-03	ci left: 7.498847e-01	ci right 7.525666e-01	k: 300491	n:400000
KS ci ratio: 5.334078e-01	ci left: 9.925312e-05	ci right 1.733097e-04	k: 53	n:400000
AHCTF1   400000 perm   194 sec   (2061 perm/sec)   p_kst 1.325000e-04   p_cons 7.512275e-01   p_joint 1.325000e-04

Joint ci ratio: 5.237956e-01	ci left: 1.010589e-04	ci right 1.746064e-04	k: 55	n:410000
Cons ci ratio: 3.523739e-03	ci left: 7.498200e-01	ci right 7.524692e-01	k: 307970	n:410000
KS ci ratio: 5.237956e-01	ci left: 1.010589e-04	ci right 1.746064e-04	k: 55	n:410000
AHCTF1   410000 perm   202 sec   (2027 perm/sec)   p_kst 1.341463e-04   p_cons 7.511463e-01   p_joint 1.341463e-04

Joint ci ratio: 5.191808e-01	ci left: 1.007201e-04	ci right 1.731410e-04	k: 56	n:420000
Cons ci ratio: 3.481059e-03	ci left: 7.498872e-01	ci right 7.525045e-01	k: 315503	n:420000
KS ci ratio: 5.191808e-01	ci left: 1.007201e-04	ci right 1.731410e-04	k: 56	n:420000
AHCTF1   420000 perm   210 sec   (2002 perm/sec)   p_kst 1.333333e-04   p_cons 7.511976e-01   p_joint 1.333333e-04

Joint ci ratio: 5.103049e-01	ci left: 1.024244e-04	ci right 1.743650e-04	k: 58	n:430000
Cons ci ratio: 3.440001e-03	ci left: 7.499399e-01	ci right 7.525265e-01	k: 323031	n:430000
KS ci ratio: 5.103049e-01	ci left: 1.024244e-04	ci right 1.743650e-04	k: 58	n:430000
AHCTF1   430000 perm   217 sec   (1982 perm/sec)   p_kst 1.348837e-04   p_cons 7.512349e-01   p_joint 1.348837e-04

Joint ci ratio: 5.060347e-01	ci left: 1.020777e-04	ci right 1.729641e-04	k: 59	n:440000
Cons ci ratio: 3.399390e-03	ci left: 7.500974e-01	ci right 7.526538e-01	k: 330606	n:440000
KS ci ratio: 5.060347e-01	ci left: 1.020777e-04	ci right 1.729641e-04	k: 59	n:440000
AHCTF1   440000 perm   224 sec   (1963 perm/sec)   p_kst 1.340909e-04   p_cons 7.513773e-01   p_joint 1.340909e-04

Joint ci ratio: 4.978056e-01	ci left: 1.036908e-04	ci right 1.741234e-04	k: 61	n:450000
Cons ci ratio: 3.361002e-03	ci left: 7.501568e-01	ci right 7.526845e-01	k: 338140	n:450000
KS ci ratio: 4.978056e-01	ci left: 1.036908e-04	ci right 1.741234e-04	k: 61	n:450000
AHCTF1   450000 perm   232 sec   (1943 perm/sec)   p_kst 1.355556e-04   p_cons 7.514222e-01   p_joint 1.355556e-04

Joint ci ratio: 4.899654e-01	ci left: 1.052427e-04	ci right 1.752235e-04	k: 63	n:460000
Cons ci ratio: 3.324351e-03	ci left: 7.501614e-01	ci right 7.526615e-01	k: 345650	n:460000
KS ci ratio: 4.899654e-01	ci left: 1.052427e-04	ci right 1.752235e-04	k: 63	n:460000
AHCTF1   460000 perm   239 sec   (1922 perm/sec)   p_kst 1.369565e-04   p_cons 7.514130e-01   p_joint 1.369565e-04

Joint ci ratio: 4.899661e-01	ci left: 1.030035e-04	ci right 1.714954e-04	k: 63	n:470000
Cons ci ratio: 3.287955e-03	ci left: 7.502705e-01	ci right 7.527435e-01	k: 353209	n:470000
KS ci ratio: 4.899661e-01	ci left: 1.030035e-04	ci right 1.714954e-04	k: 63	n:470000
AHCTF1   470000 perm   246 sec   (1909 perm/sec)   p_kst 1.340426e-04   p_cons 7.515085e-01   p_joint 1.340426e-04

Joint ci ratio: 4.861827e-01	ci left: 1.026844e-04	ci right 1.702605e-04	k: 64	n:480000
Cons ci ratio: 3.253363e-03	ci left: 7.503021e-01	ci right 7.527491e-01	k: 360733	n:480000
KS ci ratio: 4.861827e-01	ci left: 1.026844e-04	ci right 1.702605e-04	k: 64	n:480000
AHCTF1   480000 perm   253 sec   (1895 perm/sec)   p_kst 1.333333e-04   p_cons 7.515271e-01   p_joint 1.333333e-04

Joint ci ratio: 4.788710e-01	ci left: 1.041737e-04	ci right 1.713605e-04	k: 66	n:490000
Cons ci ratio: 3.219753e-03	ci left: 7.503427e-01	ci right 7.527645e-01	k: 368262	n:490000
KS ci ratio: 4.788710e-01	ci left: 1.041737e-04	ci right 1.713605e-04	k: 66	n:490000
AHCTF1   490000 perm   260 sec   (1881 perm/sec)   p_kst 1.346939e-04   p_cons 7.515551e-01   p_joint 1.346939e-04

Joint ci ratio: 4.788717e-01	ci left: 1.020902e-04	ci right 1.679333e-04	k: 66	n:500000
Cons ci ratio: 3.187402e-03	ci left: 7.503538e-01	ci right 7.527513e-01	k: 375777	n:500000
KS ci ratio: 4.788717e-01	ci left: 1.020902e-04	ci right 1.679333e-04	k: 66	n:500000
AHCTF1   500000 perm   268 sec   (1868 perm/sec)   p_kst 1.320000e-04   p_cons 7.515540e-01   p_joint 1.320000e-04

Joint ci ratio: 4.753377e-01	ci left: 1.018133e-04	ci right 1.668355e-04	k: 67	n:510000
Cons ci ratio: 3.156388e-03	ci left: 7.503194e-01	ci right 7.526934e-01	k: 383269	n:510000
KS ci ratio: 4.753377e-01	ci left: 1.018133e-04	ci right 1.668355e-04	k: 67	n:510000
AHCTF1   510000 perm   275 sec   (1855 perm/sec)   p_kst 1.313725e-04   p_cons 7.515078e-01   p_joint 1.313725e-04

Joint ci ratio: 4.684976e-01	ci left: 1.032440e-04	ci right 1.679276e-04	k: 69	n:520000
Cons ci ratio: 3.126086e-03	ci left: 7.503077e-01	ci right 7.526588e-01	k: 390772	n:520000
KS ci ratio: 4.684976e-01	ci left: 1.032440e-04	ci right 1.679276e-04	k: 69	n:520000
AHCTF1   520000 perm   283 sec   (1840 perm/sec)   p_kst 1.326923e-04   p_cons 7.514846e-01   p_joint 1.326923e-04

Joint ci ratio: 4.651868e-01	ci left: 1.029607e-04	ci right 1.668665e-04	k: 70	n:530000
Cons ci ratio: 3.095216e-03	ci left: 7.504684e-01	ci right 7.527967e-01	k: 398366	n:530000
KS ci ratio: 4.651868e-01	ci left: 1.029607e-04	ci right 1.668665e-04	k: 70	n:530000
AHCTF1   530000 perm   291 sec   (1823 perm/sec)   p_kst 1.320755e-04   p_cons 7.516340e-01   p_joint 1.320755e-04

Joint ci ratio: 4.587699e-01	ci left: 1.043265e-04	ci right 1.679084e-04	k: 72	n:540000
Cons ci ratio: 3.066184e-03	ci left: 7.505083e-01	ci right 7.528149e-01	k: 405898	n:540000
KS ci ratio: 4.587699e-01	ci left: 1.043265e-04	ci right 1.679084e-04	k: 72	n:540000
AHCTF1   540000 perm   299 sec   (1805 perm/sec)   p_kst 1.333333e-04   p_cons 7.516630e-01   p_joint 1.333333e-04

Joint ci ratio: 4.556597e-01	ci left: 1.040384e-04	ci right 1.668818e-04	k: 73	n:550000
Cons ci ratio: 3.037807e-03	ci left: 7.505651e-01	ci right 7.528504e-01	k: 413440	n:550000
KS ci ratio: 4.556597e-01	ci left: 1.040384e-04	ci right 1.668818e-04	k: 73	n:550000
AHCTF1   550000 perm   307 sec   (1792 perm/sec)   p_kst 1.327273e-04   p_cons 7.517091e-01   p_joint 1.327273e-04

Joint ci ratio: 4.556602e-01	ci left: 1.021805e-04	ci right 1.639018e-04	k: 73	n:560000
Cons ci ratio: 3.010332e-03	ci left: 7.506038e-01	ci right 7.528686e-01	k: 420973	n:560000
KS ci ratio: 4.556602e-01	ci left: 1.021805e-04	ci right 1.639018e-04	k: 73	n:560000
AHCTF1   560000 perm   315 sec   (1779 perm/sec)   p_kst 1.303571e-04   p_cons 7.517375e-01   p_joint 1.303571e-04

Joint ci ratio: 4.556608e-01	ci left: 1.003879e-04	ci right 1.610264e-04	k: 73	n:570000
Cons ci ratio: 2.983996e-03	ci left: 7.505903e-01	ci right 7.528352e-01	k: 428477	n:570000
KS ci ratio: 4.556608e-01	ci left: 1.003879e-04	ci right 1.610264e-04	k: 73	n:570000
AHCTF1   570000 perm   323 sec   (1762 perm/sec)   p_kst 1.280702e-04   p_cons 7.517140e-01   p_joint 1.280702e-04

Joint ci ratio: 4.526130e-01	ci left: 1.001839e-04	ci right 1.601702e-04	k: 74	n:580000
Cons ci ratio: 2.957179e-03	ci left: 7.507242e-01	ci right 7.529492e-01	k: 436066	n:580000
KS ci ratio: 4.526130e-01	ci left: 1.001839e-04	ci right 1.601702e-04	k: 74	n:580000
AHCTF1   580000 perm   332 sec   (1748 perm/sec)   p_kst 1.275862e-04   p_cons 7.518379e-01   p_joint 1.275862e-04

Joint ci ratio: 4.526135e-01	ci left: 9.848585e-05	ci right 1.574555e-04	k: 74	n:590000
Cons ci ratio: 2.932735e-03	ci left: 7.506414e-01	ci right 7.528477e-01	k: 443530	n:590000
KS ci ratio: 4.526135e-01	ci left: 9.848585e-05	ci right 1.574555e-04	k: 74	n:590000
AHCTF1   590000 perm   340 sec   (1736 perm/sec)   p_kst 1.254237e-04   p_cons 7.517458e-01   p_joint 1.254237e-04

Joint ci ratio: 4.466964e-01	ci left: 9.980018e-05	ci right 1.585397e-04	k: 76	n:600000
Cons ci ratio: 2.908640e-03	ci left: 7.505931e-01	ci right 7.527811e-01	k: 451013	n:600000
KS ci ratio: 4.466964e-01	ci left: 9.980018e-05	ci right 1.585397e-04	k: 76	n:600000
AHCTF1   600000 perm   349 sec   (1719 perm/sec)   p_kst 1.266667e-04   p_cons 7.516883e-01   p_joint 1.266667e-04

Joint ci ratio: 4.438239e-01	ci left: 9.961960e-05	ci right 1.577627e-04	k: 77	n:610000
Cons ci ratio: 2.884775e-03	ci left: 7.505925e-01	ci right 7.527625e-01	k: 458524	n:610000
KS ci ratio: 4.438239e-01	ci left: 9.961960e-05	ci right 1.577627e-04	k: 77	n:610000
AHCTF1   610000 perm   357 sec   (1707 perm/sec)   p_kst 1.262295e-04   p_cons 7.516787e-01   p_joint 1.262295e-04

Joint ci ratio: 4.438243e-01	ci left: 9.801281e-05	ci right 1.552182e-04	k: 77	n:620000
Cons ci ratio: 2.861871e-03	ci left: 7.505419e-01	ci right 7.526945e-01	k: 466004	n:620000
KS ci ratio: 4.438243e-01	ci left: 9.801281e-05	ci right 1.552182e-04	k: 77	n:620000
AHCTF1   620000 perm   367 sec   (1687 perm/sec)   p_kst 1.241935e-04   p_cons 7.516194e-01   p_joint 1.241935e-04

Joint ci ratio: 4.438248e-01	ci left: 9.645703e-05	ci right 1.527545e-04	k: 77	n:630000
Cons ci ratio: 2.839371e-03	ci left: 7.505104e-01	ci right 7.526460e-01	k: 473495	n:630000
KS ci ratio: 4.438248e-01	ci left: 9.645703e-05	ci right 1.527545e-04	k: 77	n:630000
AHCTF1   630000 perm   378 sec   (1668 perm/sec)   p_kst 1.222222e-04   p_cons 7.515794e-01   p_joint 1.222222e-04

Joint ci ratio: 4.410069e-01	ci left: 9.633828e-05	ci right 1.521032e-04	k: 78	n:640000
Cons ci ratio: 2.816002e-03	ci left: 7.506647e-01	ci right 7.527831e-01	k: 481104	n:640000
KS ci ratio: 4.410069e-01	ci left: 9.633828e-05	ci right 1.521032e-04	k: 78	n:640000
AHCTF1   640000 perm   388 sec   (1650 perm/sec)   p_kst 1.218750e-04   p_cons 7.517250e-01   p_joint 1.218750e-04

Joint ci ratio: 4.328639e-01	ci left: 9.896380e-05	ci right 1.548832e-04	k: 81	n:650000
Cons ci ratio: 2.794018e-03	ci left: 7.507048e-01	ci right 7.528068e-01	k: 488642	n:650000
KS ci ratio: 4.328639e-01	ci left: 9.896380e-05	ci right 1.548832e-04	k: 81	n:650000
AHCTF1   650000 perm   397 sec   (1635 perm/sec)   p_kst 1.246154e-04   p_cons 7.517569e-01   p_joint 1.246154e-04

Joint ci ratio: 4.302485e-01	ci left: 9.881487e-05	ci right 1.542153e-04	k: 82	n:660000
Cons ci ratio: 2.773227e-03	ci left: 7.506513e-01	ci right 7.527374e-01	k: 496119	n:660000
KS ci ratio: 4.302485e-01	ci left: 9.881487e-05	ci right 1.542153e-04	k: 82	n:660000
AHCTF1   660000 perm   406 sec   (1624 perm/sec)   p_kst 1.242424e-04   p_cons 7.516955e-01   p_joint 1.242424e-04

Joint ci ratio: 4.251564e-01	ci left: 1.000037e-04	ci right 1.552182e-04	k: 84	n:670000
Cons ci ratio: 2.752332e-03	ci left: 7.506756e-01	ci right 7.527461e-01	k: 503647	n:670000
KS ci ratio: 4.251564e-01	ci left: 1.000037e-04	ci right 1.552182e-04	k: 84	n:670000
AHCTF1   670000 perm   415 sec   (1613 perm/sec)   p_kst 1.253731e-04   p_cons 7.517119e-01   p_joint 1.253731e-04

Joint ci ratio: 4.154917e-01	ci left: 1.037933e-04	ci right 1.594365e-04	k: 88	n:680000
Cons ci ratio: 2.732171e-03	ci left: 7.506625e-01	ci right 7.527177e-01	k: 511150	n:680000
KS ci ratio: 4.154917e-01	ci left: 1.037933e-04	ci right 1.594365e-04	k: 88	n:680000
AHCTF1   680000 perm   424 sec   (1603 perm/sec)   p_kst 1.294118e-04   p_cons 7.516912e-01   p_joint 1.294118e-04

Joint ci ratio: 4.131770e-01	ci left: 1.035872e-04	ci right 1.587254e-04	k: 89	n:690000
Cons ci ratio: 2.712405e-03	ci left: 7.506556e-01	ci right 7.526959e-01	k: 518657	n:690000
KS ci ratio: 4.131770e-01	ci left: 1.035872e-04	ci right 1.587254e-04	k: 89	n:690000
AHCTF1   690000 perm   433 sec   (1592 perm/sec)   p_kst 1.289855e-04   p_cons 7.516768e-01   p_joint 1.289855e-04

Joint ci ratio: 4.109007e-01	ci left: 1.033878e-04	ci right 1.580338e-04	k: 90	n:700000
Cons ci ratio: 2.693164e-03	ci left: 7.506347e-01	ci right 7.526604e-01	k: 526154	n:700000
KS ci ratio: 4.109007e-01	ci left: 1.033878e-04	ci right 1.580338e-04	k: 90	n:700000
AHCTF1   700000 perm   443 sec   (1582 perm/sec)   p_kst 1.285714e-04   p_cons 7.516486e-01   p_joint 1.285714e-04

Joint ci ratio: 4.109010e-01	ci left: 1.019317e-04	ci right 1.558080e-04	k: 90	n:710000
Cons ci ratio: 2.674328e-03	ci left: 7.506144e-01	ci right 7.526258e-01	k: 533651	n:710000
KS ci ratio: 4.109010e-01	ci left: 1.019317e-04	ci right 1.558080e-04	k: 90	n:710000
AHCTF1   710000 perm   452 sec   (1571 perm/sec)   p_kst 1.267606e-04   p_cons 7.516211e-01   p_joint 1.267606e-04

Joint ci ratio: 4.064585e-01	ci left: 1.030081e-04	ci right 1.567058e-04	k: 92	n:720000
Cons ci ratio: 2.656138e-03	ci left: 7.505585e-01	ci right 7.525561e-01	k: 541122	n:720000
KS ci ratio: 4.064585e-01	ci left: 1.030081e-04	ci right 1.567058e-04	k: 92	n:720000
AHCTF1   720000 perm   461 sec   (1561 perm/sec)   p_kst 1.277778e-04   p_cons 7.515583e-01   p_joint 1.277778e-04

Joint ci ratio: 4.064589e-01	ci left: 1.015970e-04	ci right 1.545592e-04	k: 92	n:730000
Cons ci ratio: 2.638081e-03	ci left: 7.505372e-01	ci right 7.525211e-01	k: 548617	n:730000
KS ci ratio: 4.064589e-01	ci left: 1.015970e-04	ci right 1.545592e-04	k: 92	n:730000
AHCTF1   730000 perm   470 sec   (1552 perm/sec)   p_kst 1.260274e-04   p_cons 7.515301e-01   p_joint 1.260274e-04

Joint ci ratio: 4.042912e-01	ci left: 1.014377e-04	ci right 1.539590e-04	k: 93	n:740000
Cons ci ratio: 2.620436e-03	ci left: 7.505097e-01	ci right 7.524802e-01	k: 556107	n:740000
KS ci ratio: 4.042912e-01	ci left: 1.014377e-04	ci right 1.539590e-04	k: 93	n:740000
AHCTF1   740000 perm   480 sec   (1543 perm/sec)   p_kst 1.256757e-04   p_cons 7.514959e-01   p_joint 1.256757e-04

Joint ci ratio: 4.021578e-01	ci left: 1.012832e-04	ci right 1.533741e-04	k: 94	n:750000
Cons ci ratio: 2.602768e-03	ci left: 7.505364e-01	ci right 7.524937e-01	k: 563637	n:750000
KS ci ratio: 4.021578e-01	ci left: 1.012832e-04	ci right 1.533741e-04	k: 94	n:750000
AHCTF1   750000 perm   489 sec   (1533 perm/sec)   p_kst 1.253333e-04   p_cons 7.515160e-01   p_joint 1.253333e-04

Joint ci ratio: 4.021581e-01	ci left: 9.995055e-05	ci right 1.513561e-04	k: 94	n:760000
Cons ci ratio: 2.585671e-03	ci left: 7.505308e-01	ci right 7.524752e-01	k: 571143	n:760000
KS ci ratio: 4.021581e-01	ci left: 9.995055e-05	ci right 1.513561e-04	k: 94	n:760000
AHCTF1   760000 perm   500 sec   (1521 perm/sec)   p_kst 1.236842e-04   p_cons 7.515039e-01   p_joint 1.236842e-04

Joint ci ratio: 3.979904e-01	ci left: 1.009885e-04	ci right 1.522478e-04	k: 96	n:770000
Cons ci ratio: 2.568934e-03	ci left: 7.505215e-01	ci right 7.524533e-01	k: 578646	n:770000
KS ci ratio: 3.979904e-01	ci left: 1.009885e-04	ci right 1.522478e-04	k: 96	n:770000
AHCTF1   770000 perm   511 sec   (1507 perm/sec)   p_kst 1.246753e-04   p_cons 7.514883e-01   p_joint 1.246753e-04

Joint ci ratio: 3.900291e-01	ci left: 1.043140e-04	ci right 1.559296e-04	k: 100	n:780000
Cons ci ratio: 2.552710e-03	ci left: 7.504842e-01	ci right 7.524037e-01	k: 586127	n:780000
KS ci ratio: 3.900291e-01	ci left: 1.043140e-04	ci right 1.559296e-04	k: 100	n:780000
AHCTF1   780000 perm   522 sec   (1493 perm/sec)   p_kst 1.282051e-04   p_cons 7.514449e-01   p_joint 1.282051e-04

Joint ci ratio: 3.881125e-01	ci left: 1.041355e-04	ci right 1.553449e-04	k: 101	n:790000
Cons ci ratio: 2.536128e-03	ci left: 7.505455e-01	ci right 7.524526e-01	k: 593685	n:790000
KS ci ratio: 3.881125e-01	ci left: 1.041355e-04	ci right 1.553449e-04	k: 101	n:790000
AHCTF1   790000 perm   533 sec   (1483 perm/sec)   p_kst 1.278481e-04   p_cons 7.515000e-01   p_joint 1.278481e-04

Joint ci ratio: 3.862240e-01	ci left: 1.039622e-04	ci right 1.547742e-04	k: 102	n:800000
Cons ci ratio: 2.520253e-03	ci left: 7.505478e-01	ci right 7.524429e-01	k: 601197	n:800000
KS ci ratio: 3.862240e-01	ci left: 1.039622e-04	ci right 1.547742e-04	k: 102	n:800000
AHCTF1   800000 perm   543 sec   (1473 perm/sec)   p_kst 1.275000e-04   p_cons 7.514962e-01   p_joint 1.275000e-04

Joint ci ratio: 3.789354e-01	ci left: 1.071421e-04	ci right 1.582743e-04	k: 106	n:810000
Cons ci ratio: 2.504332e-03	ci left: 7.506007e-01	ci right 7.524840e-01	k: 608750	n:810000
KS ci ratio: 3.789354e-01	ci left: 1.071421e-04	ci right 1.582743e-04	k: 106	n:810000
AHCTF1   810000 perm   554 sec   (1463 perm/sec)   p_kst 1.308642e-04   p_cons 7.515432e-01   p_joint 1.308642e-04

Joint ci ratio: 3.771771e-01	ci left: 1.069391e-04	ci right 1.576790e-04	k: 107	n:820000
Cons ci ratio: 2.489368e-03	ci left: 7.505534e-01	ci right 7.524253e-01	k: 616222	n:820000
KS ci ratio: 3.771771e-01	ci left: 1.069391e-04	ci right 1.576790e-04	k: 107	n:820000
AHCTF1   820000 perm   564 sec   (1455 perm/sec)   p_kst 1.304878e-04   p_cons 7.514902e-01   p_joint 1.304878e-04

Joint ci ratio: 3.720448e-01	ci left: 1.089249e-04	ci right 1.597325e-04	k: 110	n:830000
Cons ci ratio: 2.474645e-03	ci left: 7.505109e-01	ci right 7.523717e-01	k: 623697	n:830000
KS ci ratio: 3.720448e-01	ci left: 1.089249e-04	ci right 1.597325e-04	k: 110	n:830000
AHCTF1   830000 perm   574 sec   (1447 perm/sec)   p_kst 1.325301e-04   p_cons 7.514422e-01   p_joint 1.325301e-04

Joint ci ratio: 3.720451e-01	ci left: 1.076281e-04	ci right 1.578309e-04	k: 110	n:840000
Cons ci ratio: 2.459725e-03	ci left: 7.505386e-01	ci right 7.523882e-01	k: 631230	n:840000
KS ci ratio: 3.720451e-01	ci left: 1.076281e-04	ci right 1.578309e-04	k: 110	n:840000
AHCTF1   840000 perm   584 sec   (1439 perm/sec)   p_kst 1.309524e-04   p_cons 7.514643e-01   p_joint 1.309524e-04

Joint ci ratio: 3.671168e-01	ci left: 1.095636e-04	ci right 1.598298e-04	k: 113	n:850000
Cons ci ratio: 2.445626e-03	ci left: 7.504809e-01	ci right 7.523197e-01	k: 638691	n:850000
KS ci ratio: 3.671168e-01	ci left: 1.095636e-04	ci right 1.598298e-04	k: 113	n:850000
AHCTF1   850000 perm   594 sec   (1430 perm/sec)   p_kst 1.329412e-04   p_cons 7.514012e-01   p_joint 1.329412e-04

Joint ci ratio: 3.671171e-01	ci left: 1.082896e-04	ci right 1.579713e-04	k: 113	n:860000
Cons ci ratio: 2.431412e-03	ci left: 7.504793e-01	ci right 7.523074e-01	k: 646199	n:860000
KS ci ratio: 3.671171e-01	ci left: 1.082896e-04	ci right 1.579713e-04	k: 113	n:860000
AHCTF1   860000 perm   605 sec   (1421 perm/sec)   p_kst 1.313953e-04   p_cons 7.513942e-01   p_joint 1.313953e-04

Joint ci ratio: 3.671174e-01	ci left: 1.070448e-04	ci right 1.561556e-04	k: 113	n:870000
Cons ci ratio: 2.417680e-03	ci left: 7.504409e-01	ci right 7.522586e-01	k: 653675	n:870000
KS ci ratio: 3.671174e-01	ci left: 1.070448e-04	ci right 1.561556e-04	k: 113	n:870000
AHCTF1   870000 perm   616 sec   (1413 perm/sec)   p_kst 1.298851e-04   p_cons 7.513506e-01   p_joint 1.298851e-04

Joint ci ratio: 3.671176e-01	ci left: 1.058284e-04	ci right 1.543811e-04	k: 113	n:880000
Cons ci ratio: 2.404046e-03	ci left: 7.504239e-01	ci right 7.522312e-01	k: 661169	n:880000
KS ci ratio: 3.671176e-01	ci left: 1.058284e-04	ci right 1.543811e-04	k: 113	n:880000
AHCTF1   880000 perm   627 sec   (1403 perm/sec)   p_kst 1.284091e-04   p_cons 7.513284e-01   p_joint 1.284091e-04

Joint ci ratio: 3.671179e-01	ci left: 1.046393e-04	ci right 1.526465e-04	k: 113	n:890000
Cons ci ratio: 2.390648e-03	ci left: 7.504062e-01	ci right 7.522034e-01	k: 668662	n:890000
KS ci ratio: 3.671179e-01	ci left: 1.046393e-04	ci right 1.526465e-04	k: 113	n:890000
AHCTF1   890000 perm   640 sec   (1391 perm/sec)   p_kst 1.269663e-04   p_cons 7.513056e-01   p_joint 1.269663e-04

Joint ci ratio: 3.655183e-01	ci left: 1.044855e-04	ci right 1.521634e-04	k: 114	n:900000
Cons ci ratio: 2.377040e-03	ci left: 7.504568e-01	ci right 7.522438e-01	k: 676216	n:900000
KS ci ratio: 3.655183e-01	ci left: 1.044855e-04	ci right 1.521634e-04	k: 114	n:900000
AHCTF1   900000 perm   650 sec   (1384 perm/sec)   p_kst 1.266667e-04   p_cons 7.513511e-01   p_joint 1.266667e-04

Joint ci ratio: 3.655186e-01	ci left: 1.033373e-04	ci right 1.504913e-04	k: 114	n:910000
Cons ci ratio: 2.363426e-03	ci left: 7.505437e-01	ci right 7.523207e-01	k: 683804	n:910000
KS ci ratio: 3.655186e-01	ci left: 1.033373e-04	ci right 1.504913e-04	k: 114	n:910000
AHCTF1   910000 perm   662 sec   (1374 perm/sec)   p_kst 1.252747e-04   p_cons 7.514330e-01   p_joint 1.252747e-04

Joint ci ratio: 3.639397e-01	ci left: 1.032014e-04	ci right 1.500417e-04	k: 115	n:920000
Cons ci ratio: 2.350644e-03	ci left: 7.505329e-01	ci right 7.523003e-01	k: 691304	n:920000
KS ci ratio: 3.639397e-01	ci left: 1.032014e-04	ci right 1.500417e-04	k: 115	n:920000
AHCTF1   920000 perm   676 sec   (1361 perm/sec)   p_kst 1.250000e-04   p_cons 7.514174e-01   p_joint 1.250000e-04

Joint ci ratio: 3.608422e-01	ci left: 1.040464e-04	ci right 1.507738e-04	k: 117	n:930000
Cons ci ratio: 2.338020e-03	ci left: 7.505300e-01	ci right 7.522878e-01	k: 698811	n:930000
KS ci ratio: 3.608422e-01	ci left: 1.040464e-04	ci right 1.507738e-04	k: 117	n:930000
AHCTF1   930000 perm   689 sec   (1351 perm/sec)   p_kst 1.258065e-04   p_cons 7.514097e-01   p_joint 1.258065e-04

Joint ci ratio: 3.862277e-01	ci left: 8.847830e-05	ci right 1.317230e-04	k: 102	n:940000
Cons ci ratio: 2.325651e-03	ci left: 7.505186e-01	ci right 7.522671e-01	k: 706310	n:940000
KS ci ratio: 3.593229e-01	ci left: 1.039072e-04	ci right 1.503295e-04	k: 118	n:940000
AHCTF1   940000 perm   701 sec   (1341 perm/sec)   p_kst 1.255319e-04   p_cons 7.513936e-01   p_joint 1.085106e-04

Joint ci ratio: 3.843664e-01	ci left: 8.849761e-05	ci right 1.314905e-04	k: 103	n:950000
Cons ci ratio: 2.313299e-03	ci left: 7.505359e-01	ci right 7.522752e-01	k: 713836	n:950000
KS ci ratio: 3.578226e-01	ci left: 1.037712e-04	ci right 1.498942e-04	k: 119	n:950000
AHCTF1   950000 perm   712 sec   (1333 perm/sec)   p_kst 1.252632e-04   p_cons 7.514063e-01   p_joint 1.084211e-04

Joint ci ratio: 3.843666e-01	ci left: 8.757575e-05	ci right 1.301209e-04	k: 103	n:960000
Cons ci ratio: 2.301136e-03	ci left: 7.505540e-01	ci right 7.522841e-01	k: 721363	n:960000
KS ci ratio: 3.578229e-01	ci left: 1.026902e-04	ci right 1.483328e-04	k: 119	n:960000
AHCTF1   960000 perm   724 sec   (1326 perm/sec)   p_kst 1.239583e-04   p_cons 7.514198e-01   p_joint 1.072917e-04

Joint ci ratio: 3.843668e-01	ci left: 8.667290e-05	ci right 1.287794e-04	k: 103	n:970000
Cons ci ratio: 2.289049e-03	ci left: 7.505902e-01	ci right 7.523113e-01	k: 728908	n:970000
KS ci ratio: 3.578231e-01	ci left: 1.016316e-04	ci right 1.468036e-04	k: 119	n:970000
AHCTF1   970000 perm   735 sec   (1319 perm/sec)   p_kst 1.226804e-04   p_cons 7.514515e-01   p_joint 1.061856e-04

Joint ci ratio: 3.825321e-01	ci left: 8.671053e-05	ci right 1.285837e-04	k: 104	n:980000
Cons ci ratio: 2.277443e-03	ci left: 7.505778e-01	ci right 7.522901e-01	k: 736406	n:980000
KS ci ratio: 3.563415e-01	ci left: 1.015234e-04	ci right 1.464172e-04	k: 120	n:980000
AHCTF1   980000 perm   747 sec   (1312 perm/sec)   p_kst 1.224490e-04   p_cons 7.514347e-01   p_joint 1.061224e-04

Joint ci ratio: 3.789400e-01	ci left: 8.766153e-05	ci right 1.294975e-04	k: 106	n:990000
Cons ci ratio: 2.265975e-03	ci left: 7.505717e-01	ci right 7.522753e-01	k: 743910	n:990000
KS ci ratio: 3.534324e-01	ci left: 1.023380e-04	ci right 1.471378e-04	k: 122	n:990000
AHCTF1   990000 perm   759 sec   (1304 perm/sec)   p_kst 1.232323e-04   p_cons 7.514242e-01   p_joint 1.070707e-04

Joint ci ratio: 3.789402e-01	ci left: 8.678491e-05	ci right 1.282025e-04	k: 106	n:1000000
Cons ci ratio: 2.254727e-03	ci left: 7.505577e-01	ci right 7.522529e-01	k: 751406	n:1000000
KS ci ratio: 3.534326e-01	ci left: 1.013146e-04	ci right 1.456664e-04	k: 122	n:1000000
AHCTF1   1000000 perm   771 sec   (1297 perm/sec)   p_kst 1.220000e-04   p_cons 7.514060e-01   p_joint 1.060000e-04

Joint ci ratio: 3.789404e-01	ci left: 8.592564e-05	ci right 1.269332e-04	k: 106	n:1010000
Cons ci ratio: 2.243484e-03	ci left: 7.505708e-01	ci right 7.522575e-01	k: 758929	n:1010000
KS ci ratio: 3.534328e-01	ci left: 1.003115e-04	ci right 1.442242e-04	k: 122	n:1010000
AHCTF1   1010000 perm   783 sec   (1291 perm/sec)   p_kst 1.207921e-04   p_cons 7.514149e-01   p_joint 1.049505e-04

Joint ci ratio: 3.789406e-01	ci left: 8.508323e-05	ci right 1.256888e-04	k: 106	n:1020000
Cons ci ratio: 2.232132e-03	ci left: 7.506297e-01	ci right 7.523081e-01	k: 766499	n:1020000
KS ci ratio: 3.534330e-01	ci left: 9.932804e-05	ci right 1.428103e-04	k: 122	n:1020000
AHCTF1   1020000 perm   794 sec   (1284 perm/sec)   p_kst 1.196078e-04   p_cons 7.514696e-01   p_joint 1.039216e-04

Joint ci ratio: 3.771822e-01	ci left: 8.513579e-05	ci right 1.255312e-04	k: 107	n:1030000
Cons ci ratio: 2.221165e-03	ci left: 7.506516e-01	ci right 7.523217e-01	k: 774032	n:1030000
KS ci ratio: 3.520050e-01	ci left: 9.924855e-05	ci right 1.424803e-04	k: 123	n:1030000
AHCTF1   1030000 perm   807 sec   (1277 perm/sec)   p_kst 1.194175e-04   p_cons 7.514874e-01   p_joint 1.038835e-04

Joint ci ratio: 3.737374e-01	ci left: 8.605879e-05	ci right 1.264279e-04	k: 109	n:1040000
Cons ci ratio: 2.210004e-03	ci left: 7.507328e-01	ci right 7.523947e-01	k: 781627	n:1040000
KS ci ratio: 3.492000e-01	ci left: 1.000480e-04	ci right 1.432021e-04	k: 125	n:1040000
AHCTF1   1040000 perm   818 sec   (1271 perm/sec)   p_kst 1.201923e-04   p_cons 7.515644e-01   p_joint 1.048077e-04

Joint ci ratio: 3.720501e-01	ci left: 8.610231e-05	ci right 1.262651e-04	k: 110	n:1050000
Cons ci ratio: 2.199403e-03	ci left: 7.507457e-01	ci right 7.523996e-01	k: 789152	n:1050000
KS ci ratio: 3.478225e-01	ci left: 9.996416e-05	ci right 1.428737e-04	k: 126	n:1050000
AHCTF1   1050000 perm   831 sec   (1263 perm/sec)   p_kst 1.200000e-04   p_cons 7.515733e-01   p_joint 1.047619e-04

Joint ci ratio: 3.720503e-01	ci left: 8.529001e-05	ci right 1.250739e-04	k: 110	n:1060000
Cons ci ratio: 2.188986e-03	ci left: 7.507527e-01	ci right 7.523988e-01	k: 796671	n:1060000
KS ci ratio: 3.478227e-01	ci left: 9.902109e-05	ci right 1.415258e-04	k: 126	n:1060000
AHCTF1   1060000 perm   843 sec   (1257 perm/sec)   p_kst 1.188679e-04   p_cons 7.515764e-01   p_joint 1.037736e-04

Joint ci ratio: 3.720505e-01	ci left: 8.449290e-05	ci right 1.239050e-04	k: 110	n:1070000
Cons ci ratio: 2.178590e-03	ci left: 7.507811e-01	ci right 7.524194e-01	k: 804213	n:1070000
KS ci ratio: 3.478229e-01	ci left: 9.809565e-05	ci right 1.402031e-04	k: 126	n:1070000
AHCTF1   1070000 perm   856 sec   (1251 perm/sec)   p_kst 1.177570e-04   p_cons 7.516009e-01   p_joint 1.028037e-04

Joint ci ratio: 3.687431e-01	ci left: 8.539005e-05	ci right 1.247812e-04	k: 112	n:1080000
Cons ci ratio: 2.168545e-03	ci left: 7.507738e-01	ci right 7.524045e-01	k: 811717	n:1080000
KS ci ratio: 3.451160e-01	ci left: 9.887809e-05	ci right 1.409173e-04	k: 128	n:1080000
AHCTF1   1080000 perm   868 sec   (1244 perm/sec)   p_kst 1.185185e-04   p_cons 7.515898e-01   p_joint 1.037037e-04

Joint ci ratio: 3.671223e-01	ci left: 8.543927e-05	ci right 1.246383e-04	k: 113	n:1090000
Cons ci ratio: 2.158696e-03	ci left: 7.507565e-01	ci right 7.523798e-01	k: 819210	n:1090000
KS ci ratio: 3.437861e-01	ci left: 9.880902e-05	ci right 1.406210e-04	k: 129	n:1090000
AHCTF1   1090000 perm   882 sec   (1236 perm/sec)   p_kst 1.183486e-04   p_cons 7.515688e-01   p_joint 1.036697e-04

Joint ci ratio: 3.655226e-01	ci left: 8.548796e-05	ci right 1.244976e-04	k: 114	n:1100000
Cons ci ratio: 2.148635e-03	ci left: 7.507996e-01	ci right 7.524154e-01	k: 826769	n:1100000
KS ci ratio: 3.424714e-01	ci left: 9.874151e-05	ci right 1.403298e-04	k: 130	n:1100000
AHCTF1   1100000 perm   895 sec   (1229 perm/sec)   p_kst 1.181818e-04   p_cons 7.516082e-01   p_joint 1.036364e-04

Joint ci ratio: 3.623849e-01	ci left: 8.635484e-05	ci right 1.253419e-04	k: 116	n:1110000
Cons ci ratio: 2.138501e-03	ci left: 7.508790e-01	ci right 7.524873e-01	k: 834369	n:1110000
KS ci ratio: 3.398866e-01	ci left: 9.949940e-05	ci right 1.410211e-04	k: 132	n:1110000
AHCTF1   1110000 perm   908 sec   (1223 perm/sec)   p_kst 1.189189e-04   p_cons 7.516838e-01   p_joint 1.045045e-04

Joint ci ratio: 3.608461e-01	ci left: 8.639555e-05	ci right 1.251964e-04	k: 117	n:1120000
Cons ci ratio: 2.128922e-03	ci left: 7.508845e-01	ci right 7.524856e-01	k: 841888	n:1120000
KS ci ratio: 3.386160e-01	ci left: 9.942781e-05	ci right 1.407306e-04	k: 133	n:1120000
AHCTF1   1120000 perm   920 sec   (1217 perm/sec)   p_kst 1.187500e-04   p_cons 7.516857e-01   p_joint 1.044643e-04

Joint ci ratio: 3.608462e-01	ci left: 8.563098e-05	ci right 1.240885e-04	k: 117	n:1130000
Cons ci ratio: 2.119334e-03	ci left: 7.509139e-01	ci right 7.525079e-01	k: 849434	n:1130000
KS ci ratio: 3.386162e-01	ci left: 9.854791e-05	ci right 1.394852e-04	k: 133	n:1130000
AHCTF1   1130000 perm   933 sec   (1211 perm/sec)   p_kst 1.176991e-04   p_cons 7.517115e-01   p_joint 1.035398e-04

Joint ci ratio: 3.578264e-01	ci left: 8.647585e-05	ci right 1.249121e-04	k: 119	n:1140000
Cons ci ratio: 2.109910e-03	ci left: 7.509366e-01	ci right 7.525235e-01	k: 856973	n:1140000
KS ci ratio: 3.361170e-01	ci left: 9.928924e-05	ci right 1.401641e-04	k: 135	n:1140000
AHCTF1   1140000 perm   946 sec   (1205 perm/sec)   p_kst 1.184211e-04   p_cons 7.517307e-01   p_joint 1.043860e-04

Joint ci ratio: 3.563447e-01	ci left: 8.651545e-05	ci right 1.247731e-04	k: 120	n:1150000
Cons ci ratio: 2.100424e-03	ci left: 7.509920e-01	ci right 7.525719e-01	k: 864550	n:1150000
KS ci ratio: 3.348881e-01	ci left: 9.922217e-05	ci right 1.398879e-04	k: 136	n:1150000
AHCTF1   1150000 perm   959 sec   (1199 perm/sec)   p_kst 1.182609e-04   p_cons 7.517826e-01   p_joint 1.043478e-04

Joint ci ratio: 3.324700e-01	ci left: 9.994652e-05	ci right 1.405500e-04	k: 138	n:1160000
Cons ci ratio: 2.091689e-03	ci left: 7.509352e-01	ci right 7.525084e-01	k: 871998	n:1160000
KS ci ratio: 3.324700e-01	ci left: 9.994652e-05	ci right 1.405500e-04	k: 138	n:1160000
AHCTF1   1160000 perm   972 sec   (1194 perm/sec)   p_kst 1.189655e-04   p_cons 7.517224e-01   p_joint 1.189655e-04

Joint ci ratio: 3.324702e-01	ci left: 9.909227e-05	ci right 1.393487e-04	k: 138	n:1170000
Cons ci ratio: 2.082732e-03	ci left: 7.509384e-01	ci right 7.525048e-01	k: 879515	n:1170000
KS ci ratio: 3.324702e-01	ci left: 9.909227e-05	ci right 1.393487e-04	k: 138	n:1170000
AHCTF1   1170000 perm   985 sec   (1188 perm/sec)   p_kst 1.179487e-04   p_cons 7.517222e-01   p_joint 1.179487e-04

Joint ci ratio: 3.312807e-01	ci left: 9.902935e-05	ci right 1.390856e-04	k: 139	n:1180000
Cons ci ratio: 2.074077e-03	ci left: 7.509076e-01	ci right 7.524675e-01	k: 886992	n:1180000
KS ci ratio: 3.312807e-01	ci left: 9.902935e-05	ci right 1.390856e-04	k: 139	n:1180000
AHCTF1   1180000 perm   998 sec   (1182 perm/sec)   p_kst 1.177966e-04   p_cons 7.516881e-01   p_joint 1.177966e-04

Joint ci ratio: 3.289393e-01	ci left: 9.973858e-05	ci right 1.397363e-04	k: 141	n:1190000
Cons ci ratio: 2.065344e-03	ci left: 7.509110e-01	ci right 7.524643e-01	k: 894509	n:1190000
KS ci ratio: 3.289393e-01	ci left: 9.973858e-05	ci right 1.397363e-04	k: 141	n:1190000
AHCTF1   1190000 perm   1011 sec   (1177 perm/sec)   p_kst 1.184874e-04   p_cons 7.516882e-01   p_joint 1.184874e-04

Joint ci ratio: 3.289395e-01	ci left: 9.890742e-05	ci right 1.385718e-04	k: 141	n:1200000
Cons ci ratio: 2.056949e-03	ci left: 7.508726e-01	ci right 7.524195e-01	k: 901976	n:1200000
KS ci ratio: 3.289395e-01	ci left: 9.890742e-05	ci right 1.385718e-04	k: 141	n:1200000
AHCTF1   1200000 perm   1024 sec   (1171 perm/sec)   p_kst 1.175000e-04   p_cons 7.516467e-01   p_joint 1.175000e-04

Joint ci ratio: 3.289397e-01	ci left: 9.808999e-05	ci right 1.374266e-04	k: 141	n:1210000
Cons ci ratio: 2.048533e-03	ci left: 7.508572e-01	ci right 7.523978e-01	k: 909470	n:1210000
KS ci ratio: 3.289397e-01	ci left: 9.808999e-05	ci right 1.374266e-04	k: 141	n:1210000
AHCTF1   1210000 perm   1038 sec   (1166 perm/sec)   p_kst 1.165289e-04   p_cons 7.516281e-01   p_joint 1.165289e-04

Joint ci ratio: 3.277875e-01	ci left: 9.803809e-05	ci right 1.371872e-04	k: 142	n:1220000
Cons ci ratio: 2.040108e-03	ci left: 7.508626e-01	ci right 7.523968e-01	k: 916989	n:1220000
KS ci ratio: 3.277875e-01	ci left: 9.803809e-05	ci right 1.371872e-04	k: 142	n:1220000
AHCTF1   1220000 perm   1051 sec   (1161 perm/sec)   p_kst 1.163934e-04   p_cons 7.516303e-01   p_joint 1.163934e-04

Joint ci ratio: 3.277877e-01	ci left: 9.724102e-05	ci right 1.360718e-04	k: 142	n:1230000
Cons ci ratio: 2.031530e-03	ci left: 7.509152e-01	ci right 7.524430e-01	k: 924566	n:1230000
KS ci ratio: 3.277877e-01	ci left: 9.724102e-05	ci right 1.360718e-04	k: 142	n:1230000
AHCTF1   1230000 perm   1065 sec   (1155 perm/sec)   p_kst 1.154472e-04   p_cons 7.516797e-01   p_joint 1.154472e-04

Joint ci ratio: 3.277878e-01	ci left: 9.645681e-05	ci right 1.349745e-04	k: 142	n:1240000
Cons ci ratio: 2.023500e-03	ci left: 7.508853e-01	ci right 7.524071e-01	k: 932042	n:1240000
KS ci ratio: 3.277878e-01	ci left: 9.645681e-05	ci right 1.349745e-04	k: 142	n:1240000
AHCTF1   1240000 perm   1078 sec   (1150 perm/sec)   p_kst 1.145161e-04   p_cons 7.516468e-01   p_joint 1.145161e-04

Joint ci ratio: 3.244024e-01	ci left: 9.788873e-05	ci right 1.364904e-04	k: 145	n:1250000
Cons ci ratio: 2.015435e-03	ci left: 7.508800e-01	ci right 7.523956e-01	k: 939548	n:1250000
KS ci ratio: 3.244024e-01	ci left: 9.788873e-05	ci right 1.364904e-04	k: 145	n:1250000
AHCTF1   1250000 perm   1092 sec   (1145 perm/sec)   p_kst 1.160000e-04   p_cons 7.516384e-01   p_joint 1.160000e-04

Joint ci ratio: 3.244026e-01	ci left: 9.711183e-05	ci right 1.354072e-04	k: 145	n:1260000
Cons ci ratio: 2.007815e-03	ci left: 7.508096e-01	ci right 7.523194e-01	k: 946972	n:1260000
KS ci ratio: 3.244026e-01	ci left: 9.711183e-05	ci right 1.354072e-04	k: 145	n:1260000
AHCTF1   1260000 perm   1105 sec   (1140 perm/sec)   p_kst 1.150794e-04   p_cons 7.515651e-01   p_joint 1.150794e-04

Joint ci ratio: 3.244027e-01	ci left: 9.634716e-05	ci right 1.343410e-04	k: 145	n:1270000
Cons ci ratio: 1.999957e-03	ci left: 7.508011e-01	ci right 7.523049e-01	k: 954473	n:1270000
KS ci ratio: 3.244027e-01	ci left: 9.634716e-05	ci right 1.343410e-04	k: 145	n:1270000
AHCTF1   1270000 perm   1119 sec   (1135 perm/sec)   p_kst 1.141732e-04   p_cons 7.515535e-01   p_joint 1.141732e-04

Joint ci ratio: 3.232975e-01	ci left: 9.631219e-05	ci right 1.341360e-04	k: 146	n:1280000
Cons ci ratio: 1.992135e-03	ci left: 7.508028e-01	ci right 7.523007e-01	k: 961987	n:1280000
KS ci ratio: 3.232975e-01	ci left: 9.631219e-05	ci right 1.341360e-04	k: 146	n:1280000
AHCTF1   1280000 perm   1133 sec   (1130 perm/sec)   p_kst 1.140625e-04   p_cons 7.515523e-01   p_joint 1.140625e-04

Joint ci ratio: 3.222034e-01	ci left: 9.627799e-05	ci right 1.339340e-04	k: 147	n:1290000
Cons ci ratio: 1.984500e-03	ci left: 7.507867e-01	ci right 7.522789e-01	k: 969478	n:1290000
KS ci ratio: 3.222034e-01	ci left: 9.627799e-05	ci right 1.339340e-04	k: 147	n:1290000
AHCTF1   1290000 perm   1147 sec   (1125 perm/sec)   p_kst 1.139535e-04   p_cons 7.515333e-01   p_joint 1.139535e-04

Joint ci ratio: 3.222035e-01	ci left: 9.553738e-05	ci right 1.329037e-04	k: 147	n:1300000
Cons ci ratio: 1.976687e-03	ci left: 7.508209e-01	ci right 7.523072e-01	k: 977034	n:1300000
KS ci ratio: 3.222035e-01	ci left: 9.553738e-05	ci right 1.329037e-04	k: 147	n:1300000
AHCTF1   1300000 perm   1161 sec   (1119 perm/sec)   p_kst 1.130769e-04   p_cons 7.515646e-01   p_joint 1.130769e-04

Joint ci ratio: 3.398897e-01	ci left: 8.430853e-05	ci right 1.194914e-04	k: 132	n:1310000
Cons ci ratio: 1.969034e-03	ci left: 7.508416e-01	ci right 7.523222e-01	k: 984573	n:1310000
KS ci ratio: 3.189866e-01	ci left: 9.691392e-05	ci right 1.343629e-04	k: 150	n:1310000
AHCTF1   1310000 perm   1177 sec   (1113 perm/sec)   p_kst 1.145038e-04   p_cons 7.515824e-01   p_joint 1.007634e-04

Joint ci ratio: 3.179356e-01	ci left: 9.687675e-05	ci right 1.341629e-04	k: 151	n:1320000
Cons ci ratio: 1.961724e-03	ci left: 7.508134e-01	ci right 7.522885e-01	k: 992048	n:1320000
KS ci ratio: 3.179356e-01	ci left: 9.687675e-05	ci right 1.341629e-04	k: 151	n:1320000
AHCTF1   1320000 perm   1191 sec   (1108 perm/sec)   p_kst 1.143939e-04   p_cons 7.515515e-01   p_joint 1.143939e-04

Joint ci ratio: 3.179357e-01	ci left: 9.614835e-05	ci right 1.331542e-04	k: 151	n:1330000
Cons ci ratio: 1.954451e-03	ci left: 7.507940e-01	ci right 7.522636e-01	k: 999534	n:1330000
KS ci ratio: 3.179357e-01	ci left: 9.614835e-05	ci right 1.331542e-04	k: 151	n:1330000
AHCTF1   1330000 perm   1206 sec   (1103 perm/sec)   p_kst 1.135338e-04   p_cons 7.515293e-01   p_joint 1.135338e-04

Joint ci ratio: 3.179358e-01	ci left: 9.543081e-05	ci right 1.321605e-04	k: 151	n:1340000
Cons ci ratio: 1.947235e-03	ci left: 7.507794e-01	ci right 7.522434e-01	k: 1007026	n:1340000
KS ci ratio: 3.179358e-01	ci left: 9.543081e-05	ci right 1.321605e-04	k: 151	n:1340000
AHCTF1   1340000 perm   1221 sec   (1098 perm/sec)   p_kst 1.126866e-04   p_cons 7.515119e-01   p_joint 1.126866e-04

Joint ci ratio: 3.138329e-01	ci left: 9.745203e-05	ci right 1.343786e-04	k: 155	n:1350000
Cons ci ratio: 1.939914e-03	ci left: 7.508005e-01	ci right 7.522591e-01	k: 1014566	n:1350000
KS ci ratio: 3.138329e-01	ci left: 9.745203e-05	ci right 1.343786e-04	k: 155	n:1350000
AHCTF1   1350000 perm   1235 sec   (1093 perm/sec)   p_kst 1.148148e-04   p_cons 7.515304e-01   p_joint 1.148148e-04

Joint ci ratio: 3.089209e-01	ci left: 1.001247e-04	ci right 1.373533e-04	k: 160	n:1360000
Cons ci ratio: 1.932747e-03	ci left: 7.508074e-01	ci right 7.522606e-01	k: 1022087	n:1360000
KS ci ratio: 3.089209e-01	ci left: 1.001247e-04	ci right 1.373533e-04	k: 160	n:1360000
AHCTF1   1360000 perm   1250 sec   (1088 perm/sec)   p_kst 1.176471e-04   p_cons 7.515346e-01   p_joint 1.176471e-04

Joint ci ratio: 3.060821e-01	ci left: 1.014148e-04	ci right 1.387089e-04	k: 163	n:1370000
Cons ci ratio: 1.925878e-03	ci left: 7.507718e-01	ci right 7.522198e-01	k: 1029550	n:1370000
KS ci ratio: 3.060821e-01	ci left: 1.014148e-04	ci right 1.387089e-04	k: 163	n:1370000
AHCTF1   1370000 perm   1265 sec   (1083 perm/sec)   p_kst 1.189781e-04   p_cons 7.514964e-01   p_joint 1.189781e-04

Joint ci ratio: 3.060823e-01	ci left: 1.006799e-04	ci right 1.377038e-04	k: 163	n:1380000
Cons ci ratio: 1.918805e-03	ci left: 7.507904e-01	ci right 7.522331e-01	k: 1037087	n:1380000
KS ci ratio: 3.060823e-01	ci left: 1.006799e-04	ci right 1.377038e-04	k: 163	n:1380000
AHCTF1   1380000 perm   1280 sec   (1078 perm/sec)   p_kst 1.181159e-04   p_cons 7.515123e-01   p_joint 1.181159e-04

Joint ci ratio: 3.033204e-01	ci left: 1.019488e-04	ci right 1.390359e-04	k: 166	n:1390000
Cons ci ratio: 1.911902e-03	ci left: 7.507908e-01	ci right 7.522283e-01	k: 1044599	n:1390000
KS ci ratio: 3.033204e-01	ci left: 1.019488e-04	ci right 1.390359e-04	k: 166	n:1390000
AHCTF1   1390000 perm   1295 sec   (1073 perm/sec)   p_kst 1.194245e-04   p_cons 7.515101e-01   p_joint 1.194245e-04

Joint ci ratio: 3.024163e-01	ci left: 1.018806e-04	ci right 1.388112e-04	k: 167	n:1400000
Cons ci ratio: 1.904843e-03	ci left: 7.508362e-01	ci right 7.522685e-01	k: 1052174	n:1400000
KS ci ratio: 3.024163e-01	ci left: 1.018806e-04	ci right 1.388112e-04	k: 167	n:1400000
AHCTF1   1400000 perm   1310 sec   (1068 perm/sec)   p_kst 1.192857e-04   p_cons 7.515529e-01   p_joint 1.192857e-04

Joint ci ratio: 3.015203e-01	ci left: 1.018136e-04	ci right 1.385895e-04	k: 168	n:1410000
Cons ci ratio: 1.898104e-03	ci left: 7.508334e-01	ci right 7.522606e-01	k: 1059682	n:1410000
KS ci ratio: 3.015203e-01	ci left: 1.018136e-04	ci right 1.385895e-04	k: 168	n:1410000
AHCTF1   1410000 perm   1326 sec   (1063 perm/sec)   p_kst 1.191489e-04   p_cons 7.515475e-01   p_joint 1.191489e-04

Joint ci ratio: 3.006322e-01	ci left: 1.017476e-04	ci right 1.383708e-04	k: 169	n:1420000
Cons ci ratio: 1.891371e-03	ci left: 7.508433e-01	ci right 7.522655e-01	k: 1067208	n:1420000
KS ci ratio: 3.006322e-01	ci left: 1.017476e-04	ci right 1.383708e-04	k: 169	n:1420000
AHCTF1   1420000 perm   1341 sec   (1059 perm/sec)   p_kst 1.190141e-04   p_cons 7.515549e-01   p_joint 1.190141e-04

Joint ci ratio: 2.997519e-01	ci left: 1.016827e-04	ci right 1.381549e-04	k: 170	n:1430000
Cons ci ratio: 1.884819e-03	ci left: 7.508315e-01	ci right 7.522486e-01	k: 1074703	n:1430000
KS ci ratio: 2.997519e-01	ci left: 1.016827e-04	ci right 1.381549e-04	k: 170	n:1430000
AHCTF1   1430000 perm   1357 sec   (1054 perm/sec)   p_kst 1.188811e-04   p_cons 7.515406e-01   p_joint 1.188811e-04

Joint ci ratio: 2.988792e-01	ci left: 1.016189e-04	ci right 1.379420e-04	k: 171	n:1440000
Cons ci ratio: 1.878152e-03	ci left: 7.508559e-01	ci right 7.522681e-01	k: 1082250	n:1440000
KS ci ratio: 2.988792e-01	ci left: 1.016189e-04	ci right 1.379420e-04	k: 171	n:1440000
AHCTF1   1440000 perm   1372 sec   (1049 perm/sec)   p_kst 1.187500e-04   p_cons 7.515625e-01   p_joint 1.187500e-04

Joint ci ratio: 2.988794e-01	ci left: 1.009181e-04	ci right 1.369907e-04	k: 171	n:1450000
Cons ci ratio: 1.871819e-03	ci left: 7.508275e-01	ci right 7.522349e-01	k: 1089721	n:1450000
KS ci ratio: 2.988794e-01	ci left: 1.009181e-04	ci right 1.369907e-04	k: 171	n:1450000
AHCTF1   1450000 perm   1388 sec   (1045 perm/sec)   p_kst 1.179310e-04   p_cons 7.515317e-01   p_joint 1.179310e-04

Joint ci ratio: 2.963063e-01	ci left: 1.021283e-04	ci right 1.382601e-04	k: 174	n:1460000
Cons ci ratio: 1.865457e-03	ci left: 7.508181e-01	ci right 7.522207e-01	k: 1097219	n:1460000
KS ci ratio: 2.963063e-01	ci left: 1.021283e-04	ci right 1.382601e-04	k: 174	n:1460000
AHCTF1   1460000 perm   1404 sec   (1040 perm/sec)   p_kst 1.191781e-04   p_cons 7.515199e-01   p_joint 1.191781e-04

Joint ci ratio: 2.954633e-01	ci left: 1.020633e-04	ci right 1.380502e-04	k: 175	n:1470000
Cons ci ratio: 1.859207e-03	ci left: 7.507992e-01	ci right 7.521971e-01	k: 1104703	n:1470000
KS ci ratio: 2.954633e-01	ci left: 1.020633e-04	ci right 1.380502e-04	k: 175	n:1470000
AHCTF1   1470000 perm   1420 sec   (1035 perm/sec)   p_kst 1.190476e-04   p_cons 7.514986e-01   p_joint 1.190476e-04

Joint ci ratio: 2.946275e-01	ci left: 1.019994e-04	ci right 1.378429e-04	k: 176	n:1480000
Cons ci ratio: 1.852623e-03	ci left: 7.508604e-01	ci right 7.522534e-01	k: 1112305	n:1480000
KS ci ratio: 2.946275e-01	ci left: 1.019994e-04	ci right 1.378429e-04	k: 176	n:1480000
AHCTF1   1480000 perm   1437 sec   (1030 perm/sec)   p_kst 1.189189e-04   p_cons 7.515574e-01   p_joint 1.189189e-04

Joint ci ratio: 2.946276e-01	ci left: 1.013148e-04	ci right 1.369178e-04	k: 176	n:1490000
Cons ci ratio: 1.846613e-03	ci left: 7.508187e-01	ci right 7.522071e-01	k: 1119755	n:1490000
KS ci ratio: 2.946276e-01	ci left: 1.013148e-04	ci right 1.369178e-04	k: 176	n:1490000
AHCTF1   1490000 perm   1453 sec   (1025 perm/sec)   p_kst 1.181208e-04   p_cons 7.515134e-01   p_joint 1.181208e-04

Joint ci ratio: 2.921619e-01	ci left: 1.024922e-04	ci right 1.381518e-04	k: 179	n:1500000
Cons ci ratio: 1.840438e-03	ci left: 7.508230e-01	ci right 7.522067e-01	k: 1127273	n:1500000
KS ci ratio: 2.921619e-01	ci left: 1.024922e-04	ci right 1.381518e-04	k: 179	n:1500000
AHCTF1   1500000 perm   1469 sec   (1021 perm/sec)   p_kst 1.193333e-04   p_cons 7.515153e-01   p_joint 1.193333e-04

Joint ci ratio: 2.921620e-01	ci left: 1.018135e-04	ci right 1.372369e-04	k: 179	n:1510000
Cons ci ratio: 1.834182e-03	ci left: 7.508563e-01	ci right 7.522354e-01	k: 1134835	n:1510000
KS ci ratio: 2.921620e-01	ci left: 1.018135e-04	ci right 1.372369e-04	k: 179	n:1510000
AHCTF1   1510000 perm   1485 sec   (1017 perm/sec)   p_kst 1.185430e-04   p_cons 7.515464e-01   p_joint 1.185430e-04

Joint ci ratio: 2.921622e-01	ci left: 1.011436e-04	ci right 1.363340e-04	k: 179	n:1520000
Cons ci ratio: 1.828455e-03	ci left: 7.507938e-01	ci right 7.521684e-01	k: 1142252	n:1520000
KS ci ratio: 2.921622e-01	ci left: 1.011436e-04	ci right 1.363340e-04	k: 179	n:1520000
AHCTF1   1520000 perm   1501 sec   (1012 perm/sec)   p_kst 1.177632e-04   p_cons 7.514816e-01   p_joint 1.177632e-04

Joint ci ratio: 2.921623e-01	ci left: 1.004825e-04	ci right 1.354430e-04	k: 179	n:1530000
Cons ci ratio: 1.822619e-03	ci left: 7.507654e-01	ci right 7.521356e-01	k: 1149720	n:1530000
KS ci ratio: 2.921623e-01	ci left: 1.004825e-04	ci right 1.354430e-04	k: 179	n:1530000
AHCTF1   1530000 perm   1518 sec   (1008 perm/sec)   p_kst 1.169935e-04   p_cons 7.514510e-01   p_joint 1.169935e-04

Joint ci ratio: 2.913541e-01	ci left: 1.004319e-04	ci right 1.352602e-04	k: 180	n:1540000
Cons ci ratio: 1.816596e-03	ci left: 7.507874e-01	ci right 7.521532e-01	k: 1157265	n:1540000
KS ci ratio: 2.913541e-01	ci left: 1.004319e-04	ci right 1.352602e-04	k: 180	n:1540000
AHCTF1   1540000 perm   1534 sec   (1004 perm/sec)   p_kst 1.168831e-04   p_cons 7.514708e-01   p_joint 1.168831e-04

Joint ci ratio: 2.897575e-01	ci left: 1.009802e-04	ci right 1.357716e-04	k: 182	n:1550000
Cons ci ratio: 1.810713e-03	ci left: 7.507924e-01	ci right 7.521537e-01	k: 1164784	n:1550000
KS ci ratio: 2.897575e-01	ci left: 1.009802e-04	ci right 1.357716e-04	k: 182	n:1550000
AHCTF1   1550000 perm   1552 sec   (999 perm/sec)   p_kst 1.174194e-04   p_cons 7.514735e-01   p_joint 1.174194e-04

Joint ci ratio: 2.874111e-01	ci left: 1.021168e-04	ci right 1.369632e-04	k: 185	n:1560000
Cons ci ratio: 1.804713e-03	ci left: 7.508333e-01	ci right 7.521902e-01	k: 1172359	n:1560000
KS ci ratio: 2.874111e-01	ci left: 1.021168e-04	ci right 1.369632e-04	k: 185	n:1560000
AHCTF1   1560000 perm   1569 sec   (995 perm/sec)   p_kst 1.185897e-04   p_cons 7.515122e-01   p_joint 1.185897e-04

Joint ci ratio: 2.858782e-01	ci left: 1.026487e-04	ci right 1.374560e-04	k: 187	n:1570000
Cons ci ratio: 1.798920e-03	ci left: 7.508430e-01	ci right 7.521955e-01	k: 1179886	n:1570000
KS ci ratio: 2.858782e-01	ci left: 1.026487e-04	ci right 1.374560e-04	k: 187	n:1570000
AHCTF1   1570000 perm   1585 sec   (990 perm/sec)   p_kst 1.191083e-04   p_cons 7.515197e-01   p_joint 1.191083e-04

Joint ci ratio: 2.851209e-01	ci left: 1.025867e-04	ci right 1.372642e-04	k: 188	n:1580000
Cons ci ratio: 1.793128e-03	ci left: 7.508640e-01	ci right 7.522123e-01	k: 1187431	n:1580000
KS ci ratio: 2.851209e-01	ci left: 1.025867e-04	ci right 1.372642e-04	k: 188	n:1580000
AHCTF1   1580000 perm   1602 sec   (987 perm/sec)   p_kst 1.189873e-04   p_cons 7.515386e-01   p_joint 1.189873e-04

Joint ci ratio: 2.843696e-01	ci left: 1.025255e-04	ci right 1.370746e-04	k: 189	n:1590000
Cons ci ratio: 1.787542e-03	ci left: 7.508533e-01	ci right 7.521973e-01	k: 1194926	n:1590000
KS ci ratio: 2.843696e-01	ci left: 1.025255e-04	ci right 1.370746e-04	k: 189	n:1590000
AHCTF1   1590000 perm   1618 sec   (983 perm/sec)   p_kst 1.188679e-04   p_cons 7.515258e-01   p_joint 1.188679e-04

Joint ci ratio: 2.836242e-01	ci left: 1.024652e-04	ci right 1.368873e-04	k: 190	n:1600000
Cons ci ratio: 1.781909e-03	ci left: 7.508634e-01	ci right 7.522032e-01	k: 1202454	n:1600000
KS ci ratio: 2.836242e-01	ci left: 1.024652e-04	ci right 1.368873e-04	k: 190	n:1600000
AHCTF1   1600000 perm   1635 sec   (979 perm/sec)   p_kst 1.187500e-04   p_cons 7.515338e-01   p_joint 1.187500e-04

Joint ci ratio: 2.836243e-01	ci left: 1.018288e-04	ci right 1.360370e-04	k: 190	n:1610000
Cons ci ratio: 1.776388e-03	ci left: 7.508609e-01	ci right 7.521965e-01	k: 1209962	n:1610000
KS ci ratio: 2.836243e-01	ci left: 1.018288e-04	ci right 1.360370e-04	k: 190	n:1610000
AHCTF1   1610000 perm   1652 sec   (975 perm/sec)   p_kst 1.180124e-04   p_cons 7.515292e-01   p_joint 1.180124e-04

Joint ci ratio: 2.828848e-01	ci left: 1.017736e-04	ci right 1.358583e-04	k: 191	n:1620000
Cons ci ratio: 1.770898e-03	ci left: 7.508628e-01	ci right 7.521943e-01	k: 1217477	n:1620000
KS ci ratio: 2.828848e-01	ci left: 1.017736e-04	ci right 1.358583e-04	k: 191	n:1620000
AHCTF1   1620000 perm   1669 sec   (970 perm/sec)   p_kst 1.179012e-04   p_cons 7.515290e-01   p_joint 1.179012e-04

Joint ci ratio: 2.814228e-01	ci left: 1.022894e-04	ci right 1.363384e-04	k: 193	n:1630000
Cons ci ratio: 1.765403e-03	ci left: 7.508764e-01	ci right 7.522037e-01	k: 1225011	n:1630000
KS ci ratio: 2.814228e-01	ci left: 1.022894e-04	ci right 1.363384e-04	k: 193	n:1630000
AHCTF1   1630000 perm   1688 sec   (966 perm/sec)   p_kst 1.184049e-04   p_cons 7.515405e-01   p_joint 1.184049e-04

Joint ci ratio: 2.799832e-01	ci left: 1.027994e-04	ci right 1.368122e-04	k: 195	n:1640000
Cons ci ratio: 1.760166e-03	ci left: 7.508458e-01	ci right 7.521692e-01	k: 1232473	n:1640000
KS ci ratio: 2.799832e-01	ci left: 1.027994e-04	ci right 1.368122e-04	k: 195	n:1640000
AHCTF1   1640000 perm   1706 sec   (961 perm/sec)   p_kst 1.189024e-04   p_cons 7.515079e-01   p_joint 1.189024e-04

Joint ci ratio: 2.785655e-01	ci left: 1.033036e-04	ci right 1.372798e-04	k: 197	n:1650000
Cons ci ratio: 1.754716e-03	ci left: 7.508708e-01	ci right 7.521901e-01	k: 1240026	n:1650000
KS ci ratio: 2.785655e-01	ci left: 1.033036e-04	ci right 1.372798e-04	k: 197	n:1650000
AHCTF1   1650000 perm   1725 sec   (957 perm/sec)   p_kst 1.193939e-04   p_cons 7.515309e-01   p_joint 1.193939e-04

Joint ci ratio: 2.771691e-01	ci left: 1.038022e-04	ci right 1.377414e-04	k: 199	n:1660000
Cons ci ratio: 1.749294e-03	ci left: 7.509004e-01	ci right 7.522156e-01	k: 1247587	n:1660000
KS ci ratio: 2.771691e-01	ci left: 1.038022e-04	ci right 1.377414e-04	k: 199	n:1660000
AHCTF1   1660000 perm   1742 sec   (953 perm/sec)   p_kst 1.198795e-04   p_cons 7.515584e-01   p_joint 1.198795e-04

Joint ci ratio: 2.771692e-01	ci left: 1.031806e-04	ci right 1.369166e-04	k: 199	n:1670000
Cons ci ratio: 1.744165e-03	ci left: 7.508774e-01	ci right 7.521888e-01	k: 1255061	n:1670000
KS ci ratio: 2.771692e-01	ci left: 1.031806e-04	ci right 1.369166e-04	k: 199	n:1670000
AHCTF1   1670000 perm   1761 sec   (949 perm/sec)   p_kst 1.191617e-04   p_cons 7.515335e-01   p_joint 1.191617e-04

Joint ci ratio: 2.771693e-01	ci left: 1.025664e-04	ci right 1.361016e-04	k: 199	n:1680000
Cons ci ratio: 1.738923e-03	ci left: 7.508887e-01	ci right 7.521961e-01	k: 1262592	n:1680000
KS ci ratio: 2.771693e-01	ci left: 1.025664e-04	ci right 1.361016e-04	k: 199	n:1680000
AHCTF1   1680000 perm   1779 sec   (945 perm/sec)   p_kst 1.184524e-04   p_cons 7.515429e-01   p_joint 1.184524e-04

Joint ci ratio: 2.771694e-01	ci left: 1.019595e-04	ci right 1.352963e-04	k: 199	n:1690000
Cons ci ratio: 1.733917e-03	ci left: 7.508590e-01	ci right 7.521626e-01	k: 1270054	n:1690000
KS ci ratio: 2.771694e-01	ci left: 1.019595e-04	ci right 1.352963e-04	k: 199	n:1690000
AHCTF1   1690000 perm   1797 sec   (941 perm/sec)   p_kst 1.177515e-04   p_cons 7.515112e-01   p_joint 1.177515e-04

Joint ci ratio: 2.751136e-01	ci left: 1.030023e-04	ci right 1.363870e-04	k: 202	n:1700000
Cons ci ratio: 1.728911e-03	ci left: 7.508391e-01	ci right 7.521389e-01	k: 1277532	n:1700000
KS ci ratio: 2.751136e-01	ci left: 1.030023e-04	ci right 1.363870e-04	k: 202	n:1700000
AHCTF1   1700000 perm   1815 sec   (937 perm/sec)   p_kst 1.188235e-04   p_cons 7.514894e-01   p_joint 1.188235e-04

Joint ci ratio: 2.737682e-01	ci left: 1.034891e-04	ci right 1.368393e-04	k: 204	n:1710000
Cons ci ratio: 1.723648e-03	ci left: 7.508844e-01	ci right 7.521803e-01	k: 1285121	n:1710000
KS ci ratio: 2.737682e-01	ci left: 1.034891e-04	ci right 1.368393e-04	k: 204	n:1710000
AHCTF1   1710000 perm   1833 sec   (933 perm/sec)   p_kst 1.192982e-04   p_cons 7.515327e-01   p_joint 1.192982e-04

Joint ci ratio: 2.724424e-01	ci left: 1.039706e-04	ci right 1.372859e-04	k: 206	n:1720000
Cons ci ratio: 1.718420e-03	ci left: 7.509320e-01	ci right 7.522241e-01	k: 1292715	n:1720000
KS ci ratio: 2.724424e-01	ci left: 1.039706e-04	ci right 1.372859e-04	k: 206	n:1720000
AHCTF1   1720000 perm   1853 sec   (928 perm/sec)   p_kst 1.197674e-04   p_cons 7.515785e-01   p_joint 1.197674e-04

Joint ci ratio: 2.711356e-01	ci left: 1.044469e-04	ci right 1.377270e-04	k: 208	n:1730000
Cons ci ratio: 1.713358e-03	ci left: 7.509531e-01	ci right 7.522414e-01	k: 1300264	n:1730000
KS ci ratio: 2.711356e-01	ci left: 1.044469e-04	ci right 1.377270e-04	k: 208	n:1730000
AHCTF1   1730000 perm   1873 sec   (924 perm/sec)   p_kst 1.202312e-04   p_cons 7.515977e-01   p_joint 1.202312e-04

Joint ci ratio: 2.698475e-01	ci left: 1.049181e-04	ci right 1.381627e-04	k: 210	n:1740000
Cons ci ratio: 1.708498e-03	ci left: 7.509395e-01	ci right 7.522241e-01	k: 1307753	n:1740000
KS ci ratio: 2.698475e-01	ci left: 1.049181e-04	ci right 1.381627e-04	k: 210	n:1740000
AHCTF1   1740000 perm   1892 sec   (920 perm/sec)   p_kst 1.206897e-04   p_cons 7.515822e-01   p_joint 1.206897e-04

Joint ci ratio: 2.698476e-01	ci left: 1.043186e-04	ci right 1.373732e-04	k: 210	n:1750000
Cons ci ratio: 1.703388e-03	ci left: 7.509900e-01	ci right 7.522709e-01	k: 1315354	n:1750000
KS ci ratio: 2.698476e-01	ci left: 1.043186e-04	ci right 1.373732e-04	k: 210	n:1750000
AHCTF1   1750000 perm   1910 sec   (916 perm/sec)   p_kst 1.200000e-04   p_cons 7.516309e-01   p_joint 1.200000e-04

Joint ci ratio: 2.692104e-01	ci left: 1.042556e-04	ci right 1.371991e-04	k: 211	n:1760000
Cons ci ratio: 1.698592e-03	ci left: 7.509809e-01	ci right 7.522581e-01	k: 1322851	n:1760000
KS ci ratio: 2.692104e-01	ci left: 1.042556e-04	ci right 1.371991e-04	k: 211	n:1760000
AHCTF1   1760000 perm   1931 sec   (912 perm/sec)   p_kst 1.198864e-04   p_cons 7.516199e-01   p_joint 1.198864e-04

Joint ci ratio: 2.673255e-01	ci left: 1.052476e-04	ci right 1.382326e-04	k: 214	n:1770000
Cons ci ratio: 1.693792e-03	ci left: 7.509814e-01	ci right 7.522550e-01	k: 1330365	n:1770000
KS ci ratio: 2.673255e-01	ci left: 1.052476e-04	ci right 1.382326e-04	k: 214	n:1770000
AHCTF1   1770000 perm   1950 sec   (908 perm/sec)   p_kst 1.209040e-04   p_cons 7.516186e-01   p_joint 1.209040e-04

Joint ci ratio: 2.667060e-01	ci left: 1.051805e-04	ci right 1.380553e-04	k: 215	n:1780000
Cons ci ratio: 1.689214e-03	ci left: 7.509421e-01	ci right 7.522122e-01	k: 1337808	n:1780000
KS ci ratio: 2.667060e-01	ci left: 1.051805e-04	ci right 1.380553e-04	k: 215	n:1780000
AHCTF1   1780000 perm   1968 sec   (904 perm/sec)   p_kst 1.207865e-04   p_cons 7.515775e-01   p_joint 1.207865e-04

Joint ci ratio: 2.667060e-01	ci left: 1.045929e-04	ci right 1.372841e-04	k: 215	n:1790000
Cons ci ratio: 1.684407e-03	ci left: 7.509619e-01	ci right 7.522284e-01	k: 1345356	n:1790000
KS ci ratio: 2.667060e-01	ci left: 1.045929e-04	ci right 1.372841e-04	k: 215	n:1790000
AHCTF1   1790000 perm   1987 sec   (901 perm/sec)   p_kst 1.201117e-04   p_cons 7.515955e-01   p_joint 1.201117e-04

Joint ci ratio: 2.667061e-01	ci left: 1.040118e-04	ci right 1.365214e-04	k: 215	n:1800000
Cons ci ratio: 1.679597e-03	ci left: 7.509915e-01	ci right 7.522544e-01	k: 1352922	n:1800000
KS ci ratio: 2.667061e-01	ci left: 1.040118e-04	ci right 1.365214e-04	k: 215	n:1800000
AHCTF1   1800000 perm   2007 sec   (897 perm/sec)   p_kst 1.194444e-04   p_cons 7.516233e-01   p_joint 1.194444e-04

Joint ci ratio: 2.660909e-01	ci left: 1.039527e-04	ci right 1.363564e-04	k: 216	n:1810000
Cons ci ratio: 1.674897e-03	ci left: 7.510052e-01	ci right 7.522647e-01	k: 1360460	n:1810000
KS ci ratio: 2.660909e-01	ci left: 1.039527e-04	ci right 1.363564e-04	k: 216	n:1810000
AHCTF1   1810000 perm   2029 sec   (892 perm/sec)   p_kst 1.193370e-04   p_cons 7.516354e-01   p_joint 1.193370e-04

Joint ci ratio: 2.648730e-01	ci left: 1.044073e-04	ci right 1.367791e-04	k: 218	n:1820000
Cons ci ratio: 1.670428e-03	ci left: 7.509760e-01	ci right 7.522320e-01	k: 1367920	n:1820000
KS ci ratio: 2.648730e-01	ci left: 1.044073e-04	ci right 1.367791e-04	k: 218	n:1820000
AHCTF1   1820000 perm   2049 sec   (888 perm/sec)   p_kst 1.197802e-04   p_cons 7.516044e-01   p_joint 1.197802e-04

Joint ci ratio: 2.642704e-01	ci left: 1.043470e-04	ci right 1.366143e-04	k: 219	n:1830000
Cons ci ratio: 1.665721e-03	ci left: 7.510083e-01	ci right 7.522608e-01	k: 1375492	n:1830000
KS ci ratio: 2.642704e-01	ci left: 1.043470e-04	ci right 1.366143e-04	k: 219	n:1830000
AHCTF1   1830000 perm   2070 sec   (884 perm/sec)   p_kst 1.196721e-04   p_cons 7.516350e-01   p_joint 1.196721e-04

Joint ci ratio: 2.636718e-01	ci left: 1.042874e-04	ci right 1.364512e-04	k: 220	n:1840000
Cons ci ratio: 1.661240e-03	ci left: 7.509984e-01	ci right 7.522475e-01	k: 1382987	n:1840000
KS ci ratio: 2.636718e-01	ci left: 1.042874e-04	ci right 1.364512e-04	k: 220	n:1840000
AHCTF1   1840000 perm   2091 sec   (880 perm/sec)   p_kst 1.195652e-04   p_cons 7.516234e-01   p_joint 1.195652e-04

Joint ci ratio: 2.624867e-01	ci left: 1.047335e-04	ci right 1.368658e-04	k: 222	n:1850000
Cons ci ratio: 1.656807e-03	ci left: 7.509859e-01	ci right 7.522317e-01	k: 1390477	n:1850000
KS ci ratio: 2.624867e-01	ci left: 1.047335e-04	ci right 1.368658e-04	k: 222	n:1850000
AHCTF1   1850000 perm   2111 sec   (876 perm/sec)   p_kst 1.200000e-04   p_cons 7.516092e-01   p_joint 1.200000e-04

Joint ci ratio: 2.613175e-01	ci left: 1.051751e-04	ci right 1.372756e-04	k: 224	n:1860000
Cons ci ratio: 1.652133e-03	ci left: 7.510360e-01	ci right 7.522783e-01	k: 1398083	n:1860000
KS ci ratio: 2.613175e-01	ci left: 1.051751e-04	ci right 1.372756e-04	k: 224	n:1860000
AHCTF1   1860000 perm   2133 sec   (872 perm/sec)   p_kst 1.204301e-04   p_cons 7.516575e-01   p_joint 1.204301e-04

Joint ci ratio: 2.601637e-01	ci left: 1.056123e-04	ci right 1.376808e-04	k: 226	n:1870000
Cons ci ratio: 1.647810e-03	ci left: 7.510148e-01	ci right 7.522539e-01	k: 1405557	n:1870000
KS ci ratio: 2.601637e-01	ci left: 1.056123e-04	ci right 1.376808e-04	k: 226	n:1870000
AHCTF1   1870000 perm   2154 sec   (868 perm/sec)   p_kst 1.208556e-04   p_cons 7.516348e-01   p_joint 1.208556e-04

Joint ci ratio: 2.595925e-01	ci left: 1.055478e-04	ci right 1.375150e-04	k: 227	n:1880000
Cons ci ratio: 1.643432e-03	ci left: 7.510142e-01	ci right 7.522499e-01	k: 1413069	n:1880000
KS ci ratio: 2.595925e-01	ci left: 1.055478e-04	ci right 1.375150e-04	k: 227	n:1880000
AHCTF1   1880000 perm   2173 sec   (865 perm/sec)   p_kst 1.207447e-04   p_cons 7.516324e-01   p_joint 1.207447e-04

Joint ci ratio: 2.595926e-01	ci left: 1.049893e-04	ci right 1.367874e-04	k: 227	n:1890000
Cons ci ratio: 1.638949e-03	ci left: 7.510453e-01	ci right 7.522777e-01	k: 1420641	n:1890000
KS ci ratio: 2.595926e-01	ci left: 1.049893e-04	ci right 1.367874e-04	k: 227	n:1890000
AHCTF1   1890000 perm   2193 sec   (862 perm/sec)   p_kst 1.201058e-04   p_cons 7.516619e-01   p_joint 1.201058e-04

Joint ci ratio: 2.590252e-01	ci left: 1.049289e-04	ci right 1.366279e-04	k: 228	n:1900000
Cons ci ratio: 1.634533e-03	ci left: 7.510692e-01	ci right 7.522984e-01	k: 1428200	n:1900000
KS ci ratio: 2.590252e-01	ci left: 1.049289e-04	ci right 1.366279e-04	k: 228	n:1900000
AHCTF1   1900000 perm   2212 sec   (859 perm/sec)   p_kst 1.200000e-04   p_cons 7.516842e-01   p_joint 1.200000e-04

Joint ci ratio: 2.584615e-01	ci left: 1.048691e-04	ci right 1.364700e-04	k: 229	n:1910000
Cons ci ratio: 1.630296e-03	ci left: 7.510599e-01	ci right 7.522859e-01	k: 1435696	n:1910000
KS ci ratio: 2.584615e-01	ci left: 1.048691e-04	ci right 1.364700e-04	k: 229	n:1910000
AHCTF1   1910000 perm   2233 sec   (855 perm/sec)   p_kst 1.198953e-04   p_cons 7.516733e-01   p_joint 1.198953e-04

Joint ci ratio: 2.579015e-01	ci left: 1.048101e-04	ci right 1.363137e-04	k: 230	n:1920000
Cons ci ratio: 1.626063e-03	ci left: 7.510575e-01	ci right 7.522803e-01	k: 1443205	n:1920000
KS ci ratio: 2.579015e-01	ci left: 1.048101e-04	ci right 1.363137e-04	k: 230	n:1920000
AHCTF1   1920000 perm   2253 sec   (852 perm/sec)   p_kst 1.197917e-04   p_cons 7.516693e-01   p_joint 1.197917e-04

Joint ci ratio: 2.567922e-01	ci left: 1.052364e-04	ci right 1.367104e-04	k: 232	n:1930000
Cons ci ratio: 1.621932e-03	ci left: 7.510390e-01	ci right 7.522587e-01	k: 1450683	n:1930000
KS ci ratio: 2.567922e-01	ci left: 1.052364e-04	ci right 1.367104e-04	k: 232	n:1930000
AHCTF1   1930000 perm   2273 sec   (849 perm/sec)   p_kst 1.202073e-04   p_cons 7.516492e-01   p_joint 1.202073e-04

Joint ci ratio: 2.556971e-01	ci left: 1.056587e-04	ci right 1.371027e-04	k: 234	n:1940000
Cons ci ratio: 1.617834e-03	ci left: 7.510202e-01	ci right 7.522367e-01	k: 1458160	n:1940000
KS ci ratio: 2.556971e-01	ci left: 1.056587e-04	ci right 1.371027e-04	k: 234	n:1940000
AHCTF1   1940000 perm   2293 sec   (846 perm/sec)   p_kst 1.206186e-04   p_cons 7.516289e-01   p_joint 1.206186e-04

Joint ci ratio: 2.540803e-01	ci left: 1.065571e-04	ci right 1.380361e-04	k: 237	n:1950000
Cons ci ratio: 1.613723e-03	ci left: 7.510119e-01	ci right 7.522253e-01	k: 1465657	n:1950000
KS ci ratio: 2.540803e-01	ci left: 1.065571e-04	ci right 1.380361e-04	k: 237	n:1950000
AHCTF1   1950000 perm   2315 sec   (842 perm/sec)   p_kst 1.215385e-04   p_cons 7.516190e-01   p_joint 1.215385e-04

Joint ci ratio: 2.535482e-01	ci left: 1.064912e-04	ci right 1.378744e-04	k: 238	n:1960000
Cons ci ratio: 1.609448e-03	ci left: 7.510491e-01	ci right 7.522593e-01	k: 1473243	n:1960000
KS ci ratio: 2.535482e-01	ci left: 1.064912e-04	ci right 1.378744e-04	k: 238	n:1960000
AHCTF1   1960000 perm   2335 sec   (839 perm/sec)   p_kst 1.214286e-04   p_cons 7.516546e-01   p_joint 1.214286e-04

Joint ci ratio: 2.514525e-01	ci left: 1.078526e-04	ci right 1.393332e-04	k: 242	n:1970000
Cons ci ratio: 1.605433e-03	ci left: 7.510331e-01	ci right 7.522403e-01	k: 1480725	n:1970000
KS ci ratio: 2.514525e-01	ci left: 1.078526e-04	ci right 1.393332e-04	k: 242	n:1970000
AHCTF1   1970000 perm   2356 sec   (836 perm/sec)   p_kst 1.228426e-04   p_cons 7.516371e-01   p_joint 1.228426e-04

Joint ci ratio: 2.504241e-01	ci left: 1.082544e-04	ci right 1.397030e-04	k: 244	n:1980000
Cons ci ratio: 1.601414e-03	ci left: 7.510253e-01	ci right 7.522295e-01	k: 1488223	n:1980000
KS ci ratio: 2.504241e-01	ci left: 1.082544e-04	ci right 1.397030e-04	k: 244	n:1980000
AHCTF1   1980000 perm   2379 sec   (832 perm/sec)   p_kst 1.232323e-04   p_cons 7.516278e-01   p_joint 1.232323e-04

Joint ci ratio: 2.499146e-01	ci left: 1.081815e-04	ci right 1.395349e-04	k: 245	n:1990000
Cons ci ratio: 1.597482e-03	ci left: 7.510041e-01	ci right 7.522052e-01	k: 1495694	n:1990000
KS ci ratio: 2.499146e-01	ci left: 1.081815e-04	ci right 1.395349e-04	k: 245	n:1990000
AHCTF1   1990000 perm   2399 sec   (830 perm/sec)   p_kst 1.231156e-04   p_cons 7.516050e-01   p_joint 1.231156e-04

Joint ci ratio: 2.489048e-01	ci left: 1.085781e-04	ci right 1.398996e-04	k: 247	n:2000000
Cons ci ratio: 1.593484e-03	ci left: 7.510056e-01	ci right 7.522037e-01	k: 1503210	n:2000000
KS ci ratio: 2.489048e-01	ci left: 1.085781e-04	ci right 1.398996e-04	k: 247	n:2000000
AHCTF1   2000000 perm   2420 sec   (826 perm/sec)   p_kst 1.235000e-04   p_cons 7.516050e-01   p_joint 1.235000e-04

Joint ci ratio: 2.484045e-01	ci left: 1.085044e-04	ci right 1.397320e-04	k: 248	n:2010000
Cons ci ratio: 1.589494e-03	ci left: 7.510120e-01	ci right 7.522072e-01	k: 1510736	n:2010000
KS ci ratio: 2.484045e-01	ci left: 1.085044e-04	ci right 1.397320e-04	k: 248	n:2010000
AHCTF1   2010000 perm   2441 sec   (823 perm/sec)   p_kst 1.233831e-04   p_cons 7.516100e-01   p_joint 1.233831e-04

Joint ci ratio: 2.479072e-01	ci left: 1.084315e-04	ci right 1.395661e-04	k: 249	n:2020000
Cons ci ratio: 1.585540e-03	ci left: 7.510169e-01	ci right 7.522091e-01	k: 1518259	n:2020000
KS ci ratio: 2.479072e-01	ci left: 1.084315e-04	ci right 1.395661e-04	k: 249	n:2020000
AHCTF1   2020000 perm   2461 sec   (821 perm/sec)   p_kst 1.232673e-04   p_cons 7.516134e-01   p_joint 1.232673e-04

Joint ci ratio: 2.479072e-01	ci left: 1.078974e-04	ci right 1.388786e-04	k: 249	n:2030000
Cons ci ratio: 1.581668e-03	ci left: 7.510094e-01	ci right 7.521987e-01	k: 1525757	n:2030000
KS ci ratio: 2.479072e-01	ci left: 1.078974e-04	ci right 1.388786e-04	k: 249	n:2030000
AHCTF1   2030000 perm   2482 sec   (818 perm/sec)   p_kst 1.226601e-04   p_cons 7.516044e-01   p_joint 1.226601e-04

Joint ci ratio: 2.479073e-01	ci left: 1.073684e-04	ci right 1.381978e-04	k: 249	n:2040000
Cons ci ratio: 1.577853e-03	ci left: 7.509952e-01	ci right 7.521816e-01	k: 1533241	n:2040000
KS ci ratio: 2.479073e-01	ci left: 1.073684e-04	ci right 1.381978e-04	k: 249	n:2040000
AHCTF1   2040000 perm   2503 sec   (815 perm/sec)   p_kst 1.220588e-04   p_cons 7.515887e-01   p_joint 1.220588e-04

Joint ci ratio: 2.474130e-01	ci left: 1.073022e-04	ci right 1.380417e-04	k: 250	n:2050000
Cons ci ratio: 1.574059e-03	ci left: 7.509825e-01	ci right 7.521660e-01	k: 1540728	n:2050000
KS ci ratio: 2.474130e-01	ci left: 1.073022e-04	ci right 1.380417e-04	k: 250	n:2050000
AHCTF1   2050000 perm   2524 sec   (812 perm/sec)   p_kst 1.219512e-04   p_cons 7.515746e-01   p_joint 1.219512e-04

Joint ci ratio: 2.474131e-01	ci left: 1.067813e-04	ci right 1.373716e-04	k: 250	n:2060000
Cons ci ratio: 1.570050e-03	ci left: 7.510278e-01	ci right 7.522084e-01	k: 1548334	n:2060000
KS ci ratio: 2.474131e-01	ci left: 1.067813e-04	ci right 1.373716e-04	k: 250	n:2060000
AHCTF1   2060000 perm   2545 sec   (809 perm/sec)   p_kst 1.213592e-04   p_cons 7.516184e-01   p_joint 1.213592e-04

Joint ci ratio: 2.469217e-01	ci left: 1.067187e-04	ci right 1.372209e-04	k: 251	n:2070000
Cons ci ratio: 1.566204e-03	ci left: 7.510408e-01	ci right 7.522184e-01	k: 1555874	n:2070000
KS ci ratio: 2.469217e-01	ci left: 1.067187e-04	ci right 1.372209e-04	k: 251	n:2070000
AHCTF1   2070000 perm   2566 sec   (807 perm/sec)   p_kst 1.212560e-04   p_cons 7.516300e-01   p_joint 1.212560e-04

Joint ci ratio: 2.469218e-01	ci left: 1.062056e-04	ci right 1.365612e-04	k: 251	n:2080000
Cons ci ratio: 1.562458e-03	ci left: 7.510367e-01	ci right 7.522116e-01	k: 1563379	n:2080000
KS ci ratio: 2.469218e-01	ci left: 1.062056e-04	ci right 1.365612e-04	k: 251	n:2080000
AHCTF1   2080000 perm   2587 sec   (804 perm/sec)   p_kst 1.206731e-04   p_cons 7.516245e-01   p_joint 1.206731e-04

Joint ci ratio: 2.469218e-01	ci left: 1.056974e-04	ci right 1.359078e-04	k: 251	n:2090000
Cons ci ratio: 1.558748e-03	ci left: 7.510304e-01	ci right 7.522024e-01	k: 1570879	n:2090000
KS ci ratio: 2.469218e-01	ci left: 1.056974e-04	ci right 1.359078e-04	k: 251	n:2090000
AHCTF1   2090000 perm   2608 sec   (801 perm/sec)   p_kst 1.200957e-04   p_cons 7.516167e-01   p_joint 1.200957e-04

Joint ci ratio: 2.459477e-01	ci left: 1.060877e-04	ci right 1.362717e-04	k: 253	n:2100000
Cons ci ratio: 1.555092e-03	ci left: 7.510174e-01	ci right 7.521867e-01	k: 1578365	n:2100000
KS ci ratio: 2.459477e-01	ci left: 1.060877e-04	ci right 1.362717e-04	k: 253	n:2100000
AHCTF1   2100000 perm   2629 sec   (799 perm/sec)   p_kst 1.204762e-04   p_cons 7.516024e-01   p_joint 1.204762e-04

Joint ci ratio: 2.449851e-01	ci left: 1.064745e-04	ci right 1.366319e-04	k: 255	n:2110000
Cons ci ratio: 1.551357e-03	ci left: 7.510297e-01	ci right 7.521962e-01	k: 1585904	n:2110000
KS ci ratio: 2.449851e-01	ci left: 1.064745e-04	ci right 1.366319e-04	k: 255	n:2110000
AHCTF1   2110000 perm   2651 sec   (796 perm/sec)   p_kst 1.208531e-04   p_cons 7.516133e-01   p_joint 1.208531e-04

Joint ci ratio: 2.449851e-01	ci left: 1.059722e-04	ci right 1.359874e-04	k: 255	n:2120000
Cons ci ratio: 1.547690e-03	ci left: 7.510319e-01	ci right 7.521957e-01	k: 1593422	n:2120000
KS ci ratio: 2.449851e-01	ci left: 1.059722e-04	ci right 1.359874e-04	k: 255	n:2120000
AHCTF1   2120000 perm   2671 sec   (794 perm/sec)   p_kst 1.202830e-04   p_cons 7.516142e-01   p_joint 1.202830e-04

Joint ci ratio: 2.430932e-01	ci left: 1.072378e-04	ci right 1.373415e-04	k: 259	n:2130000
Cons ci ratio: 1.544018e-03	ci left: 7.510417e-01	ci right 7.522027e-01	k: 1600956	n:2130000
KS ci ratio: 2.430932e-01	ci left: 1.072378e-04	ci right 1.373415e-04	k: 259	n:2130000
AHCTF1   2130000 perm   2693 sec   (791 perm/sec)   p_kst 1.215962e-04   p_cons 7.516225e-01   p_joint 1.215962e-04

Joint ci ratio: 2.430933e-01	ci left: 1.067367e-04	ci right 1.366997e-04	k: 259	n:2140000
Cons ci ratio: 1.540420e-03	ci left: 7.510397e-01	ci right 7.521979e-01	k: 1608465	n:2140000
KS ci ratio: 2.430933e-01	ci left: 1.067367e-04	ci right 1.366997e-04	k: 259	n:2140000
AHCTF1   2140000 perm   2713 sec   (789 perm/sec)   p_kst 1.210280e-04   p_cons 7.516192e-01   p_joint 1.210280e-04

Joint ci ratio: 2.421636e-01	ci left: 1.071139e-04	ci right 1.370506e-04	k: 261	n:2150000
Cons ci ratio: 1.536880e-03	ci left: 7.510298e-01	ci right 7.521854e-01	k: 1615957	n:2150000
KS ci ratio: 2.421636e-01	ci left: 1.071139e-04	ci right 1.370506e-04	k: 261	n:2150000
AHCTF1   2150000 perm   2735 sec   (786 perm/sec)   p_kst 1.213953e-04   p_cons 7.516079e-01   p_joint 1.213953e-04

Joint ci ratio: 2.407889e-01	ci left: 1.079229e-04	ci right 1.378888e-04	k: 264	n:2160000
Cons ci ratio: 1.533321e-03	ci left: 7.510306e-01	ci right 7.521835e-01	k: 1623472	n:2160000
KS ci ratio: 2.407889e-01	ci left: 1.079229e-04	ci right 1.378888e-04	k: 264	n:2160000
AHCTF1   2160000 perm   2756 sec   (784 perm/sec)   p_kst 1.222222e-04   p_cons 7.516074e-01   p_joint 1.222222e-04

Joint ci ratio: 2.398853e-01	ci left: 1.082917e-04	ci right 1.382305e-04	k: 266	n:2170000
Cons ci ratio: 1.529697e-03	ci left: 7.510531e-01	ci right 7.522033e-01	k: 1631034	n:2170000
KS ci ratio: 2.398853e-01	ci left: 1.082917e-04	ci right 1.382305e-04	k: 266	n:2170000
AHCTF1   2170000 perm   2777 sec   (781 perm/sec)   p_kst 1.225806e-04   p_cons 7.516286e-01   p_joint 1.225806e-04

Joint ci ratio: 2.394373e-01	ci left: 1.082261e-04	ci right 1.380826e-04	k: 267	n:2180000
Cons ci ratio: 1.526114e-03	ci left: 7.510718e-01	ci right 7.522193e-01	k: 1638588	n:2180000
KS ci ratio: 2.394373e-01	ci left: 1.082261e-04	ci right 1.380826e-04	k: 267	n:2180000
AHCTF1   2180000 perm   2799 sec   (779 perm/sec)   p_kst 1.224771e-04   p_cons 7.516459e-01   p_joint 1.224771e-04

Joint ci ratio: 2.394374e-01	ci left: 1.077319e-04	ci right 1.374521e-04	k: 267	n:2190000
Cons ci ratio: 1.522608e-03	ci left: 7.510774e-01	ci right 7.522223e-01	k: 1646114	n:2190000
KS ci ratio: 2.394374e-01	ci left: 1.077319e-04	ci right 1.374521e-04	k: 267	n:2190000
AHCTF1   2190000 perm   2820 sec   (777 perm/sec)   p_kst 1.219178e-04   p_cons 7.516502e-01   p_joint 1.219178e-04

Joint ci ratio: 2.381083e-01	ci left: 1.085243e-04	ci right 1.382724e-04	k: 270	n:2200000
Cons ci ratio: 1.519098e-03	ci left: 7.510899e-01	ci right 7.522322e-01	k: 1653655	n:2200000
KS ci ratio: 2.381083e-01	ci left: 1.085243e-04	ci right 1.382724e-04	k: 270	n:2200000
AHCTF1   2200000 perm   2842 sec   (774 perm/sec)   p_kst 1.227273e-04   p_cons 7.516614e-01   p_joint 1.227273e-04

Joint ci ratio: 2.376702e-01	ci left: 1.084588e-04	ci right 1.381261e-04	k: 271	n:2210000
Cons ci ratio: 1.515563e-03	ci left: 7.511145e-01	ci right 7.522541e-01	k: 1661223	n:2210000
KS ci ratio: 2.376702e-01	ci left: 1.084588e-04	ci right 1.381261e-04	k: 271	n:2210000
AHCTF1   2210000 perm   2863 sec   (772 perm/sec)   p_kst 1.226244e-04   p_cons 7.516846e-01   p_joint 1.226244e-04

Joint ci ratio: 2.363702e-01	ci left: 1.092413e-04	ci right 1.389353e-04	k: 274	n:2220000
Cons ci ratio: 1.512289e-03	ci left: 7.510802e-01	ci right 7.522173e-01	k: 1668661	n:2220000
KS ci ratio: 2.363702e-01	ci left: 1.092413e-04	ci right 1.389353e-04	k: 274	n:2220000
AHCTF1   2220000 perm   2885 sec   (770 perm/sec)   p_kst 1.234234e-04   p_cons 7.516491e-01   p_joint 1.234234e-04

Joint ci ratio: 2.363703e-01	ci left: 1.087515e-04	ci right 1.383123e-04	k: 274	n:2230000
Cons ci ratio: 1.508865e-03	ci left: 7.510889e-01	ci right 7.522235e-01	k: 1676194	n:2230000
KS ci ratio: 2.363703e-01	ci left: 1.087515e-04	ci right 1.383123e-04	k: 274	n:2230000
AHCTF1   2230000 perm   2907 sec   (767 perm/sec)   p_kst 1.228700e-04   p_cons 7.516565e-01   p_joint 1.228700e-04

Joint ci ratio: 2.359417e-01	ci left: 1.086860e-04	ci right 1.381677e-04	k: 275	n:2240000
Cons ci ratio: 1.505413e-03	ci left: 7.511100e-01	ci right 7.522420e-01	k: 1683755	n:2240000
KS ci ratio: 2.359417e-01	ci left: 1.086860e-04	ci right 1.381677e-04	k: 275	n:2240000
AHCTF1   2240000 perm   2929 sec   (765 perm/sec)   p_kst 1.227679e-04   p_cons 7.516763e-01   p_joint 1.227679e-04

Joint ci ratio: 2.350914e-01	ci left: 1.090394e-04	ci right 1.384948e-04	k: 277	n:2250000
Cons ci ratio: 1.502119e-03	ci left: 7.510976e-01	ci right 7.522271e-01	k: 1691241	n:2250000
KS ci ratio: 2.350914e-01	ci left: 1.090394e-04	ci right 1.384948e-04	k: 277	n:2250000
AHCTF1   2250000 perm   2950 sec   (763 perm/sec)   p_kst 1.231111e-04   p_cons 7.516627e-01   p_joint 1.231111e-04

Joint ci ratio: 2.346697e-01	ci left: 1.089733e-04	ci right 1.383505e-04	k: 278	n:2260000
Cons ci ratio: 1.498690e-03	ci left: 7.511242e-01	ci right 7.522512e-01	k: 1698815	n:2260000
KS ci ratio: 2.346697e-01	ci left: 1.089733e-04	ci right 1.383505e-04	k: 278	n:2260000
AHCTF1   2260000 perm   2972 sec   (760 perm/sec)   p_kst 1.230088e-04   p_cons 7.516881e-01   p_joint 1.230088e-04

Joint ci ratio: 2.338331e-01	ci left: 1.093226e-04	ci right 1.386737e-04	k: 280	n:2270000
Cons ci ratio: 1.495262e-03	ci left: 7.511564e-01	ci right 7.522808e-01	k: 1706402	n:2270000
KS ci ratio: 2.338331e-01	ci left: 1.093226e-04	ci right 1.386737e-04	k: 280	n:2270000
AHCTF1   2270000 perm   2995 sec   (758 perm/sec)   p_kst 1.233480e-04   p_cons 7.517189e-01   p_joint 1.233480e-04

Joint ci ratio: 2.334181e-01	ci left: 1.092561e-04	ci right 1.385297e-04	k: 281	n:2280000
Cons ci ratio: 1.491909e-03	ci left: 7.511751e-01	ci right 7.522971e-01	k: 1713959	n:2280000
KS ci ratio: 2.334181e-01	ci left: 1.092561e-04	ci right 1.385297e-04	k: 281	n:2280000
AHCTF1   2280000 perm   3017 sec   (756 perm/sec)   p_kst 1.232456e-04   p_cons 7.517364e-01   p_joint 1.232456e-04

Joint ci ratio: 2.334182e-01	ci left: 1.087790e-04	ci right 1.379247e-04	k: 281	n:2290000
Cons ci ratio: 1.488708e-03	ci left: 7.511613e-01	ci right 7.522808e-01	k: 1721442	n:2290000
KS ci ratio: 2.334182e-01	ci left: 1.087790e-04	ci right 1.379247e-04	k: 281	n:2290000
AHCTF1   2290000 perm   3039 sec   (753 perm/sec)   p_kst 1.227074e-04   p_cons 7.517214e-01   p_joint 1.227074e-04

Joint ci ratio: 2.334182e-01	ci left: 1.083060e-04	ci right 1.373251e-04	k: 281	n:2300000
Cons ci ratio: 1.485474e-03	ci left: 7.511611e-01	ci right 7.522782e-01	k: 1728956	n:2300000
KS ci ratio: 2.334182e-01	ci left: 1.083060e-04	ci right 1.373251e-04	k: 281	n:2300000
AHCTF1   2300000 perm   3061 sec   (751 perm/sec)   p_kst 1.221739e-04   p_cons 7.517200e-01   p_joint 1.221739e-04

Joint ci ratio: 2.330055e-01	ci left: 1.082448e-04	ci right 1.371887e-04	k: 282	n:2310000
Cons ci ratio: 1.482348e-03	ci left: 7.511389e-01	ci right 7.522536e-01	k: 1736419	n:2310000
KS ci ratio: 2.330055e-01	ci left: 1.082448e-04	ci right 1.371887e-04	k: 282	n:2310000
AHCTF1   2310000 perm   3084 sec   (749 perm/sec)   p_kst 1.220779e-04   p_cons 7.516965e-01   p_joint 1.220779e-04

Joint ci ratio: 2.317801e-01	ci left: 1.089960e-04	ci right 1.379657e-04	k: 285	n:2320000
Cons ci ratio: 1.479022e-03	ci left: 7.511724e-01	ci right 7.522847e-01	k: 1744011	n:2320000
KS ci ratio: 2.317801e-01	ci left: 1.089960e-04	ci right 1.379657e-04	k: 285	n:2320000
AHCTF1   2320000 perm   3107 sec   (747 perm/sec)   p_kst 1.228448e-04   p_cons 7.517289e-01   p_joint 1.228448e-04

Joint ci ratio: 2.313760e-01	ci left: 1.089325e-04	ci right 1.378276e-04	k: 286	n:2330000
Cons ci ratio: 1.475743e-03	ci left: 7.511993e-01	ci right 7.523091e-01	k: 1751588	n:2330000
KS ci ratio: 2.313760e-01	ci left: 1.089325e-04	ci right 1.378276e-04	k: 286	n:2330000
AHCTF1   2330000 perm   3129 sec   (745 perm/sec)   p_kst 1.227468e-04   p_cons 7.517545e-01   p_joint 1.227468e-04

Joint ci ratio: 2.313760e-01	ci left: 1.084670e-04	ci right 1.372386e-04	k: 286	n:2340000
Cons ci ratio: 1.472547e-03	ci left: 7.512105e-01	ci right 7.523179e-01	k: 1759129	n:2340000
KS ci ratio: 2.313760e-01	ci left: 1.084670e-04	ci right 1.372386e-04	k: 286	n:2340000
AHCTF1   2340000 perm   3152 sec   (742 perm/sec)   p_kst 1.222222e-04   p_cons 7.517645e-01   p_joint 1.222222e-04

Joint ci ratio: 2.309740e-01	ci left: 1.084063e-04	ci right 1.371047e-04	k: 287	n:2350000
Cons ci ratio: 1.469309e-03	ci left: 7.512374e-01	ci right 7.523424e-01	k: 1766707	n:2350000
KS ci ratio: 2.309740e-01	ci left: 1.084063e-04	ci right 1.371047e-04	k: 287	n:2350000
AHCTF1   2350000 perm   3175 sec   (740 perm/sec)   p_kst 1.221277e-04   p_cons 7.517902e-01   p_joint 1.221277e-04

Joint ci ratio: 2.301761e-01	ci left: 1.087455e-04	ci right 1.374201e-04	k: 289	n:2360000
Cons ci ratio: 1.466163e-03	ci left: 7.512462e-01	ci right 7.523489e-01	k: 1774243	n:2360000
KS ci ratio: 2.301761e-01	ci left: 1.087455e-04	ci right 1.374201e-04	k: 289	n:2360000
AHCTF1   2360000 perm   3198 sec   (738 perm/sec)   p_kst 1.224576e-04   p_cons 7.517979e-01   p_joint 1.224576e-04

Joint ci ratio: 2.297803e-01	ci left: 1.086843e-04	ci right 1.372865e-04	k: 290	n:2370000
Cons ci ratio: 1.463111e-03	ci left: 7.512360e-01	ci right 7.523364e-01	k: 1781734	n:2370000
KS ci ratio: 2.297803e-01	ci left: 1.086843e-04	ci right 1.372865e-04	k: 290	n:2370000
AHCTF1   2370000 perm   3221 sec   (736 perm/sec)   p_kst 1.223629e-04   p_cons 7.517865e-01   p_joint 1.223629e-04

Joint ci ratio: 2.293865e-01	ci left: 1.086236e-04	ci right 1.371539e-04	k: 291	n:2380000
Cons ci ratio: 1.460052e-03	ci left: 7.512326e-01	ci right 7.523306e-01	k: 1789241	n:2380000
KS ci ratio: 2.293865e-01	ci left: 1.086236e-04	ci right 1.371539e-04	k: 291	n:2380000
AHCTF1   2380000 perm   3244 sec   (734 perm/sec)   p_kst 1.222689e-04   p_cons 7.517819e-01   p_joint 1.222689e-04

Joint ci ratio: 2.282171e-01	ci left: 1.093524e-04	ci right 1.379071e-04	k: 294	n:2390000
Cons ci ratio: 1.457180e-03	ci left: 7.511861e-01	ci right 7.522819e-01	k: 1796645	n:2390000
KS ci ratio: 2.282171e-01	ci left: 1.093524e-04	ci right 1.379071e-04	k: 294	n:2390000
AHCTF1   2390000 perm   3267 sec   (732 perm/sec)   p_kst 1.230126e-04   p_cons 7.517343e-01   p_joint 1.230126e-04

Joint ci ratio: 2.282171e-01	ci left: 1.088968e-04	ci right 1.373325e-04	k: 294	n:2400000
Cons ci ratio: 1.454142e-03	ci left: 7.511871e-01	ci right 7.522806e-01	k: 1804162	n:2400000
KS ci ratio: 2.282171e-01	ci left: 1.088968e-04	ci right 1.373325e-04	k: 294	n:2400000
AHCTF1   2400000 perm   3291 sec   (729 perm/sec)   p_kst 1.225000e-04   p_cons 7.517342e-01   p_joint 1.225000e-04

Joint ci ratio: 2.278313e-01	ci left: 1.088362e-04	ci right 1.372012e-04	k: 295	n:2410000
Cons ci ratio: 1.451256e-03	ci left: 7.511536e-01	ci right 7.522449e-01	k: 1811596	n:2410000
KS ci ratio: 2.278313e-01	ci left: 1.088362e-04	ci right 1.372012e-04	k: 295	n:2410000
AHCTF1   2410000 perm   3314 sec   (727 perm/sec)   p_kst 1.224066e-04   p_cons 7.516996e-01   p_joint 1.224066e-04

Joint ci ratio: 2.278314e-01	ci left: 1.083864e-04	ci right 1.366343e-04	k: 295	n:2420000
Cons ci ratio: 1.448293e-03	ci left: 7.511448e-01	ci right 7.522339e-01	k: 1819089	n:2420000
KS ci ratio: 2.278314e-01	ci left: 1.083864e-04	ci right 1.366343e-04	k: 295	n:2420000
AHCTF1   2420000 perm   3337 sec   (725 perm/sec)   p_kst 1.219008e-04   p_cons 7.516897e-01   p_joint 1.219008e-04

Joint ci ratio: 2.278314e-01	ci left: 1.079404e-04	ci right 1.360720e-04	k: 295	n:2430000
Cons ci ratio: 1.445302e-03	ci left: 7.511481e-01	ci right 7.522349e-01	k: 1826611	n:2430000
KS ci ratio: 2.278314e-01	ci left: 1.079404e-04	ci right 1.360720e-04	k: 295	n:2430000
AHCTF1   2430000 perm   3361 sec   (723 perm/sec)   p_kst 1.213992e-04   p_cons 7.516918e-01   p_joint 1.213992e-04

Joint ci ratio: 2.274476e-01	ci left: 1.078845e-04	ci right 1.359475e-04	k: 296	n:2440000
Cons ci ratio: 1.442296e-03	ci left: 7.511599e-01	ci right 7.522444e-01	k: 1834154	n:2440000
KS ci ratio: 2.274476e-01	ci left: 1.078845e-04	ci right 1.359475e-04	k: 296	n:2440000
AHCTF1   2440000 perm   3385 sec   (721 perm/sec)   p_kst 1.213115e-04   p_cons 7.517025e-01   p_joint 1.213115e-04

Joint ci ratio: 2.274476e-01	ci left: 1.074441e-04	ci right 1.353926e-04	k: 296	n:2450000
Cons ci ratio: 1.439321e-03	ci left: 7.511683e-01	ci right 7.522507e-01	k: 1841689	n:2450000
KS ci ratio: 2.274476e-01	ci left: 1.074441e-04	ci right 1.353926e-04	k: 296	n:2450000
AHCTF1   2450000 perm   3409 sec   (719 perm/sec)   p_kst 1.208163e-04   p_cons 7.517098e-01   p_joint 1.208163e-04

Joint ci ratio: 2.266856e-01	ci left: 1.077741e-04	ci right 1.357014e-04	k: 298	n:2460000
Cons ci ratio: 1.436482e-03	ci left: 7.511462e-01	ci right 7.522264e-01	k: 1849149	n:2460000
KS ci ratio: 2.266856e-01	ci left: 1.077741e-04	ci right 1.357014e-04	k: 298	n:2460000
AHCTF1   2460000 perm   3432 sec   (717 perm/sec)   p_kst 1.211382e-04   p_cons 7.516866e-01   p_joint 1.211382e-04

Joint ci ratio: 2.259312e-01	ci left: 1.081016e-04	ci right 1.360076e-04	k: 300	n:2470000
Cons ci ratio: 1.433613e-03	ci left: 7.511364e-01	ci right 7.522144e-01	k: 1856639	n:2470000
KS ci ratio: 2.259312e-01	ci left: 1.081016e-04	ci right 1.360076e-04	k: 300	n:2470000
AHCTF1   2470000 perm   3456 sec   (715 perm/sec)   p_kst 1.214575e-04   p_cons 7.516757e-01   p_joint 1.214575e-04

Joint ci ratio: 2.259313e-01	ci left: 1.076657e-04	ci right 1.354591e-04	k: 300	n:2480000
Cons ci ratio: 1.430730e-03	ci left: 7.511348e-01	ci right 7.522106e-01	k: 1864149	n:2480000
KS ci ratio: 2.259313e-01	ci left: 1.076657e-04	ci right 1.354591e-04	k: 300	n:2480000
AHCTF1   2480000 perm   3481 sec   (713 perm/sec)   p_kst 1.209677e-04   p_cons 7.516730e-01   p_joint 1.209677e-04

Joint ci ratio: 2.248136e-01	ci left: 1.083701e-04	ci right 1.361879e-04	k: 303	n:2490000
Cons ci ratio: 1.427877e-03	ci left: 7.511299e-01	ci right 7.522036e-01	k: 1871651	n:2490000
KS ci ratio: 2.248136e-01	ci left: 1.083701e-04	ci right 1.361879e-04	k: 303	n:2490000
AHCTF1   2490000 perm   3504 sec   (711 perm/sec)   p_kst 1.216867e-04   p_cons 7.516671e-01   p_joint 1.216867e-04

Joint ci ratio: 2.244448e-01	ci left: 1.083142e-04	ci right 1.360656e-04	k: 304	n:2500000
Cons ci ratio: 1.425114e-03	ci left: 7.511059e-01	ci right 7.521775e-01	k: 1879105	n:2500000
KS ci ratio: 2.244448e-01	ci left: 1.083142e-04	ci right 1.360656e-04	k: 304	n:2500000
AHCTF1   2500000 perm   3528 sec   (709 perm/sec)   p_kst 1.216000e-04   p_cons 7.516420e-01   p_joint 1.216000e-04

Joint ci ratio: 2.240778e-01	ci left: 1.082587e-04	ci right 1.359442e-04	k: 305	n:2510000
Cons ci ratio: 1.422299e-03	ci left: 7.511001e-01	ci right 7.521695e-01	k: 1886604	n:2510000
KS ci ratio: 2.240778e-01	ci left: 1.082587e-04	ci right 1.359442e-04	k: 305	n:2510000
AHCTF1   2510000 perm   3552 sec   (707 perm/sec)   p_kst 1.215139e-04   p_cons 7.516351e-01   p_joint 1.215139e-04

Joint ci ratio: 2.237125e-01	ci left: 1.082036e-04	ci right 1.358238e-04	k: 306	n:2520000
Cons ci ratio: 1.419405e-03	ci left: 7.511192e-01	ci right 7.521865e-01	k: 1894166	n:2520000
KS ci ratio: 2.237125e-01	ci left: 1.082036e-04	ci right 1.358238e-04	k: 306	n:2520000
AHCTF1   2520000 perm   3577 sec   (705 perm/sec)   p_kst 1.214286e-04   p_cons 7.516532e-01   p_joint 1.214286e-04

Joint ci ratio: 2.237126e-01	ci left: 1.077759e-04	ci right 1.352870e-04	k: 306	n:2530000
Cons ci ratio: 1.416607e-03	ci left: 7.511177e-01	ci right 7.521829e-01	k: 1901676	n:2530000
KS ci ratio: 2.237126e-01	ci left: 1.077759e-04	ci right 1.352870e-04	k: 306	n:2530000
AHCTF1   2530000 perm   3601 sec   (703 perm/sec)   p_kst 1.209486e-04   p_cons 7.516506e-01   p_joint 1.209486e-04

Joint ci ratio: 2.229874e-01	ci left: 1.080950e-04	ci right 1.355857e-04	k: 308	n:2540000
Cons ci ratio: 1.413831e-03	ci left: 7.511146e-01	ci right 7.521777e-01	k: 1909182	n:2540000
KS ci ratio: 2.229874e-01	ci left: 1.080950e-04	ci right 1.355857e-04	k: 308	n:2540000
AHCTF1   2540000 perm   3625 sec   (701 perm/sec)   p_kst 1.212598e-04   p_cons 7.516465e-01   p_joint 1.212598e-04

Joint ci ratio: 2.229875e-01	ci left: 1.076711e-04	ci right 1.350540e-04	k: 308	n:2550000
Cons ci ratio: 1.410992e-03	ci left: 7.511328e-01	ci right 7.521937e-01	k: 1916742	n:2550000
KS ci ratio: 2.229875e-01	ci left: 1.076711e-04	ci right 1.350540e-04	k: 308	n:2550000
AHCTF1   2550000 perm   3650 sec   (699 perm/sec)   p_kst 1.207843e-04   p_cons 7.516635e-01   p_joint 1.207843e-04

Joint ci ratio: 2.226275e-01	ci left: 1.076193e-04	ci right 1.349388e-04	k: 309	n:2560000
Cons ci ratio: 1.408258e-03	ci left: 7.511273e-01	ci right 7.521862e-01	k: 1924242	n:2560000
KS ci ratio: 2.226275e-01	ci left: 1.076193e-04	ci right 1.349388e-04	k: 309	n:2560000
AHCTF1   2560000 perm   3674 sec   (697 perm/sec)   p_kst 1.207031e-04   p_cons 7.516570e-01   p_joint 1.207031e-04

Joint ci ratio: 2.222693e-01	ci left: 1.075680e-04	ci right 1.348245e-04	k: 310	n:2570000
Cons ci ratio: 1.405547e-03	ci left: 7.511199e-01	ci right 7.521768e-01	k: 1931737	n:2570000
KS ci ratio: 2.222693e-01	ci left: 1.075680e-04	ci right 1.348245e-04	k: 310	n:2570000
AHCTF1   2570000 perm   3699 sec   (695 perm/sec)   p_kst 1.206226e-04   p_cons 7.516486e-01   p_joint 1.206226e-04

Joint ci ratio: 2.215580e-01	ci left: 1.078832e-04	ci right 1.351202e-04	k: 312	n:2580000
Cons ci ratio: 1.402774e-03	ci left: 7.511332e-01	ci right 7.521880e-01	k: 1939285	n:2580000
KS ci ratio: 2.215580e-01	ci left: 1.078832e-04	ci right 1.351202e-04	k: 312	n:2580000
AHCTF1   2580000 perm   3724 sec   (693 perm/sec)   p_kst 1.209302e-04   p_cons 7.516609e-01   p_joint 1.209302e-04

Joint ci ratio: 2.205037e-01	ci left: 1.085608e-04	ci right 1.358208e-04	k: 315	n:2590000
Cons ci ratio: 1.399955e-03	ci left: 7.511633e-01	ci right 7.522160e-01	k: 1946877	n:2590000
KS ci ratio: 2.205037e-01	ci left: 1.085608e-04	ci right 1.358208e-04	k: 315	n:2590000
AHCTF1   2590000 perm   3749 sec   (691 perm/sec)   p_kst 1.216216e-04   p_cons 7.516900e-01   p_joint 1.216216e-04

Joint ci ratio: 2.201557e-01	ci left: 1.085067e-04	ci right 1.357042e-04	k: 316	n:2600000
Cons ci ratio: 1.397301e-03	ci left: 7.511532e-01	ci right 7.522039e-01	k: 1954365	n:2600000
KS ci ratio: 2.201557e-01	ci left: 1.085067e-04	ci right 1.357042e-04	k: 316	n:2600000
AHCTF1   2600000 perm   3774 sec   (689 perm/sec)   p_kst 1.215385e-04   p_cons 7.516788e-01   p_joint 1.215385e-04

Joint ci ratio: 2.191212e-01	ci left: 1.091771e-04	ci right 1.363968e-04	k: 319	n:2610000
Cons ci ratio: 1.394560e-03	ci left: 7.511708e-01	ci right 7.522194e-01	k: 1961925	n:2610000
KS ci ratio: 2.191212e-01	ci left: 1.091771e-04	ci right 1.363968e-04	k: 319	n:2610000
AHCTF1   2610000 perm   3799 sec   (687 perm/sec)   p_kst 1.222222e-04   p_cons 7.516954e-01   p_joint 1.222222e-04

Joint ci ratio: 2.191212e-01	ci left: 1.087604e-04	ci right 1.358762e-04	k: 319	n:2620000
Cons ci ratio: 1.391892e-03	ci left: 7.511730e-01	ci right 7.522196e-01	k: 1969445	n:2620000
KS ci ratio: 2.191212e-01	ci left: 1.087604e-04	ci right 1.358762e-04	k: 319	n:2620000
AHCTF1   2620000 perm   3824 sec   (685 perm/sec)   p_kst 1.217557e-04   p_cons 7.516966e-01   p_joint 1.217557e-04

Joint ci ratio: 2.191213e-01	ci left: 1.083469e-04	ci right 1.353596e-04	k: 319	n:2630000
Cons ci ratio: 1.389218e-03	ci left: 7.511808e-01	ci right 7.522255e-01	k: 1976980	n:2630000
KS ci ratio: 2.191213e-01	ci left: 1.083469e-04	ci right 1.353596e-04	k: 319	n:2630000
AHCTF1   2630000 perm   3849 sec   (683 perm/sec)   p_kst 1.212928e-04   p_cons 7.517034e-01   p_joint 1.212928e-04

Joint ci ratio: 2.184397e-01	ci left: 1.086525e-04	ci right 1.356459e-04	k: 321	n:2640000
Cons ci ratio: 1.386670e-03	ci left: 7.511587e-01	ci right 7.522014e-01	k: 1984436	n:2640000
KS ci ratio: 2.184397e-01	ci left: 1.086525e-04	ci right 1.356459e-04	k: 321	n:2640000
AHCTF1   2640000 perm   3875 sec   (681 perm/sec)   p_kst 1.215909e-04   p_cons 7.516803e-01   p_joint 1.215909e-04

Joint ci ratio: 2.184397e-01	ci left: 1.082425e-04	ci right 1.351340e-04	k: 321	n:2650000
Cons ci ratio: 1.383942e-03	ci left: 7.511892e-01	ci right 7.522299e-01	k: 1992031	n:2650000
KS ci ratio: 2.184397e-01	ci left: 1.082425e-04	ci right 1.351340e-04	k: 321	n:2650000
AHCTF1   2650000 perm   3900 sec   (679 perm/sec)   p_kst 1.211321e-04   p_cons 7.517098e-01   p_joint 1.211321e-04

Joint ci ratio: 2.174292e-01	ci left: 1.089019e-04	ci right 1.358153e-04	k: 324	n:2660000
Cons ci ratio: 1.381292e-03	ci left: 7.512026e-01	ci right 7.522413e-01	k: 1999581	n:2660000
KS ci ratio: 2.174292e-01	ci left: 1.089019e-04	ci right 1.358153e-04	k: 324	n:2660000
AHCTF1   2660000 perm   3925 sec   (678 perm/sec)   p_kst 1.218045e-04   p_cons 7.517222e-01   p_joint 1.218045e-04

Joint ci ratio: 2.164325e-01	ci left: 1.095565e-04	ci right 1.364911e-04	k: 327	n:2670000
Cons ci ratio: 1.378764e-03	ci left: 7.511870e-01	ci right 7.522237e-01	k: 2007054	n:2670000
KS ci ratio: 2.164325e-01	ci left: 1.095565e-04	ci right 1.364911e-04	k: 327	n:2670000
AHCTF1   2670000 perm   3950 sec   (676 perm/sec)   p_kst 1.224719e-04   p_cons 7.517056e-01   p_joint 1.224719e-04

Joint ci ratio: 2.161033e-01	ci left: 1.095007e-04	ci right 1.363752e-04	k: 328	n:2680000
Cons ci ratio: 1.376309e-03	ci left: 7.511554e-01	ci right 7.521903e-01	k: 2014484	n:2680000
KS ci ratio: 2.161033e-01	ci left: 1.095007e-04	ci right 1.363752e-04	k: 328	n:2680000
AHCTF1   2680000 perm   3976 sec   (674 perm/sec)   p_kst 1.223881e-04   p_cons 7.516731e-01   p_joint 1.223881e-04

Joint ci ratio: 2.157756e-01	ci left: 1.094453e-04	ci right 1.362600e-04	k: 329	n:2690000
Cons ci ratio: 1.373756e-03	ci left: 7.511543e-01	ci right 7.521872e-01	k: 2021995	n:2690000
KS ci ratio: 2.157756e-01	ci left: 1.094453e-04	ci right 1.362600e-04	k: 329	n:2690000
AHCTF1   2690000 perm   4002 sec   (672 perm/sec)   p_kst 1.223048e-04   p_cons 7.516710e-01   p_joint 1.223048e-04

Joint ci ratio: 2.151247e-01	ci left: 1.097407e-04	ci right 1.365360e-04	k: 331	n:2700000
Cons ci ratio: 1.371287e-03	ci left: 7.511342e-01	ci right 7.521653e-01	k: 2029455	n:2700000
KS ci ratio: 2.151247e-01	ci left: 1.097407e-04	ci right 1.365360e-04	k: 331	n:2700000
AHCTF1   2700000 perm   4029 sec   (670 perm/sec)   p_kst 1.225926e-04   p_cons 7.516500e-01   p_joint 1.225926e-04

Joint ci ratio: 2.144796e-01	ci left: 1.100340e-04	ci right 1.368098e-04	k: 333	n:2710000
Cons ci ratio: 1.368762e-03	ci left: 7.511331e-01	ci right 7.521623e-01	k: 2036966	n:2710000
KS ci ratio: 2.144796e-01	ci left: 1.100340e-04	ci right 1.368098e-04	k: 333	n:2710000
AHCTF1   2710000 perm   4054 sec   (668 perm/sec)   p_kst 1.228782e-04   p_cons 7.516480e-01   p_joint 1.228782e-04

Joint ci ratio: 2.138403e-01	ci left: 1.103254e-04	ci right 1.370815e-04	k: 335	n:2720000
Cons ci ratio: 1.366322e-03	ci left: 7.511125e-01	ci right 7.521399e-01	k: 2044424	n:2720000
KS ci ratio: 2.138403e-01	ci left: 1.103254e-04	ci right 1.370815e-04	k: 335	n:2720000
AHCTF1   2720000 perm   4081 sec   (667 perm/sec)   p_kst 1.231618e-04   p_cons 7.516265e-01   p_joint 1.231618e-04

Joint ci ratio: 2.138403e-01	ci left: 1.099212e-04	ci right 1.365794e-04	k: 335	n:2730000
Cons ci ratio: 1.363888e-03	ci left: 7.510943e-01	ci right 7.521198e-01	k: 2051888	n:2730000
KS ci ratio: 2.138403e-01	ci left: 1.099212e-04	ci right 1.365794e-04	k: 335	n:2730000
AHCTF1   2730000 perm   4107 sec   (665 perm/sec)   p_kst 1.227106e-04   p_cons 7.516073e-01   p_joint 1.227106e-04

Joint ci ratio: 2.135228e-01	ci left: 1.098655e-04	ci right 1.364654e-04	k: 336	n:2740000
Cons ci ratio: 1.361494e-03	ci left: 7.510686e-01	ci right 7.520922e-01	k: 2059331	n:2740000
KS ci ratio: 2.135228e-01	ci left: 1.098655e-04	ci right 1.364654e-04	k: 336	n:2740000
AHCTF1   2740000 perm   4133 sec   (663 perm/sec)   p_kst 1.226277e-04   p_cons 7.515807e-01   p_joint 1.226277e-04

Joint ci ratio: 2.135229e-01	ci left: 1.094660e-04	ci right 1.359692e-04	k: 336	n:2750000
Cons ci ratio: 1.359056e-03	ci left: 7.510587e-01	ci right 7.520804e-01	k: 2066817	n:2750000
KS ci ratio: 2.135229e-01	ci left: 1.094660e-04	ci right 1.359692e-04	k: 336	n:2750000
AHCTF1   2750000 perm   4160 sec   (661 perm/sec)   p_kst 1.221818e-04   p_cons 7.515698e-01   p_joint 1.221818e-04

Joint ci ratio: 2.132068e-01	ci left: 1.094123e-04	ci right 1.358582e-04	k: 337	n:2760000
Cons ci ratio: 1.356536e-03	ci left: 7.510749e-01	ci right 7.520948e-01	k: 2074375	n:2760000
KS ci ratio: 2.132068e-01	ci left: 1.094123e-04	ci right 1.358582e-04	k: 337	n:2760000
AHCTF1   2760000 perm   4187 sec   (659 perm/sec)   p_kst 1.221014e-04   p_cons 7.515851e-01   p_joint 1.221014e-04

Joint ci ratio: 2.128921e-01	ci left: 1.093591e-04	ci right 1.357479e-04	k: 338	n:2770000
Cons ci ratio: 1.354090e-03	ci left: 7.510745e-01	ci right 7.520925e-01	k: 2081887	n:2770000
KS ci ratio: 2.128921e-01	ci left: 1.093591e-04	ci right 1.357479e-04	k: 338	n:2770000
AHCTF1   2770000 perm   4213 sec   (657 perm/sec)   p_kst 1.220217e-04   p_cons 7.515838e-01   p_joint 1.220217e-04

Joint ci ratio: 2.128922e-01	ci left: 1.089657e-04	ci right 1.352596e-04	k: 338	n:2780000
Cons ci ratio: 1.351596e-03	ci left: 7.510909e-01	ci right 7.521071e-01	k: 2089446	n:2780000
KS ci ratio: 2.128922e-01	ci left: 1.089657e-04	ci right 1.352596e-04	k: 338	n:2780000
AHCTF1   2780000 perm   4240 sec   (656 perm/sec)   p_kst 1.215827e-04   p_cons 7.515993e-01   p_joint 1.215827e-04

Joint ci ratio: 2.122669e-01	ci left: 1.092538e-04	ci right 1.355298e-04	k: 340	n:2790000
Cons ci ratio: 1.349269e-03	ci left: 7.510649e-01	ci right 7.520793e-01	k: 2096887	n:2790000
KS ci ratio: 2.122669e-01	ci left: 1.092538e-04	ci right 1.355298e-04	k: 340	n:2790000
AHCTF1   2790000 perm   4267 sec   (654 perm/sec)   p_kst 1.218638e-04   p_cons 7.515724e-01   p_joint 1.218638e-04

Joint ci ratio: 2.113392e-01	ci left: 1.098782e-04	ci right 1.361739e-04	k: 343	n:2800000
Cons ci ratio: 1.346792e-03	ci left: 7.510838e-01	ci right 7.520964e-01	k: 2104453	n:2800000
KS ci ratio: 2.113392e-01	ci left: 1.098782e-04	ci right 1.361739e-04	k: 343	n:2800000
AHCTF1   2800000 perm   4293 sec   (652 perm/sec)   p_kst 1.225000e-04   p_cons 7.515904e-01   p_joint 1.225000e-04

Joint ci ratio: 2.107275e-01	ci left: 1.101613e-04	ci right 1.364386e-04	k: 345	n:2810000
Cons ci ratio: 1.344362e-03	ci left: 7.510936e-01	ci right 7.521044e-01	k: 2111994	n:2810000
KS ci ratio: 2.107275e-01	ci left: 1.101613e-04	ci right 1.364386e-04	k: 345	n:2810000
AHCTF1   2810000 perm   4320 sec   (650 perm/sec)   p_kst 1.227758e-04   p_cons 7.515993e-01   p_joint 1.227758e-04

Joint ci ratio: 2.101211e-01	ci left: 1.104426e-04	ci right 1.367013e-04	k: 347	n:2820000
Cons ci ratio: 1.341926e-03	ci left: 7.511084e-01	ci right 7.521173e-01	k: 2119549	n:2820000
KS ci ratio: 2.101211e-01	ci left: 1.104426e-04	ci right 1.367013e-04	k: 347	n:2820000
AHCTF1   2820000 perm   4347 sec   (649 perm/sec)   p_kst 1.230496e-04   p_cons 7.516131e-01   p_joint 1.230496e-04

Joint ci ratio: 2.098198e-01	ci left: 1.103871e-04	ci right 1.365902e-04	k: 348	n:2830000
Cons ci ratio: 1.339569e-03	ci left: 7.511050e-01	ci right 7.521122e-01	k: 2127053	n:2830000
KS ci ratio: 2.098198e-01	ci left: 1.103871e-04	ci right 1.365902e-04	k: 348	n:2830000
AHCTF1   2830000 perm   4374 sec   (647 perm/sec)   p_kst 1.229682e-04   p_cons 7.516088e-01   p_joint 1.229682e-04

Joint ci ratio: 2.098199e-01	ci left: 1.099984e-04	ci right 1.361093e-04	k: 348	n:2840000
Cons ci ratio: 1.337102e-03	ci left: 7.511354e-01	ci right 7.521408e-01	k: 2134653	n:2840000
KS ci ratio: 2.098199e-01	ci left: 1.099984e-04	ci right 1.361093e-04	k: 348	n:2840000
AHCTF1   2840000 perm   4401 sec   (645 perm/sec)   p_kst 1.225352e-04   p_cons 7.516384e-01   p_joint 1.225352e-04

Joint ci ratio: 2.086276e-01	ci left: 1.109424e-04	ci right 1.371086e-04	k: 352	n:2850000
Cons ci ratio: 1.334754e-03	ci left: 7.511365e-01	ci right 7.521401e-01	k: 2142170	n:2850000
KS ci ratio: 2.086276e-01	ci left: 1.109424e-04	ci right 1.371086e-04	k: 352	n:2850000
AHCTF1   2850000 perm   4428 sec   (644 perm/sec)   p_kst 1.235088e-04   p_cons 7.516386e-01   p_joint 1.235088e-04

Joint ci ratio: 2.083327e-01	ci left: 1.108859e-04	ci right 1.369971e-04	k: 353	n:2860000
Cons ci ratio: 1.332397e-03	ci left: 7.511432e-01	ci right 7.521451e-01	k: 2149703	n:2860000
KS ci ratio: 2.083327e-01	ci left: 1.108859e-04	ci right 1.369971e-04	k: 353	n:2860000
AHCTF1   2860000 perm   4455 sec   (642 perm/sec)   p_kst 1.234266e-04   p_cons 7.516444e-01   p_joint 1.234266e-04

Joint ci ratio: 2.083328e-01	ci left: 1.104995e-04	ci right 1.365197e-04	k: 353	n:2870000
Cons ci ratio: 1.330148e-03	ci left: 7.511234e-01	ci right 7.521235e-01	k: 2157160	n:2870000
KS ci ratio: 2.083328e-01	ci left: 1.104995e-04	ci right 1.365197e-04	k: 353	n:2870000
AHCTF1   2870000 perm   4482 sec   (640 perm/sec)   p_kst 1.229965e-04   p_cons 7.516237e-01   p_joint 1.229965e-04

Joint ci ratio: 2.083328e-01	ci left: 1.101158e-04	ci right 1.360457e-04	k: 353	n:2880000
Cons ci ratio: 1.327909e-03	ci left: 7.511040e-01	ci right 7.521024e-01	k: 2164618	n:2880000
KS ci ratio: 2.083328e-01	ci left: 1.101158e-04	ci right 1.360457e-04	k: 353	n:2880000
AHCTF1   2880000 perm   4510 sec   (639 perm/sec)   p_kst 1.225694e-04   p_cons 7.516035e-01   p_joint 1.225694e-04

Joint ci ratio: 2.083329e-01	ci left: 1.097348e-04	ci right 1.355750e-04	k: 353	n:2890000
Cons ci ratio: 1.325563e-03	ci left: 7.511180e-01	ci right 7.521147e-01	k: 2172172	n:2890000
KS ci ratio: 2.083329e-01	ci left: 1.097348e-04	ci right 1.355750e-04	k: 353	n:2890000
AHCTF1   2890000 perm   4537 sec   (637 perm/sec)   p_kst 1.221453e-04   p_cons 7.516166e-01   p_joint 1.221453e-04

Joint ci ratio: 2.080392e-01	ci left: 1.096833e-04	ci right 1.354703e-04	k: 354	n:2900000
Cons ci ratio: 1.323253e-03	ci left: 7.511251e-01	ci right 7.521200e-01	k: 2179706	n:2900000
KS ci ratio: 2.080392e-01	ci left: 1.096833e-04	ci right 1.354703e-04	k: 354	n:2900000
AHCTF1   2900000 perm   4565 sec   (635 perm/sec)   p_kst 1.220690e-04   p_cons 7.516228e-01   p_joint 1.220690e-04

Joint ci ratio: 2.074556e-01	ci left: 1.099579e-04	ci right 1.357277e-04	k: 356	n:2910000
Cons ci ratio: 1.321022e-03	ci left: 7.511134e-01	ci right 7.521067e-01	k: 2187186	n:2910000
KS ci ratio: 2.074556e-01	ci left: 1.099579e-04	ci right 1.357277e-04	k: 356	n:2910000
AHCTF1   2910000 perm   4592 sec   (634 perm/sec)   p_kst 1.223368e-04   p_cons 7.516103e-01   p_joint 1.223368e-04

Joint ci ratio: 2.074557e-01	ci left: 1.095813e-04	ci right 1.352629e-04	k: 356	n:2920000
Cons ci ratio: 1.318789e-03	ci left: 7.511054e-01	ci right 7.520969e-01	k: 2194676	n:2920000
KS ci ratio: 2.074557e-01	ci left: 1.095813e-04	ci right 1.352629e-04	k: 356	n:2920000
AHCTF1   2920000 perm   4620 sec   (632 perm/sec)   p_kst 1.219178e-04   p_cons 7.516014e-01   p_joint 1.219178e-04

Joint ci ratio: 2.074557e-01	ci left: 1.092073e-04	ci right 1.348013e-04	k: 356	n:2930000
Cons ci ratio: 1.316459e-03	ci left: 7.511284e-01	ci right 7.521182e-01	k: 2202257	n:2930000
KS ci ratio: 2.074557e-01	ci left: 1.092073e-04	ci right 1.348013e-04	k: 356	n:2930000
AHCTF1   2930000 perm   4648 sec   (630 perm/sec)   p_kst 1.215017e-04   p_cons 7.516235e-01   p_joint 1.215017e-04

Joint ci ratio: 2.065895e-01	ci left: 1.098034e-04	ci right 1.354160e-04	k: 359	n:2940000
Cons ci ratio: 1.314237e-03	ci left: 7.511237e-01	ci right 7.521118e-01	k: 2209757	n:2940000
KS ci ratio: 2.065895e-01	ci left: 1.098034e-04	ci right 1.354160e-04	k: 359	n:2940000
AHCTF1   2940000 perm   4676 sec   (629 perm/sec)   p_kst 1.221088e-04   p_cons 7.516180e-01   p_joint 1.221088e-04

Joint ci ratio: 2.063031e-01	ci left: 1.097526e-04	ci right 1.353134e-04	k: 360	n:2950000
Cons ci ratio: 1.312030e-03	ci left: 7.511184e-01	ci right 7.521048e-01	k: 2217255	n:2950000
KS ci ratio: 2.063031e-01	ci left: 1.097526e-04	ci right 1.353134e-04	k: 360	n:2950000
AHCTF1   2950000 perm   4704 sec   (627 perm/sec)   p_kst 1.220339e-04   p_cons 7.516119e-01   p_joint 1.220339e-04

Joint ci ratio: 2.063032e-01	ci left: 1.093818e-04	ci right 1.348563e-04	k: 360	n:2960000
Cons ci ratio: 1.309887e-03	ci left: 7.510975e-01	ci right 7.520824e-01	k: 2224707	n:2960000
KS ci ratio: 2.063032e-01	ci left: 1.093818e-04	ci right 1.348563e-04	k: 360	n:2960000
AHCTF1   2960000 perm   4732 sec   (626 perm/sec)   p_kst 1.216216e-04   p_cons 7.515902e-01   p_joint 1.216216e-04

Joint ci ratio: 2.060180e-01	ci left: 1.093329e-04	ci right 1.347563e-04	k: 361	n:2970000
Cons ci ratio: 1.307632e-03	ci left: 7.511122e-01	ci right 7.520954e-01	k: 2232264	n:2970000
KS ci ratio: 2.060180e-01	ci left: 1.093329e-04	ci right 1.347563e-04	k: 361	n:2970000
AHCTF1   2970000 perm   4760 sec   (624 perm/sec)   p_kst 1.215488e-04   p_cons 7.516040e-01   p_joint 1.215488e-04

Joint ci ratio: 2.060181e-01	ci left: 1.089660e-04	ci right 1.343041e-04	k: 361	n:2980000
Cons ci ratio: 1.305378e-03	ci left: 7.511298e-01	ci right 7.521113e-01	k: 2239830	n:2980000
KS ci ratio: 2.060181e-01	ci left: 1.089660e-04	ci right 1.343041e-04	k: 361	n:2980000
AHCTF1   2980000 perm   4788 sec   (622 perm/sec)   p_kst 1.211409e-04   p_cons 7.516208e-01   p_joint 1.211409e-04

Joint ci ratio: 2.060181e-01	ci left: 1.086015e-04	ci right 1.338549e-04	k: 361	n:2990000
Cons ci ratio: 1.303198e-03	ci left: 7.511292e-01	ci right 7.521091e-01	k: 2247342	n:2990000
KS ci ratio: 2.060181e-01	ci left: 1.086015e-04	ci right 1.338549e-04	k: 361	n:2990000
AHCTF1   2990000 perm   4816 sec   (621 perm/sec)   p_kst 1.207358e-04   p_cons 7.516194e-01   p_joint 1.207358e-04

Joint ci ratio: 2.060182e-01	ci left: 1.082395e-04	ci right 1.334087e-04	k: 361	n:3000000
Cons ci ratio: 1.301029e-03	ci left: 7.511287e-01	ci right 7.521069e-01	k: 2254854	n:3000000
KS ci ratio: 2.060182e-01	ci left: 1.082395e-04	ci right 1.334087e-04	k: 361	n:3000000
AHCTF1   3000000 perm   4845 sec   (619 perm/sec)   p_kst 1.203333e-04   p_cons 7.516180e-01   p_joint 1.203333e-04

Joint ci ratio: 2.057342e-01	ci left: 1.081950e-04	ci right 1.333148e-04	k: 362	n:3010000
Cons ci ratio: 1.298926e-03	ci left: 7.511121e-01	ci right 7.520887e-01	k: 2262318	n:3010000
KS ci ratio: 2.057342e-01	ci left: 1.081950e-04	ci right 1.333148e-04	k: 362	n:3010000
AHCTF1   3010000 perm   4873 sec   (618 perm/sec)   p_kst 1.202658e-04   p_cons 7.516007e-01   p_joint 1.202658e-04

Joint ci ratio: 2.054514e-01	ci left: 1.081509e-04	ci right 1.332215e-04	k: 363	n:3020000
Cons ci ratio: 1.296742e-03	ci left: 7.511222e-01	ci right 7.520972e-01	k: 2269862	n:3020000
KS ci ratio: 2.054514e-01	ci left: 1.081509e-04	ci right 1.332215e-04	k: 363	n:3020000
AHCTF1   3020000 perm   4902 sec   (616 perm/sec)   p_kst 1.201987e-04   p_cons 7.516099e-01   p_joint 1.201987e-04

Joint ci ratio: 2.051698e-01	ci left: 1.081070e-04	ci right 1.331288e-04	k: 364	n:3030000
Cons ci ratio: 1.294636e-03	ci left: 7.511127e-01	ci right 7.520861e-01	k: 2277347	n:3030000
KS ci ratio: 2.051698e-01	ci left: 1.081070e-04	ci right 1.331288e-04	k: 364	n:3030000
AHCTF1   3030000 perm   4930 sec   (615 perm/sec)   p_kst 1.201320e-04   p_cons 7.515997e-01   p_joint 1.201320e-04

Joint ci ratio: 2.051698e-01	ci left: 1.077514e-04	ci right 1.326909e-04	k: 364	n:3040000
Cons ci ratio: 1.292462e-03	ci left: 7.511257e-01	ci right 7.520975e-01	k: 2284900	n:3040000
KS ci ratio: 2.051698e-01	ci left: 1.077514e-04	ci right 1.326909e-04	k: 364	n:3040000
AHCTF1   3040000 perm   4959 sec   (613 perm/sec)   p_kst 1.197368e-04   p_cons 7.516118e-01   p_joint 1.197368e-04

Joint ci ratio: 2.048894e-01	ci left: 1.077091e-04	ci right 1.326006e-04	k: 365	n:3050000
Cons ci ratio: 1.290309e-03	ci left: 7.511360e-01	ci right 7.521061e-01	k: 2292445	n:3050000
KS ci ratio: 2.048894e-01	ci left: 1.077091e-04	ci right 1.326006e-04	k: 365	n:3050000
AHCTF1   3050000 perm   4988 sec   (611 perm/sec)   p_kst 1.196721e-04   p_cons 7.516213e-01   p_joint 1.196721e-04

Joint ci ratio: 2.046100e-01	ci left: 1.076672e-04	ci right 1.325107e-04	k: 366	n:3060000
Cons ci ratio: 1.288181e-03	ci left: 7.511420e-01	ci right 7.521105e-01	k: 2299977	n:3060000
KS ci ratio: 2.046100e-01	ci left: 1.076672e-04	ci right 1.325107e-04	k: 366	n:3060000
AHCTF1   3060000 perm   5017 sec   (610 perm/sec)   p_kst 1.196078e-04   p_cons 7.516265e-01   p_joint 1.196078e-04

Joint ci ratio: 2.040548e-01	ci left: 1.079346e-04	ci right 1.327639e-04	k: 368	n:3070000
Cons ci ratio: 1.286016e-03	ci left: 7.511619e-01	ci right 7.521288e-01	k: 2307552	n:3070000
KS ci ratio: 2.040548e-01	ci left: 1.079346e-04	ci right 1.327639e-04	k: 368	n:3070000
AHCTF1   3070000 perm   5046 sec   (608 perm/sec)   p_kst 1.198697e-04   p_cons 7.516456e-01   p_joint 1.198697e-04

Joint ci ratio: 2.037788e-01	ci left: 1.078923e-04	ci right 1.326740e-04	k: 369	n:3080000
Cons ci ratio: 1.283909e-03	ci left: 7.511677e-01	ci right 7.521331e-01	k: 2315084	n:3080000
KS ci ratio: 2.037788e-01	ci left: 1.078923e-04	ci right 1.326740e-04	k: 369	n:3080000
AHCTF1   3080000 perm   5075 sec   (607 perm/sec)   p_kst 1.198052e-04   p_cons 7.516506e-01   p_joint 1.198052e-04

Joint ci ratio: 2.037789e-01	ci left: 1.075431e-04	ci right 1.322447e-04	k: 369	n:3090000
Cons ci ratio: 1.281920e-03	ci left: 7.511421e-01	ci right 7.521060e-01	k: 2322519	n:3090000
KS ci ratio: 2.037789e-01	ci left: 1.075431e-04	ci right 1.322447e-04	k: 369	n:3090000
AHCTF1   3090000 perm   5104 sec   (605 perm/sec)   p_kst 1.194175e-04   p_cons 7.516243e-01   p_joint 1.194175e-04

Joint ci ratio: 2.037789e-01	ci left: 1.071962e-04	ci right 1.318181e-04	k: 369	n:3100000
Cons ci ratio: 1.279863e-03	ci left: 7.511393e-01	ci right 7.521015e-01	k: 2330024	n:3100000
KS ci ratio: 2.037789e-01	ci left: 1.071962e-04	ci right 1.318181e-04	k: 369	n:3100000
AHCTF1   3100000 perm   5133 sec   (604 perm/sec)   p_kst 1.190323e-04   p_cons 7.516206e-01   p_joint 1.190323e-04

Joint ci ratio: 2.032303e-01	ci left: 1.074618e-04	ci right 1.320700e-04	k: 371	n:3110000
Cons ci ratio: 1.277794e-03	ci left: 7.511429e-01	ci right 7.521036e-01	k: 2337549	n:3110000
KS ci ratio: 2.032303e-01	ci left: 1.074618e-04	ci right 1.320700e-04	k: 371	n:3110000
AHCTF1   3110000 perm   5162 sec   (603 perm/sec)   p_kst 1.192926e-04   p_cons 7.516235e-01   p_joint 1.192926e-04

Joint ci ratio: 2.029577e-01	ci left: 1.074216e-04	ci right 1.319835e-04	k: 372	n:3120000
Cons ci ratio: 1.275744e-03	ci left: 7.511439e-01	ci right 7.521031e-01	k: 2345066	n:3120000
KS ci ratio: 2.029577e-01	ci left: 1.074216e-04	ci right 1.319835e-04	k: 372	n:3120000
AHCTF1   3120000 perm   5191 sec   (601 perm/sec)   p_kst 1.192308e-04   p_cons 7.516237e-01   p_joint 1.192308e-04

Joint ci ratio: 2.029578e-01	ci left: 1.070784e-04	ci right 1.315619e-04	k: 372	n:3130000
Cons ci ratio: 1.273615e-03	ci left: 7.511708e-01	ci right 7.521284e-01	k: 2352664	n:3130000
KS ci ratio: 2.029578e-01	ci left: 1.070784e-04	ci right 1.315619e-04	k: 372	n:3130000
AHCTF1   3130000 perm   5221 sec   (600 perm/sec)   p_kst 1.188498e-04   p_cons 7.516498e-01   p_joint 1.188498e-04

Joint ci ratio: 2.024158e-01	ci left: 1.073420e-04	ci right 1.318121e-04	k: 374	n:3140000
Cons ci ratio: 1.271520e-03	ci left: 7.511908e-01	ci right 7.521469e-01	k: 2360241	n:3140000
KS ci ratio: 2.024158e-01	ci left: 1.073420e-04	ci right 1.318121e-04	k: 374	n:3140000
AHCTF1   3140000 perm   5250 sec   (598 perm/sec)   p_kst 1.191083e-04   p_cons 7.516691e-01   p_joint 1.191083e-04

Joint ci ratio: 2.018782e-01	ci left: 1.076040e-04	ci right 1.320607e-04	k: 376	n:3150000
Cons ci ratio: 1.269541e-03	ci left: 7.511796e-01	ci right 7.521342e-01	k: 2367720	n:3150000
KS ci ratio: 2.018782e-01	ci left: 1.076040e-04	ci right 1.320607e-04	k: 376	n:3150000
AHCTF1   3150000 perm   5279 sec   (597 perm/sec)   p_kst 1.193651e-04   p_cons 7.516571e-01   p_joint 1.193651e-04

Joint ci ratio: 2.013448e-01	ci left: 1.078645e-04	ci right 1.323076e-04	k: 378	n:3160000
Cons ci ratio: 1.267513e-03	ci left: 7.511856e-01	ci right 7.521386e-01	k: 2375253	n:3160000
KS ci ratio: 2.013448e-01	ci left: 1.078645e-04	ci right 1.323076e-04	k: 378	n:3160000
AHCTF1   3160000 perm   5309 sec   (595 perm/sec)   p_kst 1.196203e-04   p_cons 7.516623e-01   p_joint 1.196203e-04

Joint ci ratio: 2.010797e-01	ci left: 1.078238e-04	ci right 1.322215e-04	k: 379	n:3170000
Cons ci ratio: 1.265565e-03	ci left: 7.511707e-01	ci right 7.521222e-01	k: 2382720	n:3170000
KS ci ratio: 2.010797e-01	ci left: 1.078238e-04	ci right 1.322215e-04	k: 379	n:3170000
AHCTF1   3170000 perm   5339 sec   (594 perm/sec)   p_kst 1.195584e-04   p_cons 7.516467e-01   p_joint 1.195584e-04

Joint ci ratio: 2.010797e-01	ci left: 1.074847e-04	ci right 1.318057e-04	k: 379	n:3180000
Cons ci ratio: 1.263570e-03	ci left: 7.511725e-01	ci right 7.521226e-01	k: 2390240	n:3180000
KS ci ratio: 2.010797e-01	ci left: 1.074847e-04	ci right 1.318057e-04	k: 379	n:3180000
AHCTF1   3180000 perm   5369 sec   (592 perm/sec)   p_kst 1.191824e-04   p_cons 7.516478e-01   p_joint 1.191824e-04

Joint ci ratio: 2.010797e-01	ci left: 1.071477e-04	ci right 1.313926e-04	k: 379	n:3190000
Cons ci ratio: 1.261596e-03	ci left: 7.511709e-01	ci right 7.521195e-01	k: 2397749	n:3190000
KS ci ratio: 2.010797e-01	ci left: 1.071477e-04	ci right 1.313926e-04	k: 379	n:3190000
AHCTF1   3190000 perm   5399 sec   (591 perm/sec)   p_kst 1.188088e-04   p_cons 7.516455e-01   p_joint 1.188088e-04

Joint ci ratio: 1.997696e-01	ci left: 1.082970e-04	ci right 1.326228e-04	k: 384	n:3200000
Cons ci ratio: 1.259724e-03	ci left: 7.511418e-01	ci right 7.520890e-01	k: 2405170	n:3200000
KS ci ratio: 1.997696e-01	ci left: 1.082970e-04	ci right 1.326228e-04	k: 384	n:3200000
AHCTF1   3200000 perm   5429 sec   (589 perm/sec)   p_kst 1.200000e-04   p_cons 7.516156e-01   p_joint 1.200000e-04

Joint ci ratio: 1.995107e-01	ci left: 1.082556e-04	ci right 1.325367e-04	k: 385	n:3210000
Cons ci ratio: 1.257810e-03	ci left: 7.511276e-01	ci right 7.520732e-01	k: 2412638	n:3210000
KS ci ratio: 1.995107e-01	ci left: 1.082556e-04	ci right 1.325367e-04	k: 385	n:3210000
AHCTF1   3210000 perm   5459 sec   (588 perm/sec)   p_kst 1.199377e-04   p_cons 7.516006e-01   p_joint 1.199377e-04

Joint ci ratio: 1.995108e-01	ci left: 1.079194e-04	ci right 1.321251e-04	k: 385	n:3220000
Cons ci ratio: 1.255791e-03	ci left: 7.511476e-01	ci right 7.520917e-01	k: 2420216	n:3220000
KS ci ratio: 1.995108e-01	ci left: 1.079194e-04	ci right 1.321251e-04	k: 385	n:3220000
AHCTF1   3220000 perm   5489 sec   (587 perm/sec)   p_kst 1.195652e-04   p_cons 7.516199e-01   p_joint 1.195652e-04

Joint ci ratio: 1.992528e-01	ci left: 1.078794e-04	ci right 1.320411e-04	k: 386	n:3230000
Cons ci ratio: 1.253854e-03	ci left: 7.511458e-01	ci right 7.520885e-01	k: 2427724	n:3230000
KS ci ratio: 1.992528e-01	ci left: 1.078794e-04	ci right 1.320411e-04	k: 386	n:3230000
AHCTF1   3230000 perm   5519 sec   (585 perm/sec)   p_kst 1.195046e-04   p_cons 7.516173e-01   p_joint 1.195046e-04

Joint ci ratio: 1.984849e-01	ci left: 1.084263e-04	ci right 1.326055e-04	k: 389	n:3240000
Cons ci ratio: 1.251894e-03	ci left: 7.511535e-01	ci right 7.520948e-01	k: 2435263	n:3240000
KS ci ratio: 1.984849e-01	ci left: 1.084263e-04	ci right 1.326055e-04	k: 389	n:3240000
AHCTF1   3240000 perm   5549 sec   (584 perm/sec)   p_kst 1.200617e-04   p_cons 7.516244e-01   p_joint 1.200617e-04

Joint ci ratio: 1.979779e-01	ci left: 1.086775e-04	ci right 1.328434e-04	k: 391	n:3250000
Cons ci ratio: 1.249964e-03	ci left: 7.511551e-01	ci right 7.520949e-01	k: 2442782	n:3250000
KS ci ratio: 1.979779e-01	ci left: 1.086775e-04	ci right 1.328434e-04	k: 391	n:3250000
AHCTF1   3250000 perm   5580 sec   (582 perm/sec)   p_kst 1.203077e-04   p_cons 7.516252e-01   p_joint 1.203077e-04

Joint ci ratio: 1.972246e-01	ci left: 1.092189e-04	ci right 1.334016e-04	k: 394	n:3260000
Cons ci ratio: 1.248077e-03	ci left: 7.511462e-01	ci right 7.520846e-01	k: 2450267	n:3260000
KS ci ratio: 1.972246e-01	ci left: 1.092189e-04	ci right 1.334016e-04	k: 394	n:3260000
AHCTF1   3260000 perm   5610 sec   (581 perm/sec)   p_kst 1.208589e-04   p_cons 7.516156e-01   p_joint 1.208589e-04

Joint ci ratio: 1.964799e-01	ci left: 1.097571e-04	ci right 1.339562e-04	k: 397	n:3270000
Cons ci ratio: 1.246175e-03	ci left: 7.511448e-01	ci right 7.520817e-01	k: 2457776	n:3270000
KS ci ratio: 1.964799e-01	ci left: 1.097571e-04	ci right 1.339562e-04	k: 397	n:3270000
AHCTF1   3270000 perm   5640 sec   (580 perm/sec)   p_kst 1.214067e-04   p_cons 7.516135e-01   p_joint 1.214067e-04

Joint ci ratio: 1.954998e-01	ci left: 1.105821e-04	ci right 1.348271e-04	k: 401	n:3280000
Cons ci ratio: 1.244343e-03	ci left: 7.511247e-01	ci right 7.520602e-01	k: 2465224	n:3280000
KS ci ratio: 1.954998e-01	ci left: 1.105821e-04	ci right 1.348271e-04	k: 401	n:3280000
AHCTF1   3280000 perm   5671 sec   (578 perm/sec)   p_kst 1.222561e-04   p_cons 7.515927e-01   p_joint 1.222561e-04

Joint ci ratio: 1.952571e-01	ci left: 1.105351e-04	ci right 1.347361e-04	k: 402	n:3290000
Cons ci ratio: 1.242445e-03	ci left: 7.511270e-01	ci right 7.520611e-01	k: 2472745	n:3290000
KS ci ratio: 1.952571e-01	ci left: 1.105351e-04	ci right 1.347361e-04	k: 402	n:3290000
AHCTF1   3290000 perm   5702 sec   (577 perm/sec)   p_kst 1.221884e-04   p_cons 7.515942e-01   p_joint 1.221884e-04

Joint ci ratio: 1.950153e-01	ci left: 1.104884e-04	ci right 1.346456e-04	k: 403	n:3300000
Cons ci ratio: 1.240462e-03	ci left: 7.511577e-01	ci right 7.520903e-01	k: 2480360	n:3300000
KS ci ratio: 1.950153e-01	ci left: 1.104884e-04	ci right 1.346456e-04	k: 403	n:3300000
AHCTF1   3300000 perm   5733 sec   (576 perm/sec)   p_kst 1.221212e-04   p_cons 7.516242e-01   p_joint 1.221212e-04

Joint ci ratio: 1.945344e-01	ci left: 1.107293e-04	ci right 1.348725e-04	k: 405	n:3310000
Cons ci ratio: 1.238630e-03	ci left: 7.511453e-01	ci right 7.520766e-01	k: 2487833	n:3310000
KS ci ratio: 1.945344e-01	ci left: 1.107293e-04	ci right 1.348725e-04	k: 405	n:3310000
AHCTF1   3310000 perm   5764 sec   (574 perm/sec)   p_kst 1.223565e-04   p_cons 7.516112e-01   p_joint 1.223565e-04

Joint ci ratio: 1.942952e-01	ci left: 1.106824e-04	ci right 1.347821e-04	k: 406	n:3320000
Cons ci ratio: 1.236746e-03	ci left: 7.511511e-01	ci right 7.520810e-01	k: 2495366	n:3320000
KS ci ratio: 1.942952e-01	ci left: 1.106824e-04	ci right 1.347821e-04	k: 406	n:3320000
AHCTF1   3320000 perm   5795 sec   (573 perm/sec)   p_kst 1.222892e-04   p_cons 7.516163e-01   p_joint 1.222892e-04

Joint ci ratio: 1.938196e-01	ci left: 1.109214e-04	ci right 1.350071e-04	k: 408	n:3330000
Cons ci ratio: 1.234833e-03	ci left: 7.511683e-01	ci right 7.520967e-01	k: 2502937	n:3330000
KS ci ratio: 1.938196e-01	ci left: 1.109214e-04	ci right 1.350071e-04	k: 408	n:3330000
AHCTF1   3330000 perm   5826 sec   (572 perm/sec)   p_kst 1.225225e-04   p_cons 7.516327e-01   p_joint 1.225225e-04

Joint ci ratio: 1.933474e-01	ci left: 1.111591e-04	ci right 1.352306e-04	k: 410	n:3340000
Cons ci ratio: 1.232943e-03	ci left: 7.511812e-01	ci right 7.521082e-01	k: 2510494	n:3340000
KS ci ratio: 1.933474e-01	ci left: 1.111591e-04	ci right 1.352306e-04	k: 410	n:3340000
AHCTF1   3340000 perm   5857 sec   (570 perm/sec)   p_kst 1.227545e-04   p_cons 7.516449e-01   p_joint 1.227545e-04

Joint ci ratio: 1.926456e-01	ci left: 1.116795e-04	ci right 1.357657e-04	k: 413	n:3350000
Cons ci ratio: 1.231094e-03	ci left: 7.511841e-01	ci right 7.521098e-01	k: 2518018	n:3350000
KS ci ratio: 1.926456e-01	ci left: 1.116795e-04	ci right 1.357657e-04	k: 413	n:3350000
AHCTF1   3350000 perm   5889 sec   (569 perm/sec)   p_kst 1.232836e-04   p_cons 7.516472e-01   p_joint 1.232836e-04

Joint ci ratio: 1.921819e-01	ci left: 1.119137e-04	ci right 1.359855e-04	k: 415	n:3360000
Cons ci ratio: 1.229238e-03	ci left: 7.511918e-01	ci right 7.521161e-01	k: 2525558	n:3360000
KS ci ratio: 1.921819e-01	ci left: 1.119137e-04	ci right 1.359855e-04	k: 415	n:3360000
AHCTF1   3360000 perm   5921 sec   (567 perm/sec)   p_kst 1.235119e-04   p_cons 7.516542e-01   p_joint 1.235119e-04

Joint ci ratio: 1.914926e-01	ci left: 1.124291e-04	ci right 1.365149e-04	k: 418	n:3370000
Cons ci ratio: 1.227464e-03	ci left: 7.511769e-01	ci right 7.520998e-01	k: 2533022	n:3370000
KS ci ratio: 1.914926e-01	ci left: 1.124291e-04	ci right 1.365149e-04	k: 418	n:3370000
AHCTF1   3370000 perm   5956 sec   (566 perm/sec)   p_kst 1.240356e-04   p_cons 7.516386e-01   p_joint 1.240356e-04

Joint ci ratio: 1.910372e-01	ci left: 1.126598e-04	ci right 1.367310e-04	k: 420	n:3380000
Cons ci ratio: 1.225653e-03	ci left: 7.511757e-01	ci right 7.520972e-01	k: 2540532	n:3380000
KS ci ratio: 1.910372e-01	ci left: 1.126598e-04	ci right 1.367310e-04	k: 420	n:3380000
AHCTF1   3380000 perm   5988 sec   (564 perm/sec)   p_kst 1.242604e-04   p_cons 7.516367e-01   p_joint 1.242604e-04

Joint ci ratio: 1.908107e-01	ci left: 1.126084e-04	ci right 1.366367e-04	k: 421	n:3390000
Cons ci ratio: 1.223889e-03	ci left: 7.511624e-01	ci right 7.520826e-01	k: 2548001	n:3390000
KS ci ratio: 1.908107e-01	ci left: 1.126084e-04	ci right 1.366367e-04	k: 421	n:3390000
AHCTF1   3390000 perm   6020 sec   (563 perm/sec)   p_kst 1.241888e-04   p_cons 7.516227e-01   p_joint 1.241888e-04

Joint ci ratio: 1.901360e-01	ci left: 1.131175e-04	ci right 1.371592e-04	k: 424	n:3400000
Cons ci ratio: 1.222077e-03	ci left: 7.511666e-01	ci right 7.520854e-01	k: 2555529	n:3400000
KS ci ratio: 1.901360e-01	ci left: 1.131175e-04	ci right 1.371592e-04	k: 424	n:3400000
AHCTF1   3400000 perm   6053 sec   (562 perm/sec)   p_kst 1.247059e-04   p_cons 7.516262e-01   p_joint 1.247059e-04

Joint ci ratio: 1.894684e-01	ci left: 1.136237e-04	ci right 1.376785e-04	k: 427	n:3410000
Cons ci ratio: 1.220311e-03	ci left: 7.511589e-01	ci right 7.520764e-01	k: 2563017	n:3410000
KS ci ratio: 1.894684e-01	ci left: 1.136237e-04	ci right 1.376785e-04	k: 427	n:3410000
AHCTF1   3410000 perm   6085 sec   (560 perm/sec)   p_kst 1.252199e-04   p_cons 7.516179e-01   p_joint 1.252199e-04

Joint ci ratio: 1.892475e-01	ci left: 1.135700e-04	ci right 1.375822e-04	k: 428	n:3420000
Cons ci ratio: 1.218473e-03	ci left: 7.511756e-01	ci right 7.520918e-01	k: 2570588	n:3420000
KS ci ratio: 1.892475e-01	ci left: 1.135700e-04	ci right 1.375822e-04	k: 428	n:3420000
AHCTF1   3420000 perm   6117 sec   (559 perm/sec)   p_kst 1.251462e-04   p_cons 7.516339e-01   p_joint 1.251462e-04

Joint ci ratio: 1.888079e-01	ci left: 1.137944e-04	ci right 1.377917e-04	k: 430	n:3430000
Cons ci ratio: 1.216725e-03	ci left: 7.511672e-01	ci right 7.520820e-01	k: 2578073	n:3430000
KS ci ratio: 1.888079e-01	ci left: 1.137944e-04	ci right 1.377917e-04	k: 430	n:3430000
AHCTF1   3430000 perm   6149 sec   (558 perm/sec)   p_kst 1.253644e-04   p_cons 7.516248e-01   p_joint 1.253644e-04

Joint ci ratio: 1.881541e-01	ci left: 1.142946e-04	ci right 1.383044e-04	k: 433	n:3440000
Cons ci ratio: 1.215019e-03	ci left: 7.511483e-01	ci right 7.520618e-01	k: 2585522	n:3440000
KS ci ratio: 1.881541e-01	ci left: 1.142946e-04	ci right 1.383044e-04	k: 433	n:3440000
AHCTF1   3440000 perm   6181 sec   (557 perm/sec)   p_kst 1.258721e-04   p_cons 7.516052e-01   p_joint 1.258721e-04

Joint ci ratio: 1.881542e-01	ci left: 1.139633e-04	ci right 1.379035e-04	k: 433	n:3450000
Cons ci ratio: 1.213263e-03	ci left: 7.511472e-01	ci right 7.520593e-01	k: 2593032	n:3450000
KS ci ratio: 1.881542e-01	ci left: 1.139633e-04	ci right 1.379035e-04	k: 433	n:3450000
AHCTF1   3450000 perm   6213 sec   (555 perm/sec)   p_kst 1.255072e-04   p_cons 7.516035e-01   p_joint 1.255072e-04

Joint ci ratio: 1.875072e-01	ci left: 1.144602e-04	ci right 1.384127e-04	k: 436	n:3460000
Cons ci ratio: 1.211410e-03	ci left: 7.511782e-01	ci right 7.520890e-01	k: 2600653	n:3460000
KS ci ratio: 1.875072e-01	ci left: 1.144602e-04	ci right 1.384127e-04	k: 436	n:3460000
AHCTF1   3460000 perm   6245 sec   (554 perm/sec)   p_kst 1.260116e-04   p_cons 7.516338e-01   p_joint 1.260116e-04

Joint ci ratio: 1.875072e-01	ci left: 1.141303e-04	ci right 1.380138e-04	k: 436	n:3470000
Cons ci ratio: 1.209668e-03	ci left: 7.511773e-01	ci right 7.520868e-01	k: 2608164	n:3470000
KS ci ratio: 1.875072e-01	ci left: 1.141303e-04	ci right 1.380138e-04	k: 436	n:3470000
AHCTF1   3470000 perm   6277 sec   (553 perm/sec)   p_kst 1.256484e-04   p_cons 7.516323e-01   p_joint 1.256484e-04

Joint ci ratio: 1.870796e-01	ci left: 1.143501e-04	ci right 1.382189e-04	k: 438	n:3480000
Cons ci ratio: 1.207943e-03	ci left: 7.511736e-01	ci right 7.520818e-01	k: 2615665	n:3480000
KS ci ratio: 1.870796e-01	ci left: 1.143501e-04	ci right 1.382189e-04	k: 438	n:3480000
AHCTF1   3480000 perm   6310 sec   (552 perm/sec)   p_kst 1.258621e-04   p_cons 7.516279e-01   p_joint 1.258621e-04

Joint ci ratio: 1.868669e-01	ci left: 1.142956e-04	ci right 1.381227e-04	k: 439	n:3490000
Cons ci ratio: 1.206250e-03	ci left: 7.511621e-01	ci right 7.520690e-01	k: 2623139	n:3490000
KS ci ratio: 1.868669e-01	ci left: 1.142956e-04	ci right 1.381227e-04	k: 439	n:3490000
AHCTF1   3490000 perm   6342 sec   (550 perm/sec)   p_kst 1.257880e-04   p_cons 7.516158e-01   p_joint 1.257880e-04

Joint ci ratio: 1.868669e-01	ci left: 1.139690e-04	ci right 1.377281e-04	k: 439	n:3500000
Cons ci ratio: 1.204508e-03	ci left: 7.511681e-01	ci right 7.520737e-01	k: 2630674	n:3500000
KS ci ratio: 1.868669e-01	ci left: 1.139690e-04	ci right 1.377281e-04	k: 439	n:3500000
AHCTF1   3500000 perm   6375 sec   (549 perm/sec)   p_kst 1.254286e-04   p_cons 7.516211e-01   p_joint 1.254286e-04

Joint ci ratio: 1.866549e-01	ci left: 1.139159e-04	ci right 1.376339e-04	k: 440	n:3510000
Cons ci ratio: 1.202748e-03	ci left: 7.511821e-01	ci right 7.520864e-01	k: 2638237	n:3510000
KS ci ratio: 1.866549e-01	ci left: 1.139159e-04	ci right 1.376339e-04	k: 440	n:3510000
AHCTF1   3510000 perm   6407 sec   (548 perm/sec)   p_kst 1.253561e-04   p_cons 7.516345e-01   p_joint 1.253561e-04

Joint ci ratio: 1.860232e-01	ci left: 1.144048e-04	ci right 1.381349e-04	k: 443	n:3520000
Cons ci ratio: 1.201041e-03	ci left: 7.511821e-01	ci right 7.520851e-01	k: 2645751	n:3520000
KS ci ratio: 1.860232e-01	ci left: 1.144048e-04	ci right 1.381349e-04	k: 443	n:3520000
AHCTF1   3520000 perm   6440 sec   (547 perm/sec)   p_kst 1.258523e-04   p_cons 7.516338e-01   p_joint 1.258523e-04

Joint ci ratio: 1.856056e-01	ci left: 1.146209e-04	ci right 1.383365e-04	k: 445	n:3530000
Cons ci ratio: 1.199346e-03	ci left: 7.511804e-01	ci right 7.520821e-01	k: 2653259	n:3530000
KS ci ratio: 1.856056e-01	ci left: 1.146209e-04	ci right 1.383365e-04	k: 445	n:3530000
AHCTF1   3530000 perm   6474 sec   (545 perm/sec)   p_kst 1.260623e-04   p_cons 7.516314e-01   p_joint 1.260623e-04

Joint ci ratio: 1.853979e-01	ci left: 1.145665e-04	ci right 1.382413e-04	k: 446	n:3540000
Cons ci ratio: 1.197645e-03	ci left: 7.511829e-01	ci right 7.520834e-01	k: 2660782	n:3540000
KS ci ratio: 1.853979e-01	ci left: 1.145665e-04	ci right 1.382413e-04	k: 446	n:3540000
AHCTF1   3540000 perm   6507 sec   (544 perm/sec)   p_kst 1.259887e-04   p_cons 7.516333e-01   p_joint 1.259887e-04

Joint ci ratio: 1.847788e-01	ci left: 1.150497e-04	ci right 1.387361e-04	k: 449	n:3550000
Cons ci ratio: 1.195945e-03	ci left: 7.511874e-01	ci right 7.520866e-01	k: 2668312	n:3550000
KS ci ratio: 1.847788e-01	ci left: 1.150497e-04	ci right 1.387361e-04	k: 449	n:3550000
AHCTF1   3550000 perm   6540 sec   (543 perm/sec)   p_kst 1.264789e-04   p_cons 7.516372e-01   p_joint 1.264789e-04

Joint ci ratio: 1.847789e-01	ci left: 1.147265e-04	ci right 1.383463e-04	k: 449	n:3560000
Cons ci ratio: 1.194210e-03	ci left: 7.512048e-01	ci right 7.521027e-01	k: 2675888	n:3560000
KS ci ratio: 1.847789e-01	ci left: 1.147265e-04	ci right 1.383463e-04	k: 449	n:3560000
AHCTF1   3560000 perm   6574 sec   (542 perm/sec)   p_kst 1.261236e-04   p_cons 7.516539e-01   p_joint 1.261236e-04

Joint ci ratio: 1.845739e-01	ci left: 1.146723e-04	ci right 1.382519e-04	k: 450	n:3570000
Cons ci ratio: 1.192463e-03	ci left: 7.512282e-01	ci right 7.521249e-01	k: 2683486	n:3570000
KS ci ratio: 1.845739e-01	ci left: 1.146723e-04	ci right 1.382519e-04	k: 450	n:3570000
AHCTF1   3570000 perm   6607 sec   (540 perm/sec)   p_kst 1.260504e-04   p_cons 7.516768e-01   p_joint 1.260504e-04

Joint ci ratio: 1.841660e-01	ci left: 1.148849e-04	ci right 1.384501e-04	k: 452	n:3580000
Cons ci ratio: 1.190798e-03	ci left: 7.512287e-01	ci right 7.521240e-01	k: 2691002	n:3580000
KS ci ratio: 1.841660e-01	ci left: 1.148849e-04	ci right 1.384501e-04	k: 452	n:3580000
AHCTF1   3580000 perm   6640 sec   (539 perm/sec)   p_kst 1.262570e-04   p_cons 7.516765e-01   p_joint 1.262570e-04

Joint ci ratio: 1.841660e-01	ci left: 1.145649e-04	ci right 1.380645e-04	k: 452	n:3590000
Cons ci ratio: 1.189169e-03	ci left: 7.512196e-01	ci right 7.521137e-01	k: 2698484	n:3590000
KS ci ratio: 1.841660e-01	ci left: 1.145649e-04	ci right 1.380645e-04	k: 452	n:3590000
AHCTF1   3590000 perm   6673 sec   (538 perm/sec)   p_kst 1.259053e-04   p_cons 7.516669e-01   p_joint 1.259053e-04

Joint ci ratio: 1.841661e-01	ci left: 1.142467e-04	ci right 1.376809e-04	k: 452	n:3600000
Cons ci ratio: 1.187569e-03	ci left: 7.512036e-01	ci right 7.520965e-01	k: 2705941	n:3600000
KS ci ratio: 1.841661e-01	ci left: 1.142467e-04	ci right 1.376809e-04	k: 452	n:3600000
AHCTF1   3600000 perm   6707 sec   (537 perm/sec)   p_kst 1.255556e-04   p_cons 7.516503e-01   p_joint 1.255556e-04

Joint ci ratio: 1.839631e-01	ci left: 1.141944e-04	ci right 1.375893e-04	k: 453	n:3610000
Cons ci ratio: 1.185945e-03	ci left: 7.511972e-01	ci right 7.520888e-01	k: 2713432	n:3610000
KS ci ratio: 1.839631e-01	ci left: 1.141944e-04	ci right 1.375893e-04	k: 453	n:3610000
AHCTF1   3610000 perm   6740 sec   (536 perm/sec)   p_kst 1.254848e-04   p_cons 7.516432e-01   p_joint 1.254848e-04

Joint ci ratio: 1.833583e-01	ci left: 1.146696e-04	ci right 1.380760e-04	k: 456	n:3620000
Cons ci ratio: 1.184284e-03	ci left: 7.512046e-01	ci right 7.520950e-01	k: 2720973	n:3620000
KS ci ratio: 1.833583e-01	ci left: 1.146696e-04	ci right 1.380760e-04	k: 456	n:3620000
AHCTF1   3620000 perm   6774 sec   (534 perm/sec)   p_kst 1.259669e-04   p_cons 7.516500e-01   p_joint 1.259669e-04

Joint ci ratio: 1.831580e-01	ci left: 1.146166e-04	ci right 1.379837e-04	k: 457	n:3630000
Cons ci ratio: 1.182653e-03	ci left: 7.512048e-01	ci right 7.520940e-01	k: 2728488	n:3630000
KS ci ratio: 1.831580e-01	ci left: 1.146166e-04	ci right 1.379837e-04	k: 457	n:3630000
AHCTF1   3630000 perm   6808 sec   (533 perm/sec)   p_kst 1.258953e-04   p_cons 7.516496e-01   p_joint 1.258953e-04

Joint ci ratio: 1.829584e-01	ci left: 1.145638e-04	ci right 1.378920e-04	k: 458	n:3640000
Cons ci ratio: 1.181038e-03	ci left: 7.512022e-01	ci right 7.520902e-01	k: 2735993	n:3640000
KS ci ratio: 1.829584e-01	ci left: 1.145638e-04	ci right 1.378920e-04	k: 458	n:3640000
AHCTF1   3640000 perm   6842 sec   (532 perm/sec)   p_kst 1.258242e-04   p_cons 7.516464e-01   p_joint 1.258242e-04

Joint ci ratio: 1.825610e-01	ci left: 1.147728e-04	ci right 1.380872e-04	k: 460	n:3650000
Cons ci ratio: 1.179404e-03	ci left: 7.512077e-01	ci right 7.520944e-01	k: 2743527	n:3650000
KS ci ratio: 1.825610e-01	ci left: 1.147728e-04	ci right 1.380872e-04	k: 460	n:3650000
AHCTF1   3650000 perm   6876 sec   (531 perm/sec)   p_kst 1.260274e-04   p_cons 7.516512e-01   p_joint 1.260274e-04

Joint ci ratio: 1.823634e-01	ci left: 1.147200e-04	ci right 1.379956e-04	k: 461	n:3660000
Cons ci ratio: 1.177812e-03	ci left: 7.512018e-01	ci right 7.520874e-01	k: 2751020	n:3660000
KS ci ratio: 1.823634e-01	ci left: 1.147200e-04	ci right 1.379956e-04	k: 461	n:3660000
AHCTF1   3660000 perm   6910 sec   (530 perm/sec)   p_kst 1.259563e-04   p_cons 7.516448e-01   p_joint 1.259563e-04

Joint ci ratio: 1.819699e-01	ci left: 1.149275e-04	ci right 1.381893e-04	k: 463	n:3670000
Cons ci ratio: 1.176195e-03	ci left: 7.512059e-01	ci right 7.520902e-01	k: 2758549	n:3670000
KS ci ratio: 1.819699e-01	ci left: 1.149275e-04	ci right 1.381893e-04	k: 463	n:3670000
AHCTF1   3670000 perm   6944 sec   (528 perm/sec)   p_kst 1.261580e-04   p_cons 7.516482e-01   p_joint 1.261580e-04

Joint ci ratio: 1.815790e-01	ci left: 1.151339e-04	ci right 1.383820e-04	k: 465	n:3680000
Cons ci ratio: 1.174608e-03	ci left: 7.512025e-01	ci right 7.520857e-01	k: 2766051	n:3680000
KS ci ratio: 1.815790e-01	ci left: 1.151339e-04	ci right 1.383820e-04	k: 465	n:3680000
AHCTF1   3680000 perm   6978 sec   (527 perm/sec)   p_kst 1.263587e-04   p_cons 7.516443e-01   p_joint 1.263587e-04

Joint ci ratio: 1.813845e-01	ci left: 1.150806e-04	ci right 1.382903e-04	k: 466	n:3690000
Cons ci ratio: 1.173053e-03	ci left: 7.511913e-01	ci right 7.520733e-01	k: 2773524	n:3690000
KS ci ratio: 1.813845e-01	ci left: 1.150806e-04	ci right 1.382903e-04	k: 466	n:3690000
AHCTF1   3690000 perm   7012 sec   (526 perm/sec)   p_kst 1.262873e-04   p_cons 7.516325e-01   p_joint 1.262873e-04

Joint ci ratio: 1.809973e-01	ci left: 1.152856e-04	ci right 1.384816e-04	k: 468	n:3700000
Cons ci ratio: 1.171466e-03	ci left: 7.511919e-01	ci right 7.520726e-01	k: 2781040	n:3700000
KS ci ratio: 1.809973e-01	ci left: 1.152856e-04	ci right 1.384816e-04	k: 468	n:3700000
AHCTF1   3700000 perm   7047 sec   (525 perm/sec)   p_kst 1.264865e-04   p_cons 7.516324e-01   p_joint 1.264865e-04

Joint ci ratio: 1.804211e-01	ci left: 1.157469e-04	ci right 1.389535e-04	k: 471	n:3710000
Cons ci ratio: 1.169831e-03	ci left: 7.512102e-01	ci right 7.520897e-01	k: 2788622	n:3710000
KS ci ratio: 1.804211e-01	ci left: 1.157469e-04	ci right 1.389535e-04	k: 471	n:3710000
AHCTF1   3710000 perm   7081 sec   (524 perm/sec)   p_kst 1.269542e-04   p_cons 7.516501e-01   p_joint 1.269542e-04

Joint ci ratio: 1.804212e-01	ci left: 1.154358e-04	ci right 1.385799e-04	k: 471	n:3720000
Cons ci ratio: 1.168278e-03	ci left: 7.512042e-01	ci right 7.520825e-01	k: 2796114	n:3720000
KS ci ratio: 1.804212e-01	ci left: 1.154358e-04	ci right 1.385799e-04	k: 471	n:3720000
AHCTF1   3720000 perm   7116 sec   (523 perm/sec)   p_kst 1.266129e-04   p_cons 7.516435e-01   p_joint 1.266129e-04

Joint ci ratio: 1.800401e-01	ci left: 1.156383e-04	ci right 1.387688e-04	k: 473	n:3730000
Cons ci ratio: 1.166708e-03	ci left: 7.512057e-01	ci right 7.520829e-01	k: 2803634	n:3730000
KS ci ratio: 1.800401e-01	ci left: 1.156383e-04	ci right 1.387688e-04	k: 473	n:3730000
AHCTF1   3730000 perm   7150 sec   (522 perm/sec)   p_kst 1.268097e-04   p_cons 7.516445e-01   p_joint 1.268097e-04

Joint ci ratio: 1.798505e-01	ci left: 1.155844e-04	ci right 1.386771e-04	k: 474	n:3740000
Cons ci ratio: 1.165160e-03	ci left: 7.512022e-01	ci right 7.520782e-01	k: 2811135	n:3740000
KS ci ratio: 1.798505e-01	ci left: 1.155844e-04	ci right 1.386771e-04	k: 474	n:3740000
AHCTF1   3740000 perm   7185 sec   (521 perm/sec)   p_kst 1.267380e-04   p_cons 7.516404e-01   p_joint 1.267380e-04

Joint ci ratio: 1.794730e-01	ci left: 1.157856e-04	ci right 1.388646e-04	k: 476	n:3750000
Cons ci ratio: 1.163609e-03	ci left: 7.512018e-01	ci right 7.520767e-01	k: 2818648	n:3750000
KS ci ratio: 1.794730e-01	ci left: 1.157856e-04	ci right 1.388646e-04	k: 476	n:3750000
AHCTF1   3750000 perm   7219 sec   (519 perm/sec)   p_kst 1.269333e-04   p_cons 7.516395e-01   p_joint 1.269333e-04

Joint ci ratio: 1.792852e-01	ci left: 1.157316e-04	ci right 1.387732e-04	k: 477	n:3760000
Cons ci ratio: 1.162066e-03	ci left: 7.512005e-01	ci right 7.520742e-01	k: 2826157	n:3760000
KS ci ratio: 1.792852e-01	ci left: 1.157316e-04	ci right 1.387732e-04	k: 477	n:3760000
AHCTF1   3760000 perm   7254 sec   (518 perm/sec)   p_kst 1.268617e-04   p_cons 7.516375e-01   p_joint 1.268617e-04

Joint ci ratio: 1.792852e-01	ci left: 1.154247e-04	ci right 1.384051e-04	k: 477	n:3770000
Cons ci ratio: 1.160534e-03	ci left: 7.511978e-01	ci right 7.520703e-01	k: 2833661	n:3770000
KS ci ratio: 1.792852e-01	ci left: 1.154247e-04	ci right 1.384051e-04	k: 477	n:3770000
AHCTF1   3770000 perm   7288 sec   (517 perm/sec)   p_kst 1.265252e-04   p_cons 7.516342e-01   p_joint 1.265252e-04

Joint ci ratio: 1.789113e-01	ci left: 1.156247e-04	ci right 1.385917e-04	k: 479	n:3780000
Cons ci ratio: 1.159068e-03	ci left: 7.511757e-01	ci right 7.520472e-01	k: 2841092	n:3780000
KS ci ratio: 1.789113e-01	ci left: 1.156247e-04	ci right 1.385917e-04	k: 479	n:3780000
AHCTF1   3780000 perm   7323 sec   (516 perm/sec)   p_kst 1.267196e-04   p_cons 7.516116e-01   p_joint 1.267196e-04

Joint ci ratio: 1.783548e-01	ci left: 1.160758e-04	ci right 1.390530e-04	k: 482	n:3790000
Cons ci ratio: 1.157550e-03	ci left: 7.511726e-01	ci right 7.520429e-01	k: 2848594	n:3790000
KS ci ratio: 1.783548e-01	ci left: 1.160758e-04	ci right 1.390530e-04	k: 482	n:3790000
AHCTF1   3790000 perm   7358 sec   (515 perm/sec)   p_kst 1.271768e-04   p_cons 7.516079e-01   p_joint 1.271768e-04

Joint ci ratio: 1.779866e-01	ci left: 1.162732e-04	ci right 1.392368e-04	k: 484	n:3800000
Cons ci ratio: 1.155952e-03	ci left: 7.511968e-01	ci right 7.520659e-01	k: 2856200	n:3800000
KS ci ratio: 1.779866e-01	ci left: 1.162732e-04	ci right 1.392368e-04	k: 484	n:3800000
AHCTF1   3800000 perm   7393 sec   (514 perm/sec)   p_kst 1.273684e-04   p_cons 7.516316e-01   p_joint 1.273684e-04

Joint ci ratio: 1.778034e-01	ci left: 1.162188e-04	ci right 1.391455e-04	k: 485	n:3810000
Cons ci ratio: 1.154460e-03	ci left: 7.511892e-01	ci right 7.520572e-01	k: 2863685	n:3810000
KS ci ratio: 1.778034e-01	ci left: 1.162188e-04	ci right 1.391455e-04	k: 485	n:3810000
AHCTF1   3810000 perm   7428 sec   (513 perm/sec)   p_kst 1.272966e-04   p_cons 7.516234e-01   p_joint 1.272966e-04

Joint ci ratio: 1.778035e-01	ci left: 1.159145e-04	ci right 1.387812e-04	k: 485	n:3820000
Cons ci ratio: 1.152984e-03	ci left: 7.511779e-01	ci right 7.520447e-01	k: 2871156	n:3820000
KS ci ratio: 1.778035e-01	ci left: 1.159145e-04	ci right 1.387812e-04	k: 485	n:3820000
AHCTF1   3820000 perm   7462 sec   (512 perm/sec)   p_kst 1.269634e-04   p_cons 7.516115e-01   p_joint 1.269634e-04

Joint ci ratio: 1.774387e-01	ci left: 1.161109e-04	ci right 1.389643e-04	k: 487	n:3830000
Cons ci ratio: 1.151481e-03	ci left: 7.511777e-01	ci right 7.520434e-01	k: 2878669	n:3830000
KS ci ratio: 1.774387e-01	ci left: 1.161109e-04	ci right 1.389643e-04	k: 487	n:3830000
AHCTF1   3830000 perm   7498 sec   (511 perm/sec)   p_kst 1.271540e-04   p_cons 7.516107e-01   p_joint 1.271540e-04

Joint ci ratio: 1.768958e-01	ci left: 1.165551e-04	ci right 1.394182e-04	k: 490	n:3840000
Cons ci ratio: 1.150016e-03	ci left: 7.511665e-01	ci right 7.520311e-01	k: 2886140	n:3840000
KS ci ratio: 1.768958e-01	ci left: 1.165551e-04	ci right 1.394182e-04	k: 490	n:3840000
AHCTF1   3840000 perm   7533 sec   (510 perm/sec)   p_kst 1.276042e-04   p_cons 7.515990e-01   p_joint 1.276042e-04

Joint ci ratio: 1.767159e-01	ci left: 1.165006e-04	ci right 1.393273e-04	k: 491	n:3850000
Cons ci ratio: 1.148571e-03	ci left: 7.511509e-01	ci right 7.520144e-01	k: 2893594	n:3850000
KS ci ratio: 1.767159e-01	ci left: 1.165006e-04	ci right 1.393273e-04	k: 491	n:3850000
AHCTF1   3850000 perm   7569 sec   (509 perm/sec)   p_kst 1.275325e-04   p_cons 7.515829e-01   p_joint 1.275325e-04

Joint ci ratio: 1.763578e-01	ci left: 1.166940e-04	ci right 1.395074e-04	k: 493	n:3860000
Cons ci ratio: 1.147078e-03	ci left: 7.511531e-01	ci right 7.520155e-01	k: 2901116	n:3860000
KS ci ratio: 1.763578e-01	ci left: 1.166940e-04	ci right 1.395074e-04	k: 493	n:3860000
AHCTF1   3860000 perm   7605 sec   (508 perm/sec)   p_kst 1.277202e-04   p_cons 7.515845e-01   p_joint 1.277202e-04

Joint ci ratio: 1.763579e-01	ci left: 1.163925e-04	ci right 1.391469e-04	k: 493	n:3870000
Cons ci ratio: 1.145588e-03	ci left: 7.511560e-01	ci right 7.520173e-01	k: 2908641	n:3870000
KS ci ratio: 1.763579e-01	ci left: 1.163925e-04	ci right 1.391469e-04	k: 493	n:3870000
AHCTF1   3870000 perm   7641 sec   (506 perm/sec)   p_kst 1.273902e-04   p_cons 7.515868e-01   p_joint 1.273902e-04

Joint ci ratio: 1.756481e-01	ci left: 1.170780e-04	ci right 1.398646e-04	k: 497	n:3880000
Cons ci ratio: 1.144134e-03	ci left: 7.511489e-01	ci right 7.520090e-01	k: 2916127	n:3880000
KS ci ratio: 1.756481e-01	ci left: 1.170780e-04	ci right 1.398646e-04	k: 497	n:3880000
AHCTF1   3880000 perm   7677 sec   (505 perm/sec)   p_kst 1.280928e-04   p_cons 7.515791e-01   p_joint 1.280928e-04

Joint ci ratio: 1.751214e-01	ci left: 1.175144e-04	ci right 1.403100e-04	k: 500	n:3890000
Cons ci ratio: 1.142656e-03	ci left: 7.511515e-01	ci right 7.520106e-01	k: 2923651	n:3890000
KS ci ratio: 1.751214e-01	ci left: 1.175144e-04	ci right 1.403100e-04	k: 500	n:3890000
AHCTF1   3890000 perm   7714 sec   (504 perm/sec)   p_kst 1.285347e-04   p_cons 7.515812e-01   p_joint 1.285347e-04

Joint ci ratio: 1.745994e-01	ci left: 1.179487e-04	ci right 1.407531e-04	k: 503	n:3900000
Cons ci ratio: 1.141192e-03	ci left: 7.511514e-01	ci right 7.520093e-01	k: 2931164	n:3900000
KS ci ratio: 1.745994e-01	ci left: 1.179487e-04	ci right 1.407531e-04	k: 503	n:3900000
AHCTF1   3900000 perm   7750 sec   (503 perm/sec)   p_kst 1.289744e-04   p_cons 7.515805e-01   p_joint 1.289744e-04

Joint ci ratio: 1.745994e-01	ci left: 1.176470e-04	ci right 1.403932e-04	k: 503	n:3910000
Cons ci ratio: 1.139757e-03	ci left: 7.511438e-01	ci right 7.520006e-01	k: 2938648	n:3910000
KS ci ratio: 1.745994e-01	ci left: 1.176470e-04	ci right 1.403932e-04	k: 503	n:3910000
AHCTF1   3910000 perm   7787 sec   (502 perm/sec)   p_kst 1.286445e-04   p_cons 7.515724e-01   p_joint 1.286445e-04

Joint ci ratio: 1.745994e-01	ci left: 1.173469e-04	ci right 1.400350e-04	k: 503	n:3920000
Cons ci ratio: 1.138292e-03	ci left: 7.511477e-01	ci right 7.520035e-01	k: 2946177	n:3920000
KS ci ratio: 1.745994e-01	ci left: 1.173469e-04	ci right 1.400350e-04	k: 503	n:3920000
AHCTF1   3920000 perm   7823 sec   (501 perm/sec)   p_kst 1.283163e-04   p_cons 7.515758e-01   p_joint 1.283163e-04

Joint ci ratio: 1.744265e-01	ci left: 1.172916e-04	ci right 1.399442e-04	k: 504	n:3930000
Cons ci ratio: 1.136803e-03	ci left: 7.511613e-01	ci right 7.520159e-01	k: 2953744	n:3930000
KS ci ratio: 1.744265e-01	ci left: 1.172916e-04	ci right 1.399442e-04	k: 504	n:3930000
AHCTF1   3930000 perm   7859 sec   (500 perm/sec)   p_kst 1.282443e-04   p_cons 7.515888e-01   p_joint 1.282443e-04

Joint ci ratio: 1.744265e-01	ci left: 1.169939e-04	ci right 1.395891e-04	k: 504	n:3940000
Cons ci ratio: 1.135379e-03	ci left: 7.511553e-01	ci right 7.520088e-01	k: 2961234	n:3940000
KS ci ratio: 1.744265e-01	ci left: 1.169939e-04	ci right 1.395891e-04	k: 504	n:3940000
AHCTF1   3940000 perm   7896 sec   (499 perm/sec)   p_kst 1.279188e-04   p_cons 7.515822e-01   p_joint 1.279188e-04

Joint ci ratio: 1.742541e-01	ci left: 1.169399e-04	ci right 1.394999e-04	k: 505	n:3950000
Cons ci ratio: 1.133948e-03	ci left: 7.511536e-01	ci right 7.520061e-01	k: 2968741	n:3950000
KS ci ratio: 1.742541e-01	ci left: 1.169399e-04	ci right 1.394999e-04	k: 505	n:3950000
AHCTF1   3950000 perm   7933 sec   (498 perm/sec)   p_kst 1.278481e-04   p_cons 7.515800e-01   p_joint 1.278481e-04

Joint ci ratio: 1.740821e-01	ci left: 1.168861e-04	ci right 1.394111e-04	k: 506	n:3960000
Cons ci ratio: 1.132511e-03	ci left: 7.511554e-01	ci right 7.520068e-01	k: 2976262	n:3960000
KS ci ratio: 1.740821e-01	ci left: 1.168861e-04	ci right 1.394111e-04	k: 506	n:3960000
AHCTF1   3960000 perm   7969 sec   (497 perm/sec)   p_kst 1.277778e-04   p_cons 7.515813e-01   p_joint 1.277778e-04

Joint ci ratio: 1.739107e-01	ci left: 1.168326e-04	ci right 1.393228e-04	k: 507	n:3970000
Cons ci ratio: 1.131078e-03	ci left: 7.511580e-01	ci right 7.520084e-01	k: 2983786	n:3970000
KS ci ratio: 1.739107e-01	ci left: 1.168326e-04	ci right 1.393228e-04	k: 507	n:3970000
AHCTF1   3970000 perm   8006 sec   (496 perm/sec)   p_kst 1.277078e-04   p_cons 7.515834e-01   p_joint 1.277078e-04

Joint ci ratio: 1.737398e-01	ci left: 1.167793e-04	ci right 1.392349e-04	k: 508	n:3980000
Cons ci ratio: 1.129628e-03	ci left: 7.511679e-01	ci right 7.520172e-01	k: 2991339	n:3980000
KS ci ratio: 1.737398e-01	ci left: 1.167793e-04	ci right 1.392349e-04	k: 508	n:3980000
AHCTF1   3980000 perm   8043 sec   (495 perm/sec)   p_kst 1.276382e-04   p_cons 7.515927e-01   p_joint 1.276382e-04

Joint ci ratio: 1.735694e-01	ci left: 1.167264e-04	ci right 1.391475e-04	k: 509	n:3990000
Cons ci ratio: 1.128183e-03	ci left: 7.511780e-01	ci right 7.520262e-01	k: 2998893	n:3990000
KS ci ratio: 1.735694e-01	ci left: 1.167264e-04	ci right 1.391475e-04	k: 509	n:3990000
AHCTF1   3990000 perm   8080 sec   (494 perm/sec)   p_kst 1.275689e-04   p_cons 7.516023e-01   p_joint 1.275689e-04

Joint ci ratio: 1.733995e-01	ci left: 1.166737e-04	ci right 1.390604e-04	k: 510	n:4000000
Cons ci ratio: 1.126830e-03	ci left: 7.511592e-01	ci right 7.520064e-01	k: 3006332	n:4000000
KS ci ratio: 1.733995e-01	ci left: 1.166737e-04	ci right 1.390604e-04	k: 510	n:4000000
AHCTF1   4000000 perm   8117 sec   (493 perm/sec)   p_kst 1.275000e-04   p_cons 7.515830e-01   p_joint 1.275000e-04

Joint ci ratio: 1.728927e-01	ci left: 1.170985e-04	ci right 1.394942e-04	k: 513	n:4010000
Cons ci ratio: 1.125431e-03	ci left: 7.511573e-01	ci right 7.520034e-01	k: 3013838	n:4010000
KS ci ratio: 1.728927e-01	ci left: 1.170985e-04	ci right 1.394942e-04	k: 513	n:4010000
AHCTF1   4010000 perm   8153 sec   (492 perm/sec)   p_kst 1.279302e-04   p_cons 7.515805e-01   p_joint 1.279302e-04

Joint ci ratio: 1.728927e-01	ci left: 1.168072e-04	ci right 1.391472e-04	k: 513	n:4020000
Cons ci ratio: 1.124028e-03	ci left: 7.511586e-01	ci right 7.520037e-01	k: 3021357	n:4020000
KS ci ratio: 1.728927e-01	ci left: 1.168072e-04	ci right 1.391472e-04	k: 513	n:4020000
AHCTF1   4020000 perm   8190 sec   (491 perm/sec)   p_kst 1.276119e-04   p_cons 7.515813e-01   p_joint 1.276119e-04

Joint ci ratio: 1.725573e-01	ci left: 1.169922e-04	ci right 1.393196e-04	k: 515	n:4030000
Cons ci ratio: 1.122642e-03	ci left: 7.511560e-01	ci right 7.520000e-01	k: 3028860	n:4030000
KS ci ratio: 1.725573e-01	ci left: 1.169922e-04	ci right 1.393196e-04	k: 515	n:4030000
AHCTF1   4030000 perm   8227 sec   (490 perm/sec)   p_kst 1.277916e-04   p_cons 7.515782e-01   p_joint 1.277916e-04

Joint ci ratio: 1.722238e-01	ci left: 1.171763e-04	ci right 1.394911e-04	k: 517	n:4040000
Cons ci ratio: 1.121330e-03	ci left: 7.511306e-01	ci right 7.519735e-01	k: 3036271	n:4040000
KS ci ratio: 1.722238e-01	ci left: 1.171763e-04	ci right 1.394911e-04	k: 517	n:4040000
AHCTF1   4040000 perm   8264 sec   (489 perm/sec)   p_kst 1.279703e-04   p_cons 7.515522e-01   p_joint 1.279703e-04

Joint ci ratio: 1.720579e-01	ci left: 1.171232e-04	ci right 1.394043e-04	k: 518	n:4050000
Cons ci ratio: 1.119923e-03	ci left: 7.511381e-01	ci right 7.519800e-01	k: 3043815	n:4050000
KS ci ratio: 1.720579e-01	ci left: 1.171232e-04	ci right 1.394043e-04	k: 518	n:4050000
AHCTF1   4050000 perm   8302 sec   (488 perm/sec)   p_kst 1.279012e-04   p_cons 7.515593e-01   p_joint 1.279012e-04

Joint ci ratio: 1.717273e-01	ci left: 1.173062e-04	ci right 1.395747e-04	k: 520	n:4060000
Cons ci ratio: 1.118580e-03	ci left: 7.511264e-01	ci right 7.519673e-01	k: 3051281	n:4060000
KS ci ratio: 1.717273e-01	ci left: 1.173062e-04	ci right 1.395747e-04	k: 520	n:4060000
AHCTF1   4060000 perm   8340 sec   (487 perm/sec)   p_kst 1.280788e-04   p_cons 7.515470e-01   p_joint 1.280788e-04

Joint ci ratio: 1.713986e-01	ci left: 1.174882e-04	ci right 1.397442e-04	k: 522	n:4070000
Cons ci ratio: 1.117171e-03	ci left: 7.511381e-01	ci right 7.519780e-01	k: 3058842	n:4070000
KS ci ratio: 1.713986e-01	ci left: 1.174882e-04	ci right 1.397442e-04	k: 522	n:4070000
AHCTF1   4070000 perm   8379 sec   (486 perm/sec)   p_kst 1.282555e-04   p_cons 7.515582e-01   p_joint 1.282555e-04

Joint ci ratio: 1.712350e-01	ci left: 1.174349e-04	ci right 1.396573e-04	k: 523	n:4080000
Cons ci ratio: 1.115798e-03	ci left: 7.511400e-01	ci right 7.519788e-01	k: 3066363	n:4080000
KS ci ratio: 1.712350e-01	ci left: 1.174349e-04	ci right 1.396573e-04	k: 523	n:4080000
AHCTF1   4080000 perm   8417 sec   (485 perm/sec)   p_kst 1.281863e-04   p_cons 7.515596e-01   p_joint 1.281863e-04

Joint ci ratio: 1.710718e-01	ci left: 1.173818e-04	ci right 1.395708e-04	k: 524	n:4090000
Cons ci ratio: 1.114368e-03	ci left: 7.511621e-01	ci right 7.519999e-01	k: 3073967	n:4090000
KS ci ratio: 1.710718e-01	ci left: 1.173818e-04	ci right 1.395708e-04	k: 524	n:4090000
AHCTF1   4090000 perm   8455 sec   (484 perm/sec)   p_kst 1.281174e-04   p_cons 7.515812e-01   p_joint 1.281174e-04

Joint ci ratio: 1.709091e-01	ci left: 1.173289e-04	ci right 1.394847e-04	k: 525	n:4100000
Cons ci ratio: 1.113027e-03	ci left: 7.511563e-01	ci right 7.519931e-01	k: 3081457	n:4100000
KS ci ratio: 1.709091e-01	ci left: 1.173289e-04	ci right 1.394847e-04	k: 525	n:4100000
AHCTF1   4100000 perm   8494 sec   (483 perm/sec)   p_kst 1.280488e-04   p_cons 7.515749e-01   p_joint 1.280488e-04

Joint ci ratio: 1.705851e-01	ci left: 1.175093e-04	ci right 1.396528e-04	k: 527	n:4110000
Cons ci ratio: 1.111650e-03	ci left: 7.511644e-01	ci right 7.520002e-01	k: 3089004	n:4110000
KS ci ratio: 1.705851e-01	ci left: 1.175093e-04	ci right 1.396528e-04	k: 527	n:4110000
AHCTF1   4110000 perm   8532 sec   (482 perm/sec)   p_kst 1.282238e-04   p_cons 7.515825e-01   p_joint 1.282238e-04

Joint ci ratio: 1.704238e-01	ci left: 1.174564e-04	ci right 1.395669e-04	k: 528	n:4120000
Cons ci ratio: 1.110339e-03	ci left: 7.511519e-01	ci right 7.519866e-01	k: 3096466	n:4120000
KS ci ratio: 1.704238e-01	ci left: 1.174564e-04	ci right 1.395669e-04	k: 528	n:4120000
AHCTF1   4120000 perm   8570 sec   (481 perm/sec)   p_kst 1.281553e-04   p_cons 7.515694e-01   p_joint 1.281553e-04

Joint ci ratio: 1.702630e-01	ci left: 1.174038e-04	ci right 1.394814e-04	k: 529	n:4130000
Cons ci ratio: 1.109006e-03	ci left: 7.511483e-01	ci right 7.519821e-01	k: 3103965	n:4130000
KS ci ratio: 1.702630e-01	ci left: 1.174038e-04	ci right 1.394814e-04	k: 529	n:4130000
AHCTF1   4130000 perm   8608 sec   (480 perm/sec)   p_kst 1.280872e-04   p_cons 7.515654e-01   p_joint 1.280872e-04

Joint ci ratio: 1.701026e-01	ci left: 1.173515e-04	ci right 1.393963e-04	k: 530	n:4140000
Cons ci ratio: 1.107645e-03	ci left: 7.511557e-01	ci right 7.519884e-01	k: 3111509	n:4140000
KS ci ratio: 1.701026e-01	ci left: 1.173515e-04	ci right 1.393963e-04	k: 530	n:4140000
AHCTF1   4140000 perm   8646 sec   (479 perm/sec)   p_kst 1.280193e-04   p_cons 7.515722e-01   p_joint 1.280193e-04

Joint ci ratio: 1.697831e-01	ci left: 1.175302e-04	ci right 1.395628e-04	k: 532	n:4150000
Cons ci ratio: 1.106312e-03	ci left: 7.511555e-01	ci right 7.519872e-01	k: 3119022	n:4150000
KS ci ratio: 1.697831e-01	ci left: 1.175302e-04	ci right 1.395628e-04	k: 532	n:4150000
AHCTF1   4150000 perm   8684 sec   (478 perm/sec)   p_kst 1.281928e-04   p_cons 7.515716e-01   p_joint 1.281928e-04

Joint ci ratio: 1.691495e-01	ci left: 1.181684e-04	ci right 1.402296e-04	k: 536	n:4160000
Cons ci ratio: 1.104988e-03	ci left: 7.511537e-01	ci right 7.519844e-01	k: 3126528	n:4160000
KS ci ratio: 1.691495e-01	ci left: 1.181684e-04	ci right 1.402296e-04	k: 536	n:4160000
AHCTF1   4160000 perm   8722 sec   (477 perm/sec)   p_kst 1.288462e-04   p_cons 7.515692e-01   p_joint 1.288462e-04

Joint ci ratio: 1.688354e-01	ci left: 1.183444e-04	ci right 1.403932e-04	k: 538	n:4170000
Cons ci ratio: 1.103693e-03	ci left: 7.511440e-01	ci right 7.519737e-01	k: 3134001	n:4170000
KS ci ratio: 1.688354e-01	ci left: 1.183444e-04	ci right 1.403932e-04	k: 538	n:4170000
AHCTF1   4170000 perm   8761 sec   (476 perm/sec)   p_kst 1.290168e-04   p_cons 7.515590e-01   p_joint 1.290168e-04

Joint ci ratio: 1.686790e-01	ci left: 1.182904e-04	ci right 1.403066e-04	k: 539	n:4180000
Cons ci ratio: 1.102355e-03	ci left: 7.511501e-01	ci right 7.519788e-01	k: 3141540	n:4180000
KS ci ratio: 1.686790e-01	ci left: 1.182904e-04	ci right 1.403066e-04	k: 539	n:4180000
AHCTF1   4180000 perm   8799 sec   (475 perm/sec)   p_kst 1.289474e-04   p_cons 7.515646e-01   p_joint 1.289474e-04

Joint ci ratio: 1.685231e-01	ci left: 1.182366e-04	ci right 1.402205e-04	k: 540	n:4190000
Cons ci ratio: 1.101039e-03	ci left: 7.511506e-01	ci right 7.519784e-01	k: 3149056	n:4190000
KS ci ratio: 1.685231e-01	ci left: 1.182366e-04	ci right 1.402205e-04	k: 540	n:4190000
AHCTF1   4190000 perm   8837 sec   (474 perm/sec)   p_kst 1.288783e-04   p_cons 7.515647e-01   p_joint 1.288783e-04

Joint ci ratio: 1.685231e-01	ci left: 1.179551e-04	ci right 1.398866e-04	k: 540	n:4200000
Cons ci ratio: 1.099739e-03	ci left: 7.511472e-01	ci right 7.519739e-01	k: 3156555	n:4200000
KS ci ratio: 1.685231e-01	ci left: 1.179551e-04	ci right 1.398866e-04	k: 540	n:4200000
AHCTF1   4200000 perm   8877 sec   (473 perm/sec)   p_kst 1.285714e-04   p_cons 7.515607e-01   p_joint 1.285714e-04

Joint ci ratio: 1.683676e-01	ci left: 1.179025e-04	ci right 1.398019e-04	k: 541	n:4210000
Cons ci ratio: 1.098383e-03	ci left: 7.511644e-01	ci right 7.519901e-01	k: 3164141	n:4210000
KS ci ratio: 1.683676e-01	ci left: 1.179025e-04	ci right 1.398019e-04	k: 541	n:4210000
AHCTF1   4210000 perm   8916 sec   (472 perm/sec)   p_kst 1.285036e-04   p_cons 7.515774e-01   p_joint 1.285036e-04

Joint ci ratio: 1.683676e-01	ci left: 1.176231e-04	ci right 1.394706e-04	k: 541	n:4220000
Cons ci ratio: 1.097050e-03	ci left: 7.511754e-01	ci right 7.520001e-01	k: 3171701	n:4220000
KS ci ratio: 1.683676e-01	ci left: 1.176231e-04	ci right 1.394706e-04	k: 541	n:4220000
AHCTF1   4220000 perm   8956 sec   (471 perm/sec)   p_kst 1.281991e-04   p_cons 7.515879e-01   p_joint 1.281991e-04

Joint ci ratio: 1.680578e-01	ci left: 1.177979e-04	ci right 1.396336e-04	k: 543	n:4230000
Cons ci ratio: 1.095776e-03	ci left: 7.511676e-01	ci right 7.519914e-01	k: 3179182	n:4230000
KS ci ratio: 1.680578e-01	ci left: 1.177979e-04	ci right 1.396336e-04	k: 543	n:4230000
AHCTF1   4230000 perm   8996 sec   (470 perm/sec)   p_kst 1.283688e-04   p_cons 7.515797e-01   p_joint 1.283688e-04

Joint ci ratio: 1.679035e-01	ci left: 1.177460e-04	ci right 1.395500e-04	k: 544	n:4240000
Cons ci ratio: 1.094505e-03	ci left: 7.511606e-01	ci right 7.519834e-01	k: 3186666	n:4240000
KS ci ratio: 1.679035e-01	ci left: 1.177460e-04	ci right 1.395500e-04	k: 544	n:4240000
AHCTF1   4240000 perm   9035 sec   (469 perm/sec)   p_kst 1.283019e-04   p_cons 7.515722e-01   p_joint 1.283019e-04

Joint ci ratio: 1.675963e-01	ci left: 1.179198e-04	ci right 1.397120e-04	k: 546	n:4250000
Cons ci ratio: 1.093220e-03	ci left: 7.511602e-01	ci right 7.519820e-01	k: 3194178	n:4250000
KS ci ratio: 1.675963e-01	ci left: 1.179198e-04	ci right 1.397120e-04	k: 546	n:4250000
AHCTF1   4250000 perm   9075 sec   (468 perm/sec)   p_kst 1.284706e-04   p_cons 7.515713e-01   p_joint 1.284706e-04

Joint ci ratio: 1.672907e-01	ci left: 1.180928e-04	ci right 1.398732e-04	k: 548	n:4260000
Cons ci ratio: 1.091918e-03	ci left: 7.511669e-01	ci right 7.519877e-01	k: 3201720	n:4260000
KS ci ratio: 1.672907e-01	ci left: 1.180928e-04	ci right 1.398732e-04	k: 548	n:4260000
AHCTF1   4260000 perm   9115 sec   (467 perm/sec)   p_kst 1.286385e-04   p_cons 7.515775e-01   p_joint 1.286385e-04

Joint ci ratio: 1.668355e-01	ci left: 1.184895e-04	ci right 1.402775e-04	k: 551	n:4270000
Cons ci ratio: 1.090618e-03	ci left: 7.511744e-01	ci right 7.519943e-01	k: 3209266	n:4270000
KS ci ratio: 1.668355e-01	ci left: 1.184895e-04	ci right 1.402775e-04	k: 551	n:4270000
AHCTF1   4270000 perm   9155 sec   (466 perm/sec)   p_kst 1.290398e-04   p_cons 7.515845e-01   p_joint 1.290398e-04

Joint ci ratio: 1.663839e-01	ci left: 1.188843e-04	ci right 1.406799e-04	k: 554	n:4280000
Cons ci ratio: 1.089392e-03	ci left: 7.511581e-01	ci right 7.519771e-01	k: 3216710	n:4280000
KS ci ratio: 1.663839e-01	ci left: 1.188843e-04	ci right 1.406799e-04	k: 554	n:4280000
AHCTF1   4280000 perm   9194 sec   (466 perm/sec)   p_kst 1.294393e-04   p_cons 7.515678e-01   p_joint 1.294393e-04

Joint ci ratio: 1.660849e-01	ci left: 1.190540e-04	ci right 1.408376e-04	k: 556	n:4290000
Cons ci ratio: 1.088169e-03	ci left: 7.511423e-01	ci right 7.519604e-01	k: 3224156	n:4290000
KS ci ratio: 1.660849e-01	ci left: 1.190540e-04	ci right 1.408376e-04	k: 556	n:4290000
AHCTF1   4290000 perm   9234 sec   (465 perm/sec)   p_kst 1.296037e-04   p_cons 7.515515e-01   p_joint 1.296037e-04

Joint ci ratio: 1.660850e-01	ci left: 1.187771e-04	ci right 1.405100e-04	k: 556	n:4300000
Cons ci ratio: 1.086906e-03	ci left: 7.511418e-01	ci right 7.519588e-01	k: 3231667	n:4300000
KS ci ratio: 1.660850e-01	ci left: 1.187771e-04	ci right 1.405100e-04	k: 556	n:4300000
AHCTF1   4300000 perm   9274 sec   (464 perm/sec)   p_kst 1.293023e-04   p_cons 7.515505e-01   p_joint 1.293023e-04

Joint ci ratio: 1.656395e-01	ci left: 1.191687e-04	ci right 1.409090e-04	k: 559	n:4310000
Cons ci ratio: 1.085644e-03	ci left: 7.511423e-01	ci right 7.519585e-01	k: 3239183	n:4310000
KS ci ratio: 1.656395e-01	ci left: 1.191687e-04	ci right 1.409090e-04	k: 559	n:4310000
AHCTF1   4310000 perm   9314 sec   (463 perm/sec)   p_kst 1.296984e-04   p_cons 7.515506e-01   p_joint 1.296984e-04

Joint ci ratio: 1.653444e-01	ci left: 1.193367e-04	ci right 1.410649e-04	k: 561	n:4320000
Cons ci ratio: 1.084397e-03	ci left: 7.511392e-01	ci right 7.519544e-01	k: 3246683	n:4320000
KS ci ratio: 1.653444e-01	ci left: 1.193367e-04	ci right 1.410649e-04	k: 561	n:4320000
AHCTF1   4320000 perm   9354 sec   (462 perm/sec)   p_kst 1.298611e-04   p_cons 7.515470e-01   p_joint 1.298611e-04

Joint ci ratio: 1.653445e-01	ci left: 1.190610e-04	ci right 1.407391e-04	k: 561	n:4330000
Cons ci ratio: 1.083139e-03	ci left: 7.511414e-01	ci right 7.519557e-01	k: 3254206	n:4330000
KS ci ratio: 1.653445e-01	ci left: 1.190610e-04	ci right 1.407391e-04	k: 561	n:4330000
AHCTF1   4330000 perm   9394 sec   (461 perm/sec)   p_kst 1.295612e-04   p_cons 7.515487e-01   p_joint 1.295612e-04

Joint ci ratio: 1.651976e-01	ci left: 1.190076e-04	ci right 1.406548e-04	k: 562	n:4340000
Cons ci ratio: 1.081894e-03	ci left: 7.511406e-01	ci right 7.519540e-01	k: 3261716	n:4340000
KS ci ratio: 1.651976e-01	ci left: 1.190076e-04	ci right 1.406548e-04	k: 562	n:4340000
AHCTF1   4340000 perm   9434 sec   (460 perm/sec)   p_kst 1.294931e-04   p_cons 7.515475e-01   p_joint 1.294931e-04

Joint ci ratio: 1.651976e-01	ci left: 1.187340e-04	ci right 1.403314e-04	k: 562	n:4350000
Cons ci ratio: 1.080685e-03	ci left: 7.511290e-01	ci right 7.519414e-01	k: 3269179	n:4350000
KS ci ratio: 1.651976e-01	ci left: 1.187340e-04	ci right 1.403314e-04	k: 562	n:4350000
AHCTF1   4350000 perm   9474 sec   (459 perm/sec)   p_kst 1.291954e-04   p_cons 7.515354e-01   p_joint 1.291954e-04

Joint ci ratio: 1.650511e-01	ci left: 1.186816e-04	ci right 1.402484e-04	k: 563	n:4360000
Cons ci ratio: 1.079452e-03	ci left: 7.511269e-01	ci right 7.519384e-01	k: 3276683	n:4360000
KS ci ratio: 1.650511e-01	ci left: 1.186816e-04	ci right 1.402484e-04	k: 563	n:4360000
AHCTF1   4360000 perm   9514 sec   (458 perm/sec)   p_kst 1.291284e-04   p_cons 7.515328e-01   p_joint 1.291284e-04

Joint ci ratio: 1.647592e-01	ci left: 1.188488e-04	ci right 1.404040e-04	k: 565	n:4370000
Cons ci ratio: 1.078250e-03	ci left: 7.511158e-01	ci right 7.519264e-01	k: 3284148	n:4370000
KS ci ratio: 1.647592e-01	ci left: 1.188488e-04	ci right 1.404040e-04	k: 565	n:4370000
AHCTF1   4370000 perm   9554 sec   (457 perm/sec)   p_kst 1.292906e-04   p_cons 7.515213e-01   p_joint 1.292906e-04

Joint ci ratio: 1.643243e-01	ci left: 1.192342e-04	ci right 1.407965e-04	k: 568	n:4380000
Cons ci ratio: 1.077024e-03	ci left: 7.511142e-01	ci right 7.519238e-01	k: 3291654	n:4380000
KS ci ratio: 1.643243e-01	ci left: 1.192342e-04	ci right 1.407965e-04	k: 568	n:4380000
AHCTF1   4380000 perm   9595 sec   (456 perm/sec)   p_kst 1.296804e-04   p_cons 7.515192e-01   p_joint 1.296804e-04

Joint ci ratio: 1.637496e-01	ci left: 1.198363e-04	ci right 1.414243e-04	k: 572	n:4390000
Cons ci ratio: 1.075817e-03	ci left: 7.511076e-01	ci right 7.519163e-01	k: 3299138	n:4390000
KS ci ratio: 1.637496e-01	ci left: 1.198363e-04	ci right 1.414243e-04	k: 572	n:4390000
AHCTF1   4390000 perm   9636 sec   (456 perm/sec)   p_kst 1.302961e-04   p_cons 7.515121e-01   p_joint 1.302961e-04

Joint ci ratio: 1.634646e-01	ci left: 1.199999e-04	ci right 1.415761e-04	k: 574	n:4400000
Cons ci ratio: 1.074587e-03	ci left: 7.511105e-01	ci right 7.519183e-01	k: 3306664	n:4400000
KS ci ratio: 1.634646e-01	ci left: 1.199999e-04	ci right 1.415761e-04	k: 574	n:4400000
AHCTF1   4400000 perm   9676 sec   (455 perm/sec)   p_kst 1.304545e-04   p_cons 7.515145e-01   p_joint 1.304545e-04

Joint ci ratio: 1.631810e-01	ci left: 1.201628e-04	ci right 1.417271e-04	k: 576	n:4410000
Cons ci ratio: 1.073403e-03	ci left: 7.510987e-01	ci right 7.519055e-01	k: 3314125	n:4410000
KS ci ratio: 1.631810e-01	ci left: 1.201628e-04	ci right 1.417271e-04	k: 576	n:4410000
AHCTF1   4410000 perm   9717 sec   (454 perm/sec)   p_kst 1.306122e-04   p_cons 7.515023e-01   p_joint 1.306122e-04

Joint ci ratio: 1.631811e-01	ci left: 1.198909e-04	ci right 1.414064e-04	k: 576	n:4420000
Cons ci ratio: 1.072213e-03	ci left: 7.510905e-01	ci right 7.518965e-01	k: 3321602	n:4420000
KS ci ratio: 1.631811e-01	ci left: 1.198909e-04	ci right 1.414064e-04	k: 576	n:4420000
AHCTF1   4420000 perm   9760 sec   (453 perm/sec)   p_kst 1.303167e-04   p_cons 7.514937e-01   p_joint 1.303167e-04

Joint ci ratio: 1.627585e-01	ci left: 1.202698e-04	ci right 1.417920e-04	k: 579	n:4430000
Cons ci ratio: 1.070988e-03	ci left: 7.510960e-01	ci right 7.519010e-01	k: 3329139	n:4430000
KS ci ratio: 1.627585e-01	ci left: 1.202698e-04	ci right 1.417920e-04	k: 579	n:4430000
AHCTF1   4430000 perm   9802 sec   (452 perm/sec)   p_kst 1.306998e-04   p_cons 7.514986e-01   p_joint 1.306998e-04

Joint ci ratio: 1.624786e-01	ci left: 1.204311e-04	ci right 1.419414e-04	k: 581	n:4440000
Cons ci ratio: 1.069829e-03	ci left: 7.510795e-01	ci right 7.518837e-01	k: 3336579	n:4440000
KS ci ratio: 1.624786e-01	ci left: 1.204311e-04	ci right 1.419414e-04	k: 581	n:4440000
AHCTF1   4440000 perm   9842 sec   (451 perm/sec)   p_kst 1.308559e-04   p_cons 7.514818e-01   p_joint 1.308559e-04

Joint ci ratio: 1.623392e-01	ci left: 1.203760e-04	ci right 1.418563e-04	k: 582	n:4450000
Cons ci ratio: 1.068576e-03	ci left: 7.510978e-01	ci right 7.519010e-01	k: 3344173	n:4450000
KS ci ratio: 1.623392e-01	ci left: 1.203760e-04	ci right 1.418563e-04	k: 582	n:4450000
AHCTF1   4450000 perm   9885 sec   (450 perm/sec)   p_kst 1.307865e-04   p_cons 7.514996e-01   p_joint 1.307865e-04

Joint ci ratio: 1.622001e-01	ci left: 1.203213e-04	ci right 1.417715e-04	k: 583	n:4460000
Cons ci ratio: 1.067379e-03	ci left: 7.510975e-01	ci right 7.518999e-01	k: 3351685	n:4460000
KS ci ratio: 1.622001e-01	ci left: 1.203213e-04	ci right 1.417715e-04	k: 583	n:4460000
AHCTF1   4460000 perm   9927 sec   (449 perm/sec)   p_kst 1.307175e-04   p_cons 7.514989e-01   p_joint 1.307175e-04

Joint ci ratio: 1.619231e-01	ci left: 1.204814e-04	ci right 1.419199e-04	k: 585	n:4470000
Cons ci ratio: 1.066179e-03	ci left: 7.511000e-01	ci right 7.519015e-01	k: 3359209	n:4470000
KS ci ratio: 1.619231e-01	ci left: 1.204814e-04	ci right 1.419199e-04	k: 585	n:4470000
AHCTF1   4470000 perm   9969 sec   (448 perm/sec)   p_kst 1.308725e-04   p_cons 7.515009e-01   p_joint 1.308725e-04

Joint ci ratio: 1.615101e-01	ci left: 1.208550e-04	ci right 1.422999e-04	k: 588	n:4480000
Cons ci ratio: 1.064963e-03	ci left: 7.511092e-01	ci right 7.519097e-01	k: 3366763	n:4480000
KS ci ratio: 1.615101e-01	ci left: 1.208550e-04	ci right 1.422999e-04	k: 588	n:4480000
AHCTF1   4480000 perm   10011 sec   (448 perm/sec)   p_kst 1.312500e-04   p_cons 7.515096e-01   p_joint 1.312500e-04

Joint ci ratio: 1.613732e-01	ci left: 1.207995e-04	ci right 1.422147e-04	k: 589	n:4490000
Cons ci ratio: 1.063781e-03	ci left: 7.511080e-01	ci right 7.519077e-01	k: 3374271	n:4490000
KS ci ratio: 1.613732e-01	ci left: 1.207995e-04	ci right 1.422147e-04	k: 589	n:4490000
AHCTF1   4490000 perm   10052 sec   (447 perm/sec)   p_kst 1.311804e-04   p_cons 7.515080e-01   p_joint 1.311804e-04

Joint ci ratio: 1.612366e-01	ci left: 1.207443e-04	ci right 1.421298e-04	k: 590	n:4500000
Cons ci ratio: 1.062618e-03	ci left: 7.511016e-01	ci right 7.519003e-01	k: 3381755	n:4500000
KS ci ratio: 1.612366e-01	ci left: 1.207443e-04	ci right 1.421298e-04	k: 590	n:4500000
AHCTF1   4500000 perm   10093 sec   (446 perm/sec)   p_kst 1.311111e-04   p_cons 7.515011e-01   p_joint 1.311111e-04

Joint ci ratio: 1.611004e-01	ci left: 1.206894e-04	ci right 1.420453e-04	k: 591	n:4510000
Cons ci ratio: 1.061426e-03	ci left: 7.511067e-01	ci right 7.519045e-01	k: 3389291	n:4510000
KS ci ratio: 1.611004e-01	ci left: 1.206894e-04	ci right 1.420453e-04	k: 591	n:4510000
AHCTF1   4510000 perm   10135 sec   (445 perm/sec)   p_kst 1.310421e-04   p_cons 7.515058e-01   p_joint 1.310421e-04

Joint ci ratio: 1.611004e-01	ci left: 1.204224e-04	ci right 1.417311e-04	k: 591	n:4520000
Cons ci ratio: 1.060277e-03	ci left: 7.510982e-01	ci right 7.518952e-01	k: 3396766	n:4520000
KS ci ratio: 1.611004e-01	ci left: 1.204224e-04	ci right 1.417311e-04	k: 591	n:4520000
AHCTF1   4520000 perm   10176 sec   (444 perm/sec)   p_kst 1.307522e-04   p_cons 7.514969e-01   p_joint 1.307522e-04

Joint ci ratio: 1.609646e-01	ci left: 1.203684e-04	ci right 1.416478e-04	k: 592	n:4530000
Cons ci ratio: 1.059116e-03	ci left: 7.510949e-01	ci right 7.518911e-01	k: 3404264	n:4530000
KS ci ratio: 1.609646e-01	ci left: 1.203684e-04	ci right 1.416478e-04	k: 592	n:4530000
AHCTF1   4530000 perm   10219 sec   (443 perm/sec)   p_kst 1.306843e-04   p_cons 7.514932e-01   p_joint 1.306843e-04

Joint ci ratio: 1.609646e-01	ci left: 1.201033e-04	ci right 1.413358e-04	k: 592	n:4540000
Cons ci ratio: 1.057928e-03	ci left: 7.511029e-01	ci right 7.518981e-01	k: 3411813	n:4540000
KS ci ratio: 1.609646e-01	ci left: 1.201033e-04	ci right 1.413358e-04	k: 592	n:4540000
AHCTF1   4540000 perm   10261 sec   (442 perm/sec)   p_kst 1.303965e-04   p_cons 7.515007e-01   p_joint 1.303965e-04

Joint ci ratio: 1.606938e-01	ci left: 1.202612e-04	ci right 1.414824e-04	k: 594	n:4550000
Cons ci ratio: 1.056732e-03	ci left: 7.511150e-01	ci right 7.519093e-01	k: 3419381	n:4550000
KS ci ratio: 1.606938e-01	ci left: 1.202612e-04	ci right 1.414824e-04	k: 594	n:4550000
AHCTF1   4550000 perm   10303 sec   (442 perm/sec)   p_kst 1.305495e-04   p_cons 7.515123e-01   p_joint 1.305495e-04

Joint ci ratio: 1.606938e-01	ci left: 1.199975e-04	ci right 1.411722e-04	k: 594	n:4560000
Cons ci ratio: 1.055585e-03	ci left: 7.511108e-01	ci right 7.519043e-01	k: 3426875	n:4560000
KS ci ratio: 1.606938e-01	ci left: 1.199975e-04	ci right 1.411722e-04	k: 594	n:4560000
AHCTF1   4560000 perm   10345 sec   (441 perm/sec)   p_kst 1.302632e-04   p_cons 7.515077e-01   p_joint 1.302632e-04

Joint ci ratio: 1.606939e-01	ci left: 1.197349e-04	ci right 1.408633e-04	k: 594	n:4570000
Cons ci ratio: 1.054429e-03	ci left: 7.511116e-01	ci right 7.519042e-01	k: 3434392	n:4570000
KS ci ratio: 1.606939e-01	ci left: 1.197349e-04	ci right 1.408633e-04	k: 594	n:4570000
AHCTF1   4570000 perm   10387 sec   (440 perm/sec)   p_kst 1.299781e-04   p_cons 7.515081e-01   p_joint 1.299781e-04

Joint ci ratio: 1.604244e-01	ci left: 1.198926e-04	ci right 1.410099e-04	k: 596	n:4580000
Cons ci ratio: 1.053247e-03	ci left: 7.511227e-01	ci right 7.519145e-01	k: 3441956	n:4580000
KS ci ratio: 1.604244e-01	ci left: 1.198926e-04	ci right 1.410099e-04	k: 596	n:4580000
AHCTF1   4580000 perm   10429 sec   (439 perm/sec)   p_kst 1.301310e-04   p_cons 7.515188e-01   p_joint 1.301310e-04

Joint ci ratio: 1.602903e-01	ci left: 1.198405e-04	ci right 1.409293e-04	k: 597	n:4590000
Cons ci ratio: 1.052113e-03	ci left: 7.511181e-01	ci right 7.519090e-01	k: 3449448	n:4590000
KS ci ratio: 1.602903e-01	ci left: 1.198405e-04	ci right 1.409293e-04	k: 597	n:4590000
AHCTF1   4590000 perm   10473 sec   (438 perm/sec)   p_kst 1.300654e-04   p_cons 7.515137e-01   p_joint 1.300654e-04

Joint ci ratio: 1.600229e-01	ci left: 1.199973e-04	ci right 1.410751e-04	k: 599	n:4600000
Cons ci ratio: 1.050948e-03	ci left: 7.511259e-01	ci right 7.519159e-01	k: 3456997	n:4600000
KS ci ratio: 1.600229e-01	ci left: 1.199973e-04	ci right 1.410751e-04	k: 599	n:4600000
AHCTF1   4600000 perm   10517 sec   (437 perm/sec)   p_kst 1.302174e-04   p_cons 7.515211e-01   p_joint 1.302174e-04

Joint ci ratio: 1.600229e-01	ci left: 1.197370e-04	ci right 1.407691e-04	k: 599	n:4610000
Cons ci ratio: 1.049786e-03	ci left: 7.511341e-01	ci right 7.519233e-01	k: 3464548	n:4610000
KS ci ratio: 1.600229e-01	ci left: 1.197370e-04	ci right 1.407691e-04	k: 599	n:4610000
AHCTF1   4610000 perm   10560 sec   (437 perm/sec)   p_kst 1.299349e-04   p_cons 7.515289e-01   p_joint 1.299349e-04

Joint ci ratio: 1.597568e-01	ci left: 1.198934e-04	ci right 1.409146e-04	k: 601	n:4620000
Cons ci ratio: 1.048616e-03	ci left: 7.511464e-01	ci right 7.519347e-01	k: 3472118	n:4620000
KS ci ratio: 1.597568e-01	ci left: 1.198934e-04	ci right 1.409146e-04	k: 601	n:4620000
AHCTF1   4620000 perm   10603 sec   (436 perm/sec)   p_kst 1.300866e-04   p_cons 7.515407e-01   p_joint 1.300866e-04

Joint ci ratio: 1.597569e-01	ci left: 1.196345e-04	ci right 1.406103e-04	k: 601	n:4630000
Cons ci ratio: 1.047526e-03	ci left: 7.511314e-01	ci right 7.519188e-01	k: 3479562	n:4630000
KS ci ratio: 1.597569e-01	ci left: 1.196345e-04	ci right 1.406103e-04	k: 601	n:4630000
AHCTF1   4630000 perm   10646 sec   (435 perm/sec)   p_kst 1.298056e-04   p_cons 7.515253e-01   p_joint 1.298056e-04

Joint ci ratio: 1.596244e-01	ci left: 1.195836e-04	ci right 1.405314e-04	k: 602	n:4640000
Cons ci ratio: 1.046398e-03	ci left: 7.511313e-01	ci right 7.519179e-01	k: 3487075	n:4640000
KS ci ratio: 1.596244e-01	ci left: 1.195836e-04	ci right 1.405314e-04	k: 602	n:4640000
AHCTF1   4640000 perm   10689 sec   (434 perm/sec)   p_kst 1.297414e-04   p_cons 7.515248e-01   p_joint 1.297414e-04

Joint ci ratio: 1.592287e-01	ci left: 1.199458e-04	ci right 1.409000e-04	k: 605	n:4650000
Cons ci ratio: 1.045233e-03	ci left: 7.511459e-01	ci right 7.519316e-01	k: 3494656	n:4650000
KS ci ratio: 1.592287e-01	ci left: 1.199458e-04	ci right 1.409000e-04	k: 605	n:4650000
AHCTF1   4650000 perm   10732 sec   (433 perm/sec)   p_kst 1.301075e-04   p_cons 7.515389e-01   p_joint 1.301075e-04

Joint ci ratio: 1.590975e-01	ci left: 1.198945e-04	ci right 1.408208e-04	k: 606	n:4660000
Cons ci ratio: 1.044116e-03	ci left: 7.511443e-01	ci right 7.519292e-01	k: 3502162	n:4660000
KS ci ratio: 1.590975e-01	ci left: 1.198945e-04	ci right 1.408208e-04	k: 606	n:4660000
AHCTF1   4660000 perm   10774 sec   (433 perm/sec)   p_kst 1.300429e-04   p_cons 7.515369e-01   p_joint 1.300429e-04

Joint ci ratio: 1.588360e-01	ci left: 1.200490e-04	ci right 1.409645e-04	k: 608	n:4670000
Cons ci ratio: 1.042940e-03	ci left: 7.511654e-01	ci right 7.519495e-01	k: 3509774	n:4670000
KS ci ratio: 1.588360e-01	ci left: 1.200490e-04	ci right 1.409645e-04	k: 608	n:4670000
AHCTF1   4670000 perm   10818 sec   (432 perm/sec)   p_kst 1.301927e-04   p_cons 7.515576e-01   p_joint 1.301927e-04

Joint ci ratio: 1.587058e-01	ci left: 1.199976e-04	ci right 1.408855e-04	k: 609	n:4680000
Cons ci ratio: 1.041803e-03	ci left: 7.511736e-01	ci right 7.519568e-01	k: 3517326	n:4680000
KS ci ratio: 1.587058e-01	ci left: 1.199976e-04	ci right 1.408855e-04	k: 609	n:4680000
AHCTF1   4680000 perm   10861 sec   (431 perm/sec)   p_kst 1.301282e-04   p_cons 7.515654e-01   p_joint 1.301282e-04

Joint ci ratio: 1.587058e-01	ci left: 1.197418e-04	ci right 1.405851e-04	k: 609	n:4690000
Cons ci ratio: 1.040700e-03	ci left: 7.511711e-01	ci right 7.519535e-01	k: 3524828	n:4690000
KS ci ratio: 1.587058e-01	ci left: 1.197418e-04	ci right 1.405851e-04	k: 609	n:4690000
AHCTF1   4690000 perm   10905 sec   (430 perm/sec)   p_kst 1.298507e-04   p_cons 7.515625e-01   p_joint 1.298507e-04

Joint ci ratio: 1.585759e-01	ci left: 1.196913e-04	ci right 1.405072e-04	k: 610	n:4700000
Cons ci ratio: 1.039645e-03	ci left: 7.511527e-01	ci right 7.519342e-01	k: 3532255	n:4700000
KS ci ratio: 1.585759e-01	ci left: 1.196913e-04	ci right 1.405072e-04	k: 610	n:4700000
AHCTF1   4700000 perm   10948 sec   (429 perm/sec)   p_kst 1.297872e-04   p_cons 7.515436e-01   p_joint 1.297872e-04

Joint ci ratio: 1.584463e-01	ci left: 1.196411e-04	ci right 1.404296e-04	k: 611	n:4710000
Cons ci ratio: 1.038552e-03	ci left: 7.511490e-01	ci right 7.519297e-01	k: 3539751	n:4710000
KS ci ratio: 1.584463e-01	ci left: 1.196411e-04	ci right 1.404296e-04	k: 611	n:4710000
AHCTF1   4710000 perm   10991 sec   (429 perm/sec)   p_kst 1.297240e-04   p_cons 7.515395e-01   p_joint 1.297240e-04

Joint ci ratio: 1.575478e-01	ci left: 1.208120e-04	ci right 1.416737e-04	k: 618	n:4720000
Cons ci ratio: 1.037464e-03	ci left: 7.511449e-01	ci right 7.519247e-01	k: 3547245	n:4720000
KS ci ratio: 1.575478e-01	ci left: 1.208120e-04	ci right 1.416737e-04	k: 618	n:4720000
AHCTF1   4720000 perm   11037 sec   (428 perm/sec)   p_kst 1.309322e-04   p_cons 7.515350e-01   p_joint 1.309322e-04

Joint ci ratio: 1.572938e-01	ci left: 1.209628e-04	ci right 1.418137e-04	k: 620	n:4730000
Cons ci ratio: 1.036401e-03	ci left: 7.511331e-01	ci right 7.519122e-01	k: 3554703	n:4730000
KS ci ratio: 1.572938e-01	ci left: 1.209628e-04	ci right 1.418137e-04	k: 620	n:4730000
AHCTF1   4730000 perm   11080 sec   (427 perm/sec)   p_kst 1.310782e-04   p_cons 7.515228e-01   p_joint 1.310782e-04

Joint ci ratio: 1.571674e-01	ci left: 1.209103e-04	ci right 1.417337e-04	k: 621	n:4740000
Cons ci ratio: 1.035324e-03	ci left: 7.511272e-01	ci right 7.519054e-01	k: 3562188	n:4740000
KS ci ratio: 1.571674e-01	ci left: 1.209103e-04	ci right 1.417337e-04	k: 621	n:4740000
AHCTF1   4740000 perm   11124 sec   (426 perm/sec)   p_kst 1.310127e-04   p_cons 7.515165e-01   p_joint 1.310127e-04

Joint ci ratio: 1.569153e-01	ci left: 1.210602e-04	ci right 1.418729e-04	k: 623	n:4750000
Cons ci ratio: 1.034231e-03	ci left: 7.511288e-01	ci right 7.519063e-01	k: 3569709	n:4750000
KS ci ratio: 1.569153e-01	ci left: 1.210602e-04	ci right 1.418729e-04	k: 623	n:4750000
AHCTF1   4750000 perm   11168 sec   (425 perm/sec)   p_kst 1.311579e-04   p_cons 7.515177e-01   p_joint 1.311579e-04

Joint ci ratio: 1.569153e-01	ci left: 1.208059e-04	ci right 1.415749e-04	k: 623	n:4760000
Cons ci ratio: 1.033129e-03	ci left: 7.511344e-01	ci right 7.519111e-01	k: 3577249	n:4760000
KS ci ratio: 1.569153e-01	ci left: 1.208059e-04	ci right 1.415749e-04	k: 623	n:4760000
AHCTF1   4760000 perm   11212 sec   (425 perm/sec)   p_kst 1.308824e-04   p_cons 7.515229e-01   p_joint 1.308824e-04

Joint ci ratio: 1.566644e-01	ci left: 1.209555e-04	ci right 1.417138e-04	k: 625	n:4770000
Cons ci ratio: 1.032100e-03	ci left: 7.511153e-01	ci right 7.518911e-01	k: 3584671	n:4770000
KS ci ratio: 1.566644e-01	ci left: 1.209555e-04	ci right 1.417138e-04	k: 625	n:4770000
AHCTF1   4770000 perm   11257 sec   (424 perm/sec)   p_kst 1.310273e-04   p_cons 7.515034e-01   p_joint 1.310273e-04

Joint ci ratio: 1.565394e-01	ci left: 1.209034e-04	ci right 1.416347e-04	k: 626	n:4780000
Cons ci ratio: 1.031035e-03	ci left: 7.511100e-01	ci right 7.518851e-01	k: 3592159	n:4780000
KS ci ratio: 1.565394e-01	ci left: 1.209034e-04	ci right 1.416347e-04	k: 626	n:4780000
AHCTF1   4780000 perm   11302 sec   (423 perm/sec)   p_kst 1.309623e-04   p_cons 7.514977e-01   p_joint 1.309623e-04

Joint ci ratio: 1.565395e-01	ci left: 1.206510e-04	ci right 1.413390e-04	k: 626	n:4790000
Cons ci ratio: 1.029955e-03	ci left: 7.511115e-01	ci right 7.518857e-01	k: 3599679	n:4790000
KS ci ratio: 1.565395e-01	ci left: 1.206510e-04	ci right 1.413390e-04	k: 626	n:4790000
AHCTF1   4790000 perm   11346 sec   (422 perm/sec)   p_kst 1.306889e-04   p_cons 7.514987e-01   p_joint 1.306889e-04

Joint ci ratio: 1.560425e-01	ci left: 1.212004e-04	ci right 1.419105e-04	k: 630	n:4800000
Cons ci ratio: 1.028910e-03	ci left: 7.511019e-01	ci right 7.518753e-01	k: 3607146	n:4800000
KS ci ratio: 1.560425e-01	ci left: 1.212004e-04	ci right 1.419105e-04	k: 630	n:4800000
AHCTF1   4800000 perm   11390 sec   (421 perm/sec)   p_kst 1.312500e-04   p_cons 7.514888e-01   p_joint 1.312500e-04

Joint ci ratio: 1.559190e-01	ci left: 1.211482e-04	ci right 1.418315e-04	k: 631	n:4810000
Cons ci ratio: 1.027855e-03	ci left: 7.510967e-01	ci right 7.518693e-01	k: 3614634	n:4810000
KS ci ratio: 1.559190e-01	ci left: 1.211482e-04	ci right 1.418315e-04	k: 631	n:4810000
AHCTF1   4810000 perm   11435 sec   (421 perm/sec)   p_kst 1.311850e-04   p_cons 7.514832e-01   p_joint 1.311850e-04

Joint ci ratio: 1.555502e-01	ci left: 1.214950e-04	ci right 1.421838e-04	k: 634	n:4820000
Cons ci ratio: 1.026814e-03	ci left: 7.510876e-01	ci right 7.518594e-01	k: 3622103	n:4820000
KS ci ratio: 1.555502e-01	ci left: 1.214950e-04	ci right 1.421838e-04	k: 634	n:4820000
AHCTF1   4820000 perm   11479 sec   (420 perm/sec)   p_kst 1.315353e-04   p_cons 7.514737e-01   p_joint 1.315353e-04

Joint ci ratio: 1.554279e-01	ci left: 1.214425e-04	ci right 1.421046e-04	k: 635	n:4830000
Cons ci ratio: 1.025749e-03	ci left: 7.510887e-01	ci right 7.518597e-01	k: 3629621	n:4830000
KS ci ratio: 1.554279e-01	ci left: 1.214425e-04	ci right 1.421046e-04	k: 635	n:4830000
AHCTF1   4830000 perm   11523 sec   (419 perm/sec)   p_kst 1.314700e-04   p_cons 7.514743e-01   p_joint 1.314700e-04

Joint ci ratio: 1.551840e-01	ci left: 1.215887e-04	ci right 1.422402e-04	k: 637	n:4840000
Cons ci ratio: 1.024682e-03	ci left: 7.510916e-01	ci right 7.518618e-01	k: 3637148	n:4840000
KS ci ratio: 1.551840e-01	ci left: 1.215887e-04	ci right 1.422402e-04	k: 637	n:4840000
AHCTF1   4840000 perm   11567 sec   (418 perm/sec)   p_kst 1.316116e-04   p_cons 7.514769e-01   p_joint 1.316116e-04

Joint ci ratio: 1.548204e-01	ci left: 1.219326e-04	ci right 1.425895e-04	k: 640	n:4850000
Cons ci ratio: 1.023600e-03	ci left: 7.511009e-01	ci right 7.518703e-01	k: 3644706	n:4850000
KS ci ratio: 1.548204e-01	ci left: 1.219326e-04	ci right 1.425895e-04	k: 640	n:4850000
AHCTF1   4850000 perm   11611 sec   (418 perm/sec)   p_kst 1.319588e-04   p_cons 7.514858e-01   p_joint 1.319588e-04

Joint ci ratio: 1.546998e-01	ci left: 1.218795e-04	ci right 1.425098e-04	k: 641	n:4860000
Cons ci ratio: 1.022595e-03	ci left: 7.510836e-01	ci right 7.518523e-01	k: 3652135	n:4860000
KS ci ratio: 1.546998e-01	ci left: 1.218795e-04	ci right 1.425098e-04	k: 641	n:4860000
AHCTF1   4860000 perm   11656 sec   (417 perm/sec)   p_kst 1.318930e-04   p_cons 7.514681e-01   p_joint 1.318930e-04

Joint ci ratio: 1.544594e-01	ci left: 1.220240e-04	ci right 1.426437e-04	k: 643	n:4870000
Cons ci ratio: 1.021528e-03	ci left: 7.510901e-01	ci right 7.518579e-01	k: 3659679	n:4870000
KS ci ratio: 1.544594e-01	ci left: 1.220240e-04	ci right 1.426437e-04	k: 643	n:4870000
AHCTF1   4870000 perm   11702 sec   (416 perm/sec)   p_kst 1.320329e-04   p_cons 7.514741e-01   p_joint 1.320329e-04

Joint ci ratio: 1.542201e-01	ci left: 1.221680e-04	ci right 1.427771e-04	k: 645	n:4880000
Cons ci ratio: 1.020451e-03	ci left: 7.511016e-01	ci right 7.518686e-01	k: 3667248	n:4880000
KS ci ratio: 1.542201e-01	ci left: 1.221680e-04	ci right 1.427771e-04	k: 645	n:4880000
AHCTF1   4880000 perm   11747 sec   (415 perm/sec)   p_kst 1.321721e-04   p_cons 7.514852e-01   p_joint 1.321721e-04

Joint ci ratio: 1.542201e-01	ci left: 1.219182e-04	ci right 1.424851e-04	k: 645	n:4890000
Cons ci ratio: 1.019416e-03	ci left: 7.510987e-01	ci right 7.518650e-01	k: 3674747	n:4890000
KS ci ratio: 1.542201e-01	ci left: 1.219182e-04	ci right 1.424851e-04	k: 645	n:4890000
AHCTF1   4890000 perm   11797 sec   (415 perm/sec)   p_kst 1.319018e-04   p_cons 7.514820e-01   p_joint 1.319018e-04

Joint ci ratio: 1.541009e-01	ci left: 1.218656e-04	ci right 1.424063e-04	k: 646	n:4900000
Cons ci ratio: 1.018381e-03	ci left: 7.510967e-01	ci right 7.518622e-01	k: 3682250	n:4900000
KS ci ratio: 1.541009e-01	ci left: 1.218656e-04	ci right 1.424063e-04	k: 646	n:4900000
AHCTF1   4900000 perm   11843 sec   (414 perm/sec)   p_kst 1.318367e-04   p_cons 7.514796e-01   p_joint 1.318367e-04

Joint ci ratio: 1.539820e-01	ci left: 1.218132e-04	ci right 1.423277e-04	k: 647	n:4910000
Cons ci ratio: 1.017304e-03	ci left: 7.511118e-01	ci right 7.518765e-01	k: 3689837	n:4910000
KS ci ratio: 1.539820e-01	ci left: 1.218132e-04	ci right 1.423277e-04	k: 647	n:4910000
AHCTF1   4910000 perm   11887 sec   (413 perm/sec)   p_kst 1.317719e-04   p_cons 7.514943e-01   p_joint 1.317719e-04

Joint ci ratio: 1.533913e-01	ci left: 1.225428e-04	ci right 1.430938e-04	k: 652	n:4920000
Cons ci ratio: 1.016296e-03	ci left: 7.511024e-01	ci right 7.518664e-01	k: 3697304	n:4920000
KS ci ratio: 1.533913e-01	ci left: 1.225428e-04	ci right 1.430938e-04	k: 652	n:4920000
AHCTF1   4920000 perm   11933 sec   (412 perm/sec)   p_kst 1.325203e-04   p_cons 7.514846e-01   p_joint 1.325203e-04

Joint ci ratio: 1.533913e-01	ci left: 1.222942e-04	ci right 1.428035e-04	k: 652	n:4930000
Cons ci ratio: 1.015263e-03	ci left: 7.511035e-01	ci right 7.518666e-01	k: 3704822	n:4930000
KS ci ratio: 1.533913e-01	ci left: 1.222942e-04	ci right 1.428035e-04	k: 652	n:4930000
AHCTF1   4930000 perm   11981 sec   (412 perm/sec)   p_kst 1.322515e-04   p_cons 7.514852e-01   p_joint 1.322515e-04

Joint ci ratio: 1.531569e-01	ci left: 1.224360e-04	ci right 1.429348e-04	k: 654	n:4940000
Cons ci ratio: 1.014237e-03	ci left: 7.511031e-01	ci right 7.518655e-01	k: 3712333	n:4940000
KS ci ratio: 1.531569e-01	ci left: 1.224360e-04	ci right 1.429348e-04	k: 654	n:4940000
AHCTF1   4940000 perm   12026 sec   (411 perm/sec)   p_kst 1.323887e-04   p_cons 7.514844e-01   p_joint 1.323887e-04

Joint ci ratio: 1.531569e-01	ci left: 1.221886e-04	ci right 1.426460e-04	k: 654	n:4950000
Cons ci ratio: 1.013166e-03	ci left: 7.511203e-01	ci right 7.518819e-01	k: 3719931	n:4950000
KS ci ratio: 1.531569e-01	ci left: 1.221886e-04	ci right 1.426460e-04	k: 654	n:4950000
AHCTF1   4950000 perm   12071 sec   (410 perm/sec)   p_kst 1.321212e-04   p_cons 7.515012e-01   p_joint 1.321212e-04

Joint ci ratio: 1.528074e-01	ci left: 1.225240e-04	ci right 1.429864e-04	k: 657	n:4960000
Cons ci ratio: 1.012151e-03	ci left: 7.511182e-01	ci right 7.518791e-01	k: 3727434	n:4960000
KS ci ratio: 1.528074e-01	ci left: 1.225240e-04	ci right 1.429864e-04	k: 657	n:4960000
AHCTF1   4960000 perm   12117 sec   (409 perm/sec)   p_kst 1.324597e-04   p_cons 7.514988e-01   p_joint 1.324597e-04

Joint ci ratio: 1.525756e-01	ci left: 1.226645e-04	ci right 1.431165e-04	k: 659	n:4970000
Cons ci ratio: 1.011139e-03	ci left: 7.511160e-01	ci right 7.518761e-01	k: 3734936	n:4970000
KS ci ratio: 1.525756e-01	ci left: 1.226645e-04	ci right 1.431165e-04	k: 659	n:4970000
AHCTF1   4970000 perm   12162 sec   (409 perm/sec)   p_kst 1.325956e-04   p_cons 7.514962e-01   p_joint 1.325956e-04

Joint ci ratio: 1.524602e-01	ci left: 1.226113e-04	ci right 1.430376e-04	k: 660	n:4980000
Cons ci ratio: 1.010110e-03	ci left: 7.511214e-01	ci right 7.518807e-01	k: 3742476	n:4980000
KS ci ratio: 1.524602e-01	ci left: 1.226113e-04	ci right 1.430376e-04	k: 660	n:4980000
AHCTF1   4980000 perm   12209 sec   (408 perm/sec)   p_kst 1.325301e-04   p_cons 7.515012e-01   p_joint 1.325301e-04

Joint ci ratio: 1.524602e-01	ci left: 1.223656e-04	ci right 1.427509e-04	k: 660	n:4990000
Cons ci ratio: 1.009139e-03	ci left: 7.511064e-01	ci right 7.518649e-01	k: 3749914	n:4990000
KS ci ratio: 1.524602e-01	ci left: 1.223656e-04	ci right 1.427509e-04	k: 660	n:4990000
AHCTF1   4990000 perm   12255 sec   (407 perm/sec)   p_kst 1.322645e-04   p_cons 7.514858e-01   p_joint 1.322645e-04

Joint ci ratio: 1.520010e-01	ci left: 1.228904e-04	ci right 1.432959e-04	k: 664	n:5000000
Cons ci ratio: 1.008142e-03	ci left: 7.511020e-01	ci right 7.518597e-01	k: 3757405	n:5000000
KS ci ratio: 1.520010e-01	ci left: 1.228904e-04	ci right 1.432959e-04	k: 664	n:5000000
AHCTF1   5000000 perm   12301 sec   (406 perm/sec)   p_kst 1.328000e-04   p_cons 7.514810e-01   p_joint 1.328000e-04

Outputting figure to mutsig2_images.part000000000005/AHCTF1.2_6972_5000000_0.0001328_0.75148_0.0001328.png
                gene_name: AHCTF1
               theta_stop: 0.15 
                    nperm: 5000000 
                     p_ks: 0.00013 
        ci_ks_bounds_left: 0.00012 
       ci_ks_bounds_right: 0.00014 
                   p_cons: 0.75 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.75 
                  p_joint: 0.00013 
     ci_joint_bounds_left: 0.00012 
    ci_joint_bounds_right: 0.00014 

Current progress: 67 percent done.
AHR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.778118e-03	ci left: 9.935271e-01	ci right 9.963728e-01	k: 9951	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: 1.094953e-01	ci left: 1.073461e-01	ci right 1.198799e-01	k: 1135	n:10000
AHR   10000 perm   2 sec   (5694 perm/sec)   p_kst 1.135000e-01   p_cons 9.906000e-01   p_joint 9.951000e-01

Joint ci ratio: 4.171258e-03	ci left: 9.757668e-01	ci right 9.798927e-01	k: 19558	n:20000
Cons ci ratio: 2.848104e-03	ci left: 9.880955e-01	ci right 9.909595e-01	k: 19792	n:20000
KS ci ratio: 7.810667e-02	ci left: 1.074644e-01	ci right 1.162488e-01	k: 2236	n:20000
AHR   20000 perm   4 sec   (4782 perm/sec)   p_kst 1.118000e-01   p_cons 9.896000e-01   p_joint 9.779000e-01

Outputting figure to mutsig2_images.part000000000005/AHR.2_2591_20000_0.1118_0.9896_0.9779.png
                gene_name: AHR
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 83 percent done.
AIFM2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.404691e-02	ci left: 2.107297e-01	ci right 2.270344e-01	k: 2188	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: 5.633897e-02	ci left: 3.169137e-01	ci right 3.353876e-01	k: 3261	n:10000
AIFM2   10000 perm   2 sec   (6508 perm/sec)   p_kst 3.261000e-01   p_cons 1.890000e-01   p_joint 2.188000e-01

Outputting figure to mutsig2_images.part000000000005/AIFM2.2_1154_10000_0.3261_0.189_0.2188.png
                gene_name: AIFM2
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    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.165.3896/
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/181708/iteration1/scatter.0000000005
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 5 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119492: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000006> was used as the working directory.
Started at Wed Oct 10 10:41:37 2012
Results reported at Wed Oct 10 10:44:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000006.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000006.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 6  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    177.51 sec.
    Max Memory :      1409 MB
    Max Swap   :      3854 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.165.3896/
-whichjob
6
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 6: processing genes 453 - 543
Calculating significance of each gene.
Using projection method.
453	AKAP5	1
454	AKAP6	1.988552e-01
455	AKAP7	1
456	AKAP8	1
457	AKAP8L	2.222401e-01
458	AKAP9	2.296428e-01
459	AKD1	2.778954e-02
460	AKIRIN1	1
461	AKIRIN2	1
462	AKNA	1
463	AKNAD1	1
464	AKR1A1	1
465	AKR1B1	1
466	AKR1B10	1
467	AKR1B15	7.254706e-02
468	AKR1C1	1
469	AKR1C2	1
470	AKR1C3	1
471	AKR1C4	3.503388e-02
472	AKR1D1	1
473	AKR1E2	1
474	AKR7A2	1
475	AKR7A3	1
476	AKR7L	8.488358e-02
477	AKT1	1
478	AKT1S1	1
479	AKT2	1
480	AKT3	1
481	AKTIP	1
482	ALAD	1
483	ALAS1	1
484	ALAS2	1
485	ALB	1
486	ALCAM	1.559017e-01
487	ALDH16A1	1
488	ALDH18A1	1
489	ALDH1A1	1
490	ALDH1A2	1
491	ALDH1A3	1
492	ALDH1B1	1
493	ALDH1L1	1
494	ALDH1L2	1
495	ALDH2	1
496	ALDH3A1	1
497	ALDH3A2	1
498	ALDH3B1	1.410111e-01
499	ALDH3B2	1.185174e-01
500	ALDH4A1	1
501	ALDH5A1	1
502	ALDH6A1	1
503	ALDH7A1	1
504	ALDH8A1	1
505	ALDH9A1	1.848058e-01
506	ALDOA	1
507	ALDOB	1
508	ALDOC	1
509	ALG1	1
510	ALG10	1
511	ALG10B	1
512	ALG11	1
513	ALG12	1
514	ALG13	1
515	ALG14	1
516	ALG1L	1
517	ALG1L2	1
518	ALG2	1
519	ALG3	1
520	ALG5	1
521	ALG6	1.245542e-01
522	ALG8	1
523	ALG9	1
524	ALK	1
525	ALKBH1	1
526	ALKBH2	1
527	ALKBH3	1
528	ALKBH4	1
529	ALKBH5	1
530	ALKBH6	1
531	ALKBH7	1
532	ALKBH8	1
533	ALLC	1
534	ALMS1	5.950402e-01
535	ALOX12	1
536	ALOX12B	1
537	ALOX15	2.890601e-01
538	ALOX15B	1
539	ALOX5	1.153916e-01
540	ALOX5AP	1
541	ALOXE3	1
542	ALPI	1
543	ALPK1	3.064109e-01
Done

Running MutSig 2:
Scatter job 6: processing genes 453 - 543
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
AKAP9
Processing conservation and coverage...
83% 
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: 1.645643e-02	ci left: 8.430535e-01	ci right 8.571419e-01	k: 8502	n:10000
KS ci ratio: 2.513674e-02	ci left: 6.995839e-01	ci right 7.174944e-01	k: 7086	n:10000
AKAP9   10000 perm   4 sec   (2354 perm/sec)   p_kst 7.086000e-01   p_cons 8.502000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000006/AKAP9.3_11924_10000_0.7086_0.8502_1.png
                gene_name: AKAP9
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.85 
      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: 25 percent done.
AKAP6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.440949e-02	ci left: 1.698592e-01	ci right 1.849292e-01	k: 1773	n:10000
Cons ci ratio: 2.289722e-02	ci left: 7.369431e-01	ci right 7.541136e-01	k: 7456	n:10000
KS ci ratio: 2.198857e-01	ci left: 2.740624e-02	ci right 3.427066e-02	k: 307	n:10000
AKAP6   10000 perm   3 sec   (3853 perm/sec)   p_kst 3.070000e-02   p_cons 7.456000e-01   p_joint 1.773000e-01

Joint ci ratio: 3.984223e-02	ci left: 3.196038e-01	ci right 3.326468e-01	k: 6522	n:20000
Cons ci ratio: 1.625069e-02	ci left: 7.380929e-01	ci right 7.502360e-01	k: 14884	n:20000
KS ci ratio: 1.588432e-01	ci left: 2.719860e-02	ci right 3.193948e-02	k: 590	n:20000
AKAP6   20000 perm   6 sec   (3384 perm/sec)   p_kst 2.950000e-02   p_cons 7.442000e-01   p_joint 3.261000e-01

Joint ci ratio: 4.685089e-02	ci left: 1.847485e-01	ci right 1.936451e-01	k: 5675	n:30000
Cons ci ratio: 1.281921e-02	ci left: 7.522059e-01	ci right 7.619442e-01	k: 22713	n:30000
KS ci ratio: 1.275258e-01	ci left: 2.858305e-02	ci right 3.250857e-02	k: 915	n:30000
AKAP6   30000 perm   9 sec   (3261 perm/sec)   p_kst 3.050000e-02   p_cons 7.571000e-01   p_joint 1.891667e-01

Joint ci ratio: 4.073688e-02	ci left: 1.841317e-01	ci right 1.918136e-01	k: 7518	n:40000
Cons ci ratio: 1.112440e-02	ci left: 7.521121e-01	ci right 7.605507e-01	k: 30254	n:40000
KS ci ratio: 1.118339e-01	ci left: 2.813107e-02	ci right 3.148765e-02	k: 1191	n:40000
AKAP6   40000 perm   13 sec   (3173 perm/sec)   p_kst 2.977500e-02   p_cons 7.563500e-01   p_joint 1.879500e-01

Joint ci ratio: 3.643802e-02	ci left: 1.845239e-01	ci right 1.913923e-01	k: 9397	n:50000
Cons ci ratio: 9.978317e-03	ci left: 7.515070e-01	ci right 7.590633e-01	k: 37765	n:50000
KS ci ratio: 9.978618e-02	ci left: 2.844404e-02	ci right 3.145086e-02	k: 1496	n:50000
AKAP6   50000 perm   16 sec   (3107 perm/sec)   p_kst 2.992000e-02   p_cons 7.553000e-01   p_joint 1.879400e-01

Outputting figure to mutsig2_images.part000000000006/AKAP6.2_7008_50000_0.02992_0.7553_0.18794.png
                gene_name: AKAP6
               theta_stop: 0.100 
                    nperm: 50000 
                     p_ks: 0.030 
        ci_ks_bounds_left: 0.028 
       ci_ks_bounds_right: 0.031 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.76 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.19 

Current progress: 50 percent done.
AKD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.766254e-02	ci left: 3.937641e-01	ci right 4.130922e-01	k: 4034	n:10000
Cons ci ratio: 5.728790e-02	ci left: 3.096702e-01	ci right 3.280354e-01	k: 3188	n:10000
KS ci ratio: 9.526235e-02	ci left: 1.378591e-01	ci right 1.517485e-01	k: 1447	n:10000
AKD1   10000 perm   2 sec   (4077 perm/sec)   p_kst 1.447000e-01   p_cons 3.188000e-01   p_joint 4.034000e-01

Outputting figure to mutsig2_images.part000000000006/AKD1.2_5908_10000_0.1447_0.3188_0.4034.png
                gene_name: AKD1
               theta_stop: 0.095 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.40 
     ci_joint_bounds_left: 0.39 
    ci_joint_bounds_right: 0.41 

Current progress: 75 percent done.
ALMS1
Processing conservation and coverage...
79% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.569727e-02	ci left: 5.367804e-01	ci right 5.563924e-01	k: 5466	n:10000
Cons ci ratio: 5.305878e-03	ci left: 9.793064e-01	ci right 9.846075e-01	k: 9821	n:10000
KS ci ratio: 1.356182e-01	ci left: 7.184865e-02	ci right 8.239926e-02	k: 770	n:10000
ALMS1   10000 perm   4 sec   (2605 perm/sec)   p_kst 7.700000e-02   p_cons 9.821000e-01   p_joint 5.466000e-01

Joint ci ratio: 2.411785e-02	ci left: 5.622023e-01	ci right 5.759776e-01	k: 11382	n:20000
Cons ci ratio: 3.650168e-03	ci left: 9.811116e-01	ci right 9.847461e-01	k: 19660	n:20000
KS ci ratio: 9.671650e-02	ci left: 7.221756e-02	ci right 7.960630e-02	k: 1517	n:20000
ALMS1   20000 perm   8 sec   (2428 perm/sec)   p_kst 7.585000e-02   p_cons 9.830000e-01   p_joint 5.691000e-01

Outputting figure to mutsig2_images.part000000000006/ALMS1.2_12596_20000_0.07585_0.983_0.5691.png
                gene_name: ALMS1
               theta_stop: 0.097 
                    nperm: 20000 
                     p_ks: 0.076 
        ci_ks_bounds_left: 0.072 
       ci_ks_bounds_right: 0.080 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.98 
                  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.165.3896/
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/181708/iteration1/scatter.0000000006
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 6 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119495: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000007> was used as the working directory.
Started at Wed Oct 10 10:41:37 2012
Results reported at Wed Oct 10 10:45:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000007.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000007.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 7  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    280.46 sec.
    Max Memory :      1562 MB
    Max Swap   :      3892 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.165.3896/
-whichjob
7
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 7: processing genes 544 - 633
Calculating significance of each gene.
Using projection method.
544	ALPK2	1
545	ALPK3	1
546	ALPL	2.508673e-01
547	ALPP	1
548	ALPPL2	1
549	ALS2	1
550	ALS2CL	1
551	ALS2CR11	1
552	ALS2CR12	1
553	ALS2CR4	1
554	ALS2CR8	1
555	ALX1	1
556	ALX3	1
557	ALX4	1
558	AMAC1	7.412187e-02
559	AMAC1L2	1
560	AMAC1L3	1
561	AMACR	1.025052e-02
562	AMBN	1
563	AMBP	1
564	AMBRA1	3.827604e-01
565	AMD1	1
566	AMDHD1	1
567	AMDHD2	2.262268e-01
568	AMELX	1
569	AMELY	1
570	AMFR	1
571	AMH	1
572	AMHR2	1
573	AMICA1	1
574	AMIGO1	1.269658e-01
575	AMIGO2	1.287106e-01
576	AMIGO3	7.630016e-02
577	AMMECR1	1
578	AMMECR1L	1
579	AMN	1
580	AMN1	7.204644e-02
581	AMOT	1
582	AMOTL1	3.616069e-02
583	AMOTL2	1
584	AMPD1	1
585	AMPD2	1
586	AMPD3	1
587	AMPH	1
588	AMT	1
589	AMTN	1
590	AMY2A	1.197826e-01
591	AMY2B	4.761995e-02
592	AMZ1	1
593	AMZ2	1
594	ANAPC1	5.193392e-01
595	ANAPC10	1
596	ANAPC11	1
597	ANAPC13	1
598	ANAPC16	1
599	ANAPC2	1
600	ANAPC4	1
601	ANAPC5	1
602	ANAPC7	1
603	ANG	1
604	ANGEL1	1
605	ANGEL2	1
606	ANGPT1	1
607	ANGPT2	1
608	ANGPT4	1
609	ANGPTL1	1
610	ANGPTL2	1
611	ANGPTL3	2.006677e-01
612	ANGPTL4	1
613	ANGPTL5	1
614	ANGPTL6	1
615	ANGPTL7	1
616	ANK1	1.826062e-02
617	ANK2	3.312840e-01
618	ANK3	8.569987e-01
619	ANKAR	1.093049e-01
620	ANKDD1A	1
621	ANKFN1	1
622	ANKFY1	3.068201e-01
623	ANKH	1
624	ANKHD1	1
625	ANKHD1-EIF4EBP3	7.471222e-01
626	ANKIB1	1
627	ANKK1	1
628	ANKLE1	1
629	ANKLE2	5.448851e-02
630	ANKMY1	1.768198e-01
631	ANKMY2	1
632	ANKRA2	1
633	ANKRD1	1
Done

Running MutSig 2:
Scatter job 7: processing genes 544 - 633
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ANK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.946732e-02	ci left: 1.878651e-01	ci right 2.035126e-01	k: 1956	n:10000
Cons ci ratio: 5.205220e-02	ci left: 3.523733e-01	ci right 3.713072e-01	k: 3618	n:10000
KS ci ratio: 9.995174e-02	ci left: 1.265977e-01	ci right 1.400167e-01	k: 1332	n:10000
ANK1   10000 perm   3 sec   (3526 perm/sec)   p_kst 1.332000e-01   p_cons 3.618000e-01   p_joint 1.956000e-01

Outputting figure to mutsig2_images.part000000000007/ANK1.3_6298_10000_0.1332_0.3618_0.1956.png
                gene_name: ANK1
               theta_stop: 0.100 
                    nperm: 10000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.20 

Current progress: 14 percent done.
AMACR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.284655e-01	ci left: 6.526864e-03	ci right 1.016828e-02	k: 82	n:10000
Cons ci ratio: 7.561906e-02	ci left: 2.037281e-01	ci right 2.198401e-01	k: 2117	n:10000
KS ci ratio: 2.198857e-01	ci left: 2.740624e-02	ci right 3.427066e-02	k: 307	n:10000
AMACR   10000 perm   2 sec   (5720 perm/sec)   p_kst 3.070000e-02   p_cons 2.117000e-01   p_joint 8.200000e-03

Joint ci ratio: 3.232272e-01	ci left: 6.121310e-03	ci right 8.525270e-03	k: 145	n:20000
Cons ci ratio: 5.577657e-02	ci left: 1.924965e-01	ci right 2.035914e-01	k: 3960	n:20000
KS ci ratio: 1.556167e-01	ci left: 2.835269e-02	ci right 3.318501e-02	k: 614	n:20000
AMACR   20000 perm   4 sec   (4906 perm/sec)   p_kst 3.070000e-02   p_cons 1.980000e-01   p_joint 7.250000e-03

Joint ci ratio: 2.278841e-01	ci left: 8.653395e-03	ci right 1.090973e-02	k: 292	n:30000
Cons ci ratio: 4.548669e-02	ci left: 1.939000e-01	ci right 2.029585e-01	k: 5952	n:30000
KS ci ratio: 1.272395e-01	ci left: 2.871225e-02	ci right 3.264600e-02	k: 919	n:30000
AMACR   30000 perm   7 sec   (4539 perm/sec)   p_kst 3.063333e-02   p_cons 1.984000e-01   p_joint 9.733333e-03

Joint ci ratio: 1.965093e-01	ci left: 8.881628e-03	ci right 1.084051e-02	k: 393	n:40000
Cons ci ratio: 3.948375e-02	ci left: 1.937818e-01	ci right 2.016121e-01	k: 7907	n:40000
KS ci ratio: 1.091269e-01	ci left: 2.954216e-02	ci right 3.297633e-02	k: 1249	n:40000
AMACR   40000 perm   9 sec   (4517 perm/sec)   p_kst 3.122500e-02   p_cons 1.976750e-01   p_joint 9.825000e-03

Joint ci ratio: 1.740760e-01	ci left: 9.165546e-03	ci right 1.093203e-02	k: 501	n:50000
Cons ci ratio: 3.523100e-02	ci left: 1.949518e-01	ci right 2.019633e-01	k: 9922	n:50000
KS ci ratio: 9.739737e-02	ci left: 2.984958e-02	ci right 3.292515e-02	k: 1568	n:50000
AMACR   50000 perm   11 sec   (4490 perm/sec)   p_kst 3.136000e-02   p_cons 1.984400e-01   p_joint 1.002000e-02

Joint ci ratio: 1.696804e-01	ci left: 8.068202e-03	ci right 9.579883e-03	k: 528	n:60000
Cons ci ratio: 3.210690e-02	ci left: 1.957951e-01	ci right 2.022007e-01	k: 11939	n:60000
KS ci ratio: 8.924960e-02	ci left: 2.975803e-02	ci right 3.255423e-02	k: 1868	n:60000
AMACR   60000 perm   14 sec   (4437 perm/sec)   p_kst 3.113333e-02   p_cons 1.989833e-01   p_joint 8.800000e-03

Joint ci ratio: 1.588118e-01	ci left: 7.942983e-03	ci right 9.326782e-03	k: 603	n:70000
Cons ci ratio: 2.978932e-02	ci left: 1.953517e-01	ci right 2.012733e-01	k: 13881	n:70000
KS ci ratio: 8.337203e-02	ci left: 2.933646e-02	ci right 3.190264e-02	k: 2142	n:70000
AMACR   70000 perm   16 sec   (4376 perm/sec)   p_kst 3.060000e-02   p_cons 1.983000e-01   p_joint 8.614286e-03

Joint ci ratio: 1.485860e-01	ci left: 7.983811e-03	ci right 9.277202e-03	k: 689	n:80000
Cons ci ratio: 2.785786e-02	ci left: 1.956288e-01	ci right 2.011681e-01	k: 15871	n:80000
KS ci ratio: 7.832032e-02	ci left: 2.917206e-02	ci right 3.156216e-02	k: 2428	n:80000
AMACR   80000 perm   19 sec   (4313 perm/sec)   p_kst 3.035000e-02   p_cons 1.983875e-01   p_joint 8.612500e-03

Joint ci ratio: 1.313442e-01	ci left: 9.155955e-03	ci right 1.045371e-02	k: 881	n:90000
Cons ci ratio: 2.619330e-02	ci left: 1.966501e-01	ci right 2.018804e-01	k: 17933	n:90000
KS ci ratio: 7.384987e-02	ci left: 2.923338e-02	ci right 3.148591e-02	k: 2731	n:90000
AMACR   90000 perm   21 sec   (4244 perm/sec)   p_kst 3.034444e-02   p_cons 1.992556e-01   p_joint 9.788889e-03

Joint ci ratio: 1.317866e-01	ci left: 8.191733e-03	ci right 9.357027e-03	k: 876	n:100000
Cons ci ratio: 2.478058e-02	ci left: 1.976639e-01	ci right 2.026335e-01	k: 20014	n:100000
KS ci ratio: 7.029402e-02	ci left: 2.909880e-02	ci right 3.122857e-02	k: 3015	n:100000
AMACR   100000 perm   24 sec   (4172 perm/sec)   p_kst 3.015000e-02   p_cons 2.001400e-01   p_joint 8.760000e-03

Joint ci ratio: 1.254374e-01	ci left: 8.247711e-03	ci right 9.360238e-03	k: 967	n:110000
Cons ci ratio: 2.368285e-02	ci left: 1.970332e-01	ci right 2.017645e-01	k: 21933	n:110000
KS ci ratio: 6.718580e-02	ci left: 2.900872e-02	ci right 3.103435e-02	k: 3301	n:110000
AMACR   110000 perm   27 sec   (4106 perm/sec)   p_kst 3.000909e-02   p_cons 1.993909e-01   p_joint 8.790909e-03

Joint ci ratio: 1.199827e-01	ci left: 8.287395e-03	ci right 9.353212e-03	k: 1057	n:120000
Cons ci ratio: 2.267875e-02	ci left: 1.970761e-01	ci right 2.016051e-01	k: 23920	n:120000
KS ci ratio: 6.428122e-02	ci left: 2.909125e-02	ci right 3.103155e-02	k: 3606	n:120000
AMACR   120000 perm   30 sec   (4044 perm/sec)   p_kst 3.005000e-02   p_cons 1.993333e-01   p_joint 8.808333e-03

Joint ci ratio: 1.149305e-01	ci left: 8.359225e-03	ci right 9.385939e-03	k: 1152	n:130000
Cons ci ratio: 2.177509e-02	ci left: 1.973688e-01	ci right 2.017215e-01	k: 25940	n:130000
KS ci ratio: 6.181312e-02	ci left: 2.907934e-02	ci right 3.094170e-02	k: 3900	n:130000
AMACR   130000 perm   33 sec   (3958 perm/sec)   p_kst 3.000000e-02   p_cons 1.995385e-01   p_joint 8.861538e-03

Joint ci ratio: 9.728440e-02	ci left: 1.090624e-02	ci right 1.202842e-02	k: 1604	n:140000
Cons ci ratio: 2.099496e-02	ci left: 1.972671e-01	ci right 2.014597e-01	k: 27910	n:140000
KS ci ratio: 5.957981e-02	ci left: 2.909852e-02	ci right 3.089245e-02	k: 4198	n:140000
AMACR   140000 perm   36 sec   (3895 perm/sec)   p_kst 2.998571e-02   p_cons 1.993571e-01   p_joint 1.145714e-02

Outputting figure to mutsig2_images.part000000000007/AMACR.2_1499_140000_0.029986_0.19936_0.011457.png
                gene_name: AMACR
               theta_stop: 0.097 
                    nperm: 140000 
                     p_ks: 0.030 
        ci_ks_bounds_left: 0.029 
       ci_ks_bounds_right: 0.031 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.011 
     ci_joint_bounds_left: 0.011 
    ci_joint_bounds_right: 0.012 

Current progress: 29 percent done.
AMOTL1
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: 1.810553e-02	ci left: 8.165953e-01	ci right 8.316154e-01	k: 8242	n:10000
KS ci ratio: 2.027820e-02	ci left: 7.807680e-01	ci right 7.968634e-01	k: 7889	n:10000
AMOTL1   10000 perm   2 sec   (5471 perm/sec)   p_kst 7.889000e-01   p_cons 8.242000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000007/AMOTL1.2_2923_10000_0.7889_0.8242_1.png
                gene_name: AMOTL1
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.80 
                   p_cons: 0.82 
      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: 43 percent done.
ANK2
Processing conservation and coverage...
82% 
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: 4.055801e-02	ci left: 4.730621e-01	ci right 4.927479e-01	k: 4829	n:10000
KS ci ratio: 4.037047e-03	ci left: 9.874126e-01	ci right 9.914948e-01	k: 9896	n:10000
ANK2   10000 perm   4 sec   (2569 perm/sec)   p_kst 9.896000e-01   p_cons 4.829000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000007/ANK2.2_12123_10000_0.9896_0.4829_1.png
                gene_name: ANK2
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 0.99 
        ci_ks_bounds_left: 0.99 
       ci_ks_bounds_right: 0.99 
                   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: 57 percent done.
ANKAR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.116412e-02	ci left: 7.659773e-01	ci right 7.824627e-01	k: 7743	n:10000
Cons ci ratio: 3.249207e-02	ci left: 5.829942e-01	ci right 6.023518e-01	k: 5927	n:10000
KS ci ratio: 2.873093e-02	ci left: 6.410619e-01	ci right 6.598504e-01	k: 6505	n:10000
ANKAR   10000 perm   3 sec   (3990 perm/sec)   p_kst 6.505000e-01   p_cons 5.927000e-01   p_joint 7.743000e-01

Outputting figure to mutsig2_images.part000000000007/ANKAR.2_4393_10000_0.6505_0.5927_0.7743.png
                gene_name: ANKAR
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.60 
                  p_joint: 0.77 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.78 

Current progress: 71 percent done.
ANKHD1-EIF4EBP3
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: 1.726249e-02	ci left: 8.302232e-01	ci right 8.447796e-01	k: 8376	n:10000
KS ci ratio: 3.634162e-01	ci left: 9.412543e-03	ci right 1.367914e-02	k: 114	n:10000
ANKHD1-EIF4EBP3   10000 perm   3 sec   (3465 perm/sec)   p_kst 1.140000e-02   p_cons 8.376000e-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: 1.217441e-02	ci left: 8.331233e-01	ci right 8.433781e-01	k: 16766	n:20000
KS ci ratio: 2.564170e-01	ci left: 1.006870e-02	ci right 1.307582e-02	k: 230	n:20000
ANKHD1-EIF4EBP3   20000 perm   6 sec   (3222 perm/sec)   p_kst 1.150000e-02   p_cons 8.383000e-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: 9.976835e-03	ci left: 8.330741e-01	ci right 8.414604e-01	k: 25119	n:30000
KS ci ratio: 2.136156e-01	ci left: 9.913730e-03	ci right 1.231569e-02	k: 332	n:30000
ANKHD1-EIF4EBP3   30000 perm   10 sec   (3079 perm/sec)   p_kst 1.106667e-02   p_cons 8.373000e-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: 8.690803e-03	ci left: 8.320319e-01	ci right 8.393193e-01	k: 33428	n:40000
KS ci ratio: 1.845774e-01	ci left: 1.012024e-02	ci right 1.220164e-02	k: 445	n:40000
ANKHD1-EIF4EBP3   40000 perm   13 sec   (3037 perm/sec)   p_kst 1.112500e-02   p_cons 8.357000e-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: 8.193612e-03	ci left: 8.173292e-01	ci right 8.240735e-01	k: 41036	n:50000
KS ci ratio: 1.676181e-01	ci left: 9.912512e-03	ci right 1.174495e-02	k: 540	n:50000
ANKHD1-EIF4EBP3   50000 perm   17 sec   (2993 perm/sec)   p_kst 1.080000e-02   p_cons 8.207200e-01   p_joint 1

Joint ci ratio: 6.533116e-05	ci left: 9.999385e-01	ci right 1	k: 60000	n:60000
Cons ci ratio: 7.491635e-03	ci left: 8.171538e-01	ci right 8.233152e-01	k: 49215	n:60000
KS ci ratio: 1.543657e-01	ci left: 9.812005e-03	ci right 1.146917e-02	k: 637	n:60000
ANKHD1-EIF4EBP3   60000 perm   20 sec   (2954 perm/sec)   p_kst 1.061667e-02   p_cons 8.202500e-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: 6.937072e-03	ci left: 8.173348e-01	ci right 8.230386e-01	k: 57414	n:70000
KS ci ratio: 1.418910e-01	ci left: 1.001993e-02	ci right 1.156388e-02	k: 754	n:70000
ANKHD1-EIF4EBP3   70000 perm   24 sec   (2918 perm/sec)   p_kst 1.077143e-02   p_cons 8.202000e-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: 6.176832e-03	ci left: 8.316926e-01	ci right 8.368581e-01	k: 66743	n:80000
KS ci ratio: 1.334209e-01	ci left: 9.962326e-03	ci right 1.139849e-02	k: 853	n:80000
ANKHD1-EIF4EBP3   80000 perm   28 sec   (2882 perm/sec)   p_kst 1.066250e-02   p_cons 8.342875e-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: 5.830789e-03	ci left: 8.314969e-01	ci right 8.363704e-01	k: 75055	n:90000
KS ci ratio: 1.246642e-01	ci left: 1.018881e-02	ci right 1.155410e-02	k: 977	n:90000
ANKHD1-EIF4EBP3   90000 perm   32 sec   (2848 perm/sec)   p_kst 1.085556e-02   p_cons 8.339444e-01   p_joint 1

Joint ci ratio: 3.919922e-05	ci left: 9.999631e-01	ci right 1	k: 100000	n:100000
Cons ci ratio: 5.527861e-03	ci left: 8.318099e-01	ci right 8.364307e-01	k: 83413	n:100000
KS ci ratio: 1.186354e-01	ci left: 1.015889e-02	ci right 1.144972e-02	k: 1079	n:100000
ANKHD1-EIF4EBP3   100000 perm   36 sec   (2815 perm/sec)   p_kst 1.079000e-02   p_cons 8.341300e-01   p_joint 1

Joint ci ratio: 3.563572e-05	ci left: 9.999665e-01	ci right 1	k: 110000	n:110000
Cons ci ratio: 5.276715e-03	ci left: 8.315959e-01	ci right 8.360046e-01	k: 91719	n:110000
KS ci ratio: 1.133558e-01	ci left: 1.014455e-02	ci right 1.137236e-02	k: 1182	n:110000
ANKHD1-EIF4EBP3   110000 perm   40 sec   (2780 perm/sec)   p_kst 1.074545e-02   p_cons 8.338091e-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: 5.316957e-03	ci left: 8.169688e-01	ci right 8.213324e-01	k: 98299	n:120000
KS ci ratio: 1.082989e-01	ci left: 1.021476e-02	ci right 1.139239e-02	k: 1295	n:120000
ANKHD1-EIF4EBP3   120000 perm   44 sec   (2738 perm/sec)   p_kst 1.079167e-02   p_cons 8.191583e-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: 5.103136e-03	ci left: 8.173597e-01	ci right 8.215491e-01	k: 106530	n:130000
KS ci ratio: 1.038262e-01	ci left: 1.028270e-02	ci right 1.141621e-02	k: 1409	n:130000
ANKHD1-EIF4EBP3   130000 perm   48 sec   (2707 perm/sec)   p_kst 1.083846e-02   p_cons 8.194615e-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: 4.921612e-03	ci left: 8.171882e-01	ci right 8.212271e-01	k: 114690	n:140000
KS ci ratio: 9.970024e-02	ci left: 1.037661e-02	ci right 1.147236e-02	k: 1528	n:140000
ANKHD1-EIF4EBP3   140000 perm   52 sec   (2667 perm/sec)   p_kst 1.091429e-02   p_cons 8.192143e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000007/ANKHD1-EIF4EBP3.2_7998_140000_0.010914_0.81921_1.png
                gene_name: ANKHD1-EIF4EBP3
               theta_stop: 0.100 
                    nperm: 140000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.010 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.82 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 86 percent done.
ANKLE2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.831909e-02	ci left: 3.020326e-01	ci right 3.202776e-01	k: 3111	n:10000
Cons ci ratio: 6.390347e-03	ci left: 9.709012e-01	ci right 9.772186e-01	k: 9742	n:10000
KS ci ratio: 1.127108e-01	ci left: 1.017865e-01	ci right 1.140430e-01	k: 1078	n:10000
ANKLE2   10000 perm   2 sec   (4363 perm/sec)   p_kst 1.078000e-01   p_cons 9.742000e-01   p_joint 3.111000e-01

Joint ci ratio: 6.026635e-02	ci left: 1.693119e-01	ci right 1.798828e-01	k: 3491	n:20000
Cons ci ratio: 4.401416e-03	ci left: 9.732099e-01	ci right 9.775503e-01	k: 19509	n:20000
KS ci ratio: 8.013786e-02	ci left: 1.025519e-01	ci right 1.111628e-01	k: 2136	n:20000
ANKLE2   20000 perm   5 sec   (4300 perm/sec)   p_kst 1.068000e-01   p_cons 9.754500e-01   p_joint 1.745500e-01

Outputting figure to mutsig2_images.part000000000007/ANKLE2.2_2869_20000_0.1068_0.97545_0.17455.png
                gene_name: ANKLE2
               theta_stop: 0.080 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.98 
                  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.165.3896/
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/181708/iteration1/scatter.0000000007
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 7 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1708>
Subject: Job 1119498: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, 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/181708/iteration1/scatter.0000000008> was used as the working directory.
Started at Wed Oct 10 10:41:37 2012
Results reported at Wed Oct 10 10:44:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000008.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000008.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 8  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    166.33 sec.
    Max Memory :      1209 MB
    Max Swap   :      3867 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.165.3896/
-whichjob
8
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 8: processing genes 634 - 724
Calculating significance of each gene.
Using projection method.
634	ANKRD10	1
635	ANKRD11	5.624747e-01
636	ANKRD12	2.637943e-01
637	ANKRD13A	1
638	ANKRD13B	1
639	ANKRD13C	2.395430e-01
640	ANKRD13D	1
641	ANKRD16	1
642	ANKRD17	1
643	ANKRD2	1
644	ANKRD20A1	1
645	ANKRD20A4	1
646	ANKRD22	1
647	ANKRD23	1
648	ANKRD24	1
649	ANKRD26	6.064585e-01
650	ANKRD27	5.335497e-02
651	ANKRD28	2.849243e-01
652	ANKRD29	1
653	ANKRD30A	2.818880e-03
654	ANKRD30B	1
655	ANKRD32	1
656	ANKRD33	1
657	ANKRD34A	1
658	ANKRD34B	1.837381e-01
659	ANKRD35	3.338060e-01
660	ANKRD36	1
661	ANKRD36B	1
662	ANKRD37	1
663	ANKRD39	1
664	ANKRD40	6.852569e-02
665	ANKRD42	1
666	ANKRD44	1
667	ANKRD45	1
668	ANKRD46	1
669	ANKRD49	1
670	ANKRD5	1.304219e-01
671	ANKRD50	1
672	ANKRD52	1
673	ANKRD53	1
674	ANKRD54	1
675	ANKRD55	1
676	ANKRD56	1
677	ANKRD57	1
678	ANKRD6	1
679	ANKRD7	1
680	ANKS1A	1
681	ANKS1B	1
682	ANKS3	1
683	ANKS4B	1
684	ANKS6	1
685	ANKZF1	3.048576e-01
686	ANLN	1
687	ANO1	1
688	ANO10	1
689	ANO2	1
690	ANO3	1
691	ANO4	7.839748e-02
692	ANO5	1
693	ANO6	3.677295e-01
694	ANO7	1
695	ANO8	1
696	ANO9	1
697	ANP32A	1
698	ANP32B	1
699	ANP32C	1
700	ANP32D	1
701	ANP32E	1.263867e-01
702	ANPEP	7.614478e-02
703	ANTXR1	1
704	ANTXR2	1
705	ANUBL1	1.373901e-01
706	ANXA1	1
707	ANXA10	1
708	ANXA11	9.655113e-02
709	ANXA13	1
710	ANXA2	1
711	ANXA3	1
712	ANXA4	1
713	ANXA5	1
714	ANXA6	1
715	ANXA7	1
716	ANXA9	1
717	AOAH	1.856165e-01
718	AOC2	1
719	AOC3	1
720	AOX1	3.498979e-01
721	AP1AR	1
722	AP1B1	9.989158e-02
723	AP1G1	1
724	AP1G2	1
Done

Running MutSig 2:
Scatter job 8: processing genes 634 - 724
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ANKRD30A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.425194e-02	ci left: 5.572202e-01	ci right 5.767407e-01	k: 5670	n:10000
Cons ci ratio: 1.375648e-02	ci left: 8.841132e-01	ci right 8.964584e-01	k: 8904	n:10000
KS ci ratio: 6.565379e-02	ci left: 2.540943e-01	ci right 2.714441e-01	k: 2627	n:10000
ANKRD30A   10000 perm   4 sec   (2644 perm/sec)   p_kst 2.627000e-01   p_cons 8.904000e-01   p_joint 5.670000e-01

Outputting figure to mutsig2_images.part000000000008/ANKRD30A.3_4166_10000_0.2627_0.8904_0.567.png
                gene_name: ANKRD30A
               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: 0.90 
                  p_joint: 0.57 
     ci_joint_bounds_left: 0.56 
    ci_joint_bounds_right: 0.58 

Current progress: 20 percent done.
ANKRD12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.069390e-02	ci left: 9.256491e-01	ci right 9.356983e-01	k: 9308	n:10000
Cons ci ratio: 2.332572e-02	ci left: 7.297682e-01	ci right 7.470927e-01	k: 7385	n:10000
KS ci ratio: 1.177263e-01	ci left: 9.389515e-02	ci right 1.057391e-01	k: 997	n:10000
ANKRD12   10000 perm   3 sec   (3571 perm/sec)   p_kst 9.970000e-02   p_cons 7.385000e-01   p_joint 9.308000e-01

Joint ci ratio: 7.450707e-03	ci left: 9.290882e-01	ci right 9.360854e-01	k: 18653	n:20000
Cons ci ratio: 1.616534e-02	ci left: 7.401082e-01	ci right 7.522201e-01	k: 14924	n:20000
KS ci ratio: 8.267273e-02	ci left: 9.685709e-02	ci right 1.052593e-01	k: 2020	n:20000
ANKRD12   20000 perm   6 sec   (3337 perm/sec)   p_kst 1.010000e-01   p_cons 7.462000e-01   p_joint 9.326500e-01

Outputting figure to mutsig2_images.part000000000008/ANKRD12.2_6237_20000_0.101_0.7462_0.93265.png
                gene_name: ANKRD12
               theta_stop: 0.083 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.097 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.75 
      ci_cons_bounds_left: 0.74 
     ci_cons_bounds_right: 0.75 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 40 percent done.
ANKRD26
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.639045e-01	ci left: 4.965055e-02	ci right 5.861142e-02	k: 540	n:10000
Cons ci ratio: 1.455778e-01	ci left: 6.265923e-02	ci right 7.259445e-02	k: 675	n:10000
KS ci ratio: 2.022577e-01	ci left: 3.252956e-02	ci right 3.994377e-02	k: 361	n:10000
ANKRD26   10000 perm   3 sec   (3398 perm/sec)   p_kst 3.610000e-02   p_cons 6.750000e-02   p_joint 5.400000e-02

Joint ci ratio: 1.125835e-01	ci left: 5.392380e-02	ci right 6.040569e-02	k: 1142	n:20000
Cons ci ratio: 1.068055e-01	ci left: 5.972022e-02	ci right 6.650747e-02	k: 1261	n:20000
KS ci ratio: 1.365022e-01	ci left: 3.689100e-02	ci right 4.234388e-02	k: 791	n:20000
ANKRD26   20000 perm   6 sec   (3577 perm/sec)   p_kst 3.955000e-02   p_cons 6.305000e-02   p_joint 5.710000e-02

Joint ci ratio: 9.157119e-02	ci left: 5.492461e-02	ci right 6.022814e-02	k: 1726	n:30000
Cons ci ratio: 8.737952e-02	ci left: 6.011316e-02	ci right 6.563853e-02	k: 1885	n:30000
KS ci ratio: 1.112110e-01	ci left: 3.755099e-02	ci right 4.200537e-02	k: 1192	n:30000
ANKRD26   30000 perm   8 sec   (3676 perm/sec)   p_kst 3.973333e-02   p_cons 6.283333e-02   p_joint 5.753333e-02

Joint ci ratio: 5.914505e-02	ci left: 9.601584e-02	ci right 1.018925e-01	k: 3957	n:40000
Cons ci ratio: 7.603951e-02	ci left: 5.992617e-02	ci right 6.468762e-02	k: 2491	n:40000
KS ci ratio: 9.586298e-02	ci left: 3.819829e-02	ci right 4.206884e-02	k: 1604	n:40000
ANKRD26   40000 perm   11 sec   (3739 perm/sec)   p_kst 4.010000e-02   p_cons 6.227500e-02   p_joint 9.892500e-02

Outputting figure to mutsig2_images.part000000000008/ANKRD26.2_5269_40000_0.0401_0.062275_0.098925.png
                gene_name: ANKRD26
               theta_stop: 0.096 
                    nperm: 40000 
                     p_ks: 0.040 
        ci_ks_bounds_left: 0.038 
       ci_ks_bounds_right: 0.042 
                   p_cons: 0.062 
      ci_cons_bounds_left: 0.060 
     ci_cons_bounds_right: 0.065 
                  p_joint: 0.099 
     ci_joint_bounds_left: 0.096 
    ci_joint_bounds_right: 0.10 

Current progress: 60 percent done.
ANKRD27
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: 6.015053e-02	ci left: 2.890454e-01	ci right 3.070724e-01	k: 2980	n:10000
KS ci ratio: 2.065500e-02	ci left: 7.744852e-01	ci right 7.907498e-01	k: 7827	n:10000
ANKRD27   10000 perm   2 sec   (5582 perm/sec)   p_kst 7.827000e-01   p_cons 2.980000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000008/ANKRD27.2_3265_10000_0.7827_0.298_1.png
                gene_name: ANKRD27
               theta_stop: 0.060 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.79 
                   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: 80 percent done.
ANPEP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.837333e-02	ci left: 1.570859e-01	ci right 1.717101e-01	k: 1643	n:10000
Cons ci ratio: 9.117616e-02	ci left: 1.488410e-01	ci right 1.631600e-01	k: 1559	n:10000
KS ci ratio: 1.019464e-01	ci left: 1.221955e-01	ci right 1.354215e-01	k: 1287	n:10000
ANPEP   10000 perm   2 sec   (5871 perm/sec)   p_kst 1.287000e-01   p_cons 1.559000e-01   p_joint 1.643000e-01

Joint ci ratio: 6.066666e-02	ci left: 1.674349e-01	ci right 1.779604e-01	k: 3453	n:20000
Cons ci ratio: 6.470589e-02	ci left: 1.500098e-01	ci right 1.600907e-01	k: 3100	n:20000
KS ci ratio: 7.157880e-02	ci left: 1.257128e-01	ci right 1.350949e-01	k: 2607	n:20000
ANPEP   20000 perm   4 sec   (5219 perm/sec)   p_kst 1.303500e-01   p_cons 1.550000e-01   p_joint 1.726500e-01

Outputting figure to mutsig2_images.part000000000008/ANPEP.2_2984_20000_0.13035_0.155_0.17265.png
                gene_name: ANPEP
               theta_stop: 0.072 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.16 
                  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.165.3896/
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/181708/iteration1/scatter.0000000008
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 8 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119500: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000009> was used as the working directory.
Started at Wed Oct 10 10:41:37 2012
Results reported at Wed Oct 10 10:43:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000009.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000009.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 9  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    147.74 sec.
    Max Memory :      1224 MB
    Max Swap   :      3893 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.165.3896/
-whichjob
9
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 9: processing genes 725 - 814
Calculating significance of each gene.
Using projection method.
725	AP1M1	1
726	AP1M2	1
727	AP1S1	1
728	AP1S2	1
729	AP1S3	1
730	AP2A1	1
731	AP2A2	1
732	AP2B1	1
733	AP2M1	1
734	AP2S1	1
735	AP3B1	3.027867e-01
736	AP3B2	1.081758e-01
737	AP3D1	1
738	AP3M1	1
739	AP3M2	1
740	AP3S1	3.298091e-02
741	AP3S2	8.880289e-02
742	AP4B1	1
743	AP4E1	1
744	AP4M1	1
745	AP4S1	1
746	APAF1	1
747	APBA1	1
748	APBA2	1
749	APBA3	1
750	APBB1	2.373637e-01
751	APBB1IP	1
752	APBB2	1
753	APBB3	1
754	APC	1
755	APC2	1
756	APCDD1	1.596749e-01
757	APCDD1L	1
758	APCS	1
759	APEH	2.815831e-01
760	APEX1	1
761	APEX2	8.923748e-02
762	APH1A	9.737771e-02
763	APH1B	1
764	API5	7.761816e-02
765	APIP	1
766	APITD1	1
767	APLF	1
768	APLNR	1
769	APLP1	1
770	APLP2	1.576149e-01
771	APOA1	1
772	APOA1BP	1
773	APOA2	1
774	APOA4	4.752168e-02
775	APOA5	1.592177e-01
776	APOB	1.973309e-01
777	APOB48R	1
778	APOBEC1	1
779	APOBEC2	1
780	APOBEC3A	1
781	APOBEC3B	1
782	APOBEC3C	1
783	APOBEC3D	1
784	APOBEC3F	1
785	APOBEC3G	1
786	APOBEC3H	1
787	APOBEC4	1
788	APOC1	1
789	APOC2	1
790	APOC3	1
791	APOC4	1
792	APOD	1
793	APOE	1
794	APOF	1
795	APOH	1
796	APOL1	1.340905e-01
797	APOL2	1.331291e-01
798	APOL3	1
799	APOL4	1
800	APOL5	1
801	APOL6	1
802	APOLD1	1
803	APOM	1
804	APOO	1
805	APOOL	1
806	APP	1
807	APPBP2	1.993794e-01
808	APPL1	1
809	APPL2	1.506621e-01
810	APRT	1
811	APTX	1
812	AQP1	1
813	AQP10	1
814	AQP11	1
Done

Running MutSig 2:
Scatter job 9: processing genes 725 - 814
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: 1.664969e-02	ci left: 8.399972e-01	ci right 8.542000e-01	k: 8472	n:10000
Cons ci ratio: 2.317481e-02	ci left: 7.322943e-01	ci right 7.495652e-01	k: 7410	n:10000
KS ci ratio: 3.009633e-02	ci left: 6.195460e-01	ci right 6.385788e-01	k: 6291	n:10000
APOB   10000 perm   5 sec   (2089 perm/sec)   p_kst 6.291000e-01   p_cons 7.410000e-01   p_joint 8.472000e-01

Outputting figure to mutsig2_images.part000000000009/APOB.6_13808_10000_0.6291_0.741_0.8472.png
                gene_name: APOB
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.75 
                  p_joint: 0.85 
     ci_joint_bounds_left: 0.84 
    ci_joint_bounds_right: 0.85 

Current progress: 33 percent done.
APH1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.526754e-03	ci left: 9.777025e-01	ci right 9.832126e-01	k: 9806	n:10000
Cons ci ratio: 1.299056e-02	ci left: 8.950816e-01	ci right 9.068836e-01	k: 9011	n:10000
KS ci ratio: 1.518912e-02	ci left: 8.627401e-01	ci right 8.760439e-01	k: 8695	n:10000
APH1A   10000 perm   2 sec   (6542 perm/sec)   p_kst 8.695000e-01   p_cons 9.011000e-01   p_joint 9.806000e-01

Outputting figure to mutsig2_images.part000000000009/APH1A.2_837_10000_0.8695_0.9011_0.9806.png
                gene_name: APH1A
               theta_stop: 0.015 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.88 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.91 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 67 percent done.
APPL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.375114e-02	ci left: 3.377653e-01	ci right 3.565238e-01	k: 3471	n:10000
Cons ci ratio: 2.958900e-02	ci left: 6.274864e-01	ci right 6.464337e-01	k: 6370	n:10000
KS ci ratio: 8.119962e-02	ci left: 1.812696e-01	ci right 1.967120e-01	k: 1889	n:10000
APPL2   10000 perm   2 sec   (5795 perm/sec)   p_kst 1.889000e-01   p_cons 6.370000e-01   p_joint 3.471000e-01

Outputting figure to mutsig2_images.part000000000009/APPL2.2_2079_10000_0.1889_0.637_0.3471.png
                gene_name: APPL2
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.35 
     ci_joint_bounds_left: 0.34 
    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.165.3896/
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/181708/iteration1/scatter.0000000009
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 9 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119502: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000010> was used as the working directory.
Started at Wed Oct 10 10:41:48 2012
Results reported at Wed Oct 10 10:43:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000010.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000010.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 10  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     99.22 sec.
    Max Memory :      1485 MB
    Max Swap   :      3937 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.165.3896/
-whichjob
10
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 10: processing genes 815 - 905
Calculating significance of each gene.
Using projection method.
815	AQP12A	1
816	AQP12B	1
817	AQP2	1
818	AQP3	1
819	AQP4	1
820	AQP5	1
821	AQP6	1
822	AQP7	1
823	AQP8	1
824	AQP9	1
825	AQPEP	1
826	AQR	1
827	AR	1
828	ARAF	2.240700e-01
829	ARAP1	2.044617e-01
830	ARAP2	4.409608e-01
831	ARAP3	1
832	ARC	1
833	ARCN1	1.224937e-01
834	AREG	1
835	ARF1	1
836	ARF3	1
837	ARF4	1
838	ARF5	1
839	ARF6	1
840	ARFGAP1	1
841	ARFGAP2	1
842	ARFGAP3	1
843	ARFGEF1	6.297614e-01
844	ARFGEF2	1
845	ARFIP1	1.272992e-01
846	ARFIP2	1
847	ARFRP1	1
848	ARG1	1
849	ARG2	1
850	ARGFX	5.395121e-02
851	ARGLU1	1
852	ARHGAP1	1
853	ARHGAP10	1
854	ARHGAP11A	1.692171e-01
855	ARHGAP11B	1.477065e-02
856	ARHGAP12	8.354923e-02
857	ARHGAP15	1
858	ARHGAP17	1.421280e-01
859	ARHGAP18	1
860	ARHGAP19	2.298756e-01
861	ARHGAP20	1
862	ARHGAP21	4.996078e-01
863	ARHGAP22	1
864	ARHGAP24	1.792335e-01
865	ARHGAP25	1.865051e-01
866	ARHGAP26	1
867	ARHGAP27	1
868	ARHGAP28	6.432418e-02
869	ARHGAP29	2.623830e-01
870	ARHGAP30	3.637308e-02
871	ARHGAP31	5.713439e-01
872	ARHGAP32	1
873	ARHGAP33	1
874	ARHGAP36	9.117432e-03
875	ARHGAP39	3.329922e-02
876	ARHGAP4	1
877	ARHGAP5	1.469355e-02
878	ARHGAP6	2.339915e-01
879	ARHGAP8	1
880	ARHGAP9	1
881	ARHGDIA	1
882	ARHGDIB	1
883	ARHGDIG	1
884	ARHGEF1	1.468788e-01
885	ARHGEF10	5.070167e-01
886	ARHGEF10L	1
887	ARHGEF11	1.647205e-01
888	ARHGEF12	1
889	ARHGEF15	1.731536e-01
890	ARHGEF16	1
891	ARHGEF17	1
892	ARHGEF18	1
893	ARHGEF19	1
894	ARHGEF2	1
895	ARHGEF3	1.149578e-01
896	ARHGEF35	1
897	ARHGEF37	1
898	ARHGEF38	1
899	ARHGEF4	1
900	ARHGEF5	2.145297e-01
901	ARHGEF6	1
902	ARHGEF7	1
903	ARHGEF9	1
904	ARID1A	6.182635e-05
905	ARID1B	1.453481e-01
Done

Running MutSig 2:
Scatter job 10: processing genes 815 - 905
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: 6.485020e-02	ci left: 2.588428e-01	ci right 2.762928e-01	k: 2675	n:10000
Cons ci ratio: 1.378463e-02	ci left: 8.837035e-01	ci right 8.960683e-01	k: 8900	n:10000
KS ci ratio: 8.872880e-02	ci left: 1.560058e-01	ci right 1.705909e-01	k: 1632	n:10000
ARID1A   10000 perm   3 sec   (3919 perm/sec)   p_kst 1.632000e-01   p_cons 8.900000e-01   p_joint 2.675000e-01

Outputting figure to mutsig2_images.part000000000010/ARID1A.8_6938_10000_0.1632_0.89_0.2675.png
                gene_name: ARID1A
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.90 
                  p_joint: 0.27 
     ci_joint_bounds_left: 0.26 
    ci_joint_bounds_right: 0.28 

Current progress: 12 percent done.
ARHGAP5
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: 1.823653e-02	ci left: 8.144611e-01	ci right 8.295509e-01	k: 8221	n:10000
KS ci ratio: 1.195306e-01	ci left: 9.126730e-02	ci right 1.029686e-01	k: 970	n:10000
ARHGAP5   10000 perm   2 sec   (4978 perm/sec)   p_kst 9.700000e-02   p_cons 8.221000e-01   p_joint 1.939000e-01

Joint ci ratio: 7.140574e-02	ci left: 1.262544e-01	ci right 1.356532e-01	k: 2618	n:20000
Cons ci ratio: 1.292336e-02	ci left: 8.160707e-01	ci right 8.267357e-01	k: 16429	n:20000
KS ci ratio: 8.406786e-02	ci left: 9.391315e-02	ci right 1.022041e-01	k: 1960	n:20000
ARHGAP5   20000 perm   5 sec   (4438 perm/sec)   p_kst 9.800000e-02   p_cons 8.214500e-01   p_joint 1.309000e-01

Outputting figure to mutsig2_images.part000000000010/ARHGAP5.4_4533_20000_0.098_0.82145_0.1309.png
                gene_name: ARHGAP5
               theta_stop: 0.084 
                    nperm: 20000 
                     p_ks: 0.098 
        ci_ks_bounds_left: 0.094 
       ci_ks_bounds_right: 0.10 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.83 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 25 percent done.
ARHGAP30
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.965300e-02	ci left: 6.264811e-01	ci right 6.454396e-01	k: 6360	n:10000
Cons ci ratio: 3.273486e-02	ci left: 5.793822e-01	ci right 5.987658e-01	k: 5891	n:10000
KS ci ratio: 5.715629e-02	ci left: 3.106623e-01	ci right 3.290427e-01	k: 3198	n:10000
ARHGAP30   10000 perm   2 sec   (5733 perm/sec)   p_kst 3.198000e-01   p_cons 5.891000e-01   p_joint 6.360000e-01

Outputting figure to mutsig2_images.part000000000010/ARHGAP30.2_3354_10000_0.3198_0.5891_0.636.png
                gene_name: ARHGAP30
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.60 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.65 

Current progress: 38 percent done.
ARHGAP32
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: 9.990851e-02	ci left: 1.266956e-01	ci right 1.401187e-01	k: 1333	n:10000
KS ci ratio: 1.265292e-02	ci left: 8.998033e-01	ci right 9.113592e-01	k: 9057	n:10000
ARHGAP32   10000 perm   2 sec   (4707 perm/sec)   p_kst 9.057000e-01   p_cons 1.333000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000010/ARHGAP32.2_6352_10000_0.9057_0.1333_1.png
                gene_name: ARHGAP32
               theta_stop: 0.100 
                    nperm: 10000 
                     p_ks: 0.91 
        ci_ks_bounds_left: 0.90 
       ci_ks_bounds_right: 0.91 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
ARHGAP36
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: 5.697756e-03	ci left: 9.764223e-01	ci right 9.820937e-01	k: 9794	n:10000
KS ci ratio: 5.872968e-02	ci left: 2.990576e-01	ci right 3.172542e-01	k: 3081	n:10000
ARHGAP36   10000 perm   2 sec   (5829 perm/sec)   p_kst 3.081000e-01   p_cons 9.794000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000010/ARHGAP36.2_1688_10000_0.3081_0.9794_1.png
                gene_name: ARHGAP36
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.98 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 62 percent done.
ARHGAP39
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.484940e-02	ci left: 4.232593e-01	ci right 4.427798e-01	k: 4330	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: 2.365790e-02	ci left: 7.242122e-01	ci right 7.416519e-01	k: 7330	n:10000
ARHGAP39   10000 perm   2 sec   (5684 perm/sec)   p_kst 7.330000e-01   p_cons 2.362000e-01   p_joint 4.330000e-01

Outputting figure to mutsig2_images.part000000000010/ARHGAP39.2_3389_10000_0.733_0.2362_0.433.png
                gene_name: ARHGAP39
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 75 percent done.
ARHGEF11
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: 3.123541e-02	ci left: 6.019660e-01	ci right 6.211689e-01	k: 6116	n:10000
KS ci ratio: 1.565400e-02	ci left: 8.555948e-01	ci right 8.691933e-01	k: 8625	n:10000
ARHGEF11   10000 perm   2 sec   (5142 perm/sec)   p_kst 8.625000e-01   p_cons 6.116000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000010/ARHGEF11.2_4853_10000_0.8625_0.6116_1.png
                gene_name: ARHGEF11
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.87 
                   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: 88 percent done.
ARID1B
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: 6.105377e-02	ci left: 2.829019e-01	ci right 3.008195e-01	k: 2918	n:10000
KS ci ratio: 7.728861e-02	ci left: 1.966317e-01	ci right 2.125408e-01	k: 2045	n:10000
ARID1B   10000 perm   2 sec   (4406 perm/sec)   p_kst 2.045000e-01   p_cons 2.918000e-01   p_joint 2.520000e-01

Outputting figure to mutsig2_images.part000000000010/ARID1B.2_6830_10000_0.2045_0.2918_0.252.png
                gene_name: ARID1B
               theta_stop: 0.077 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.28 
     ci_cons_bounds_right: 0.30 
                  p_joint: 0.25 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.26 

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.165.3896/
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/181708/iteration1/scatter.0000000010
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 10 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119505: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000011> was used as the working directory.
Started at Wed Oct 10 10:41:48 2012
Results reported at Wed Oct 10 10:44:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000011.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000011.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 11  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    161.06 sec.
    Max Memory :      1463 MB
    Max Swap   :      3826 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.165.3896/
-whichjob
11
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 11: processing genes 906 - 995
Calculating significance of each gene.
Using projection method.
906	ARID2	1
907	ARID3A	1
908	ARID3B	1
909	ARID3C	1
910	ARID4A	5.197466e-01
911	ARID4B	3.373837e-01
912	ARID5A	1.326971e-02
913	ARID5B	3.954739e-02
914	ARIH1	1
915	ARIH2	1
916	ARL1	1
917	ARL10	1
918	ARL11	1
919	ARL13A	1
920	ARL13B	6.376167e-02
921	ARL14	1
922	ARL15	1
923	ARL16	1
924	ARL2	1
925	ARL2BP	8.383594e-02
926	ARL3	1
927	ARL4A	1
928	ARL4C	1
929	ARL4D	1
930	ARL5A	1
931	ARL5B	1
932	ARL6	1
933	ARL6IP1	1
934	ARL6IP4	1
935	ARL6IP5	1
936	ARL6IP6	1
937	ARL8A	1
938	ARL8B	1
939	ARL9	1
940	ARMC1	1
941	ARMC10	1
942	ARMC2	1
943	ARMC3	2.218160e-02
944	ARMC4	5.947669e-02
945	ARMC5	1
946	ARMC6	1
947	ARMC7	1
948	ARMC8	1
949	ARMC9	3.236597e-01
950	ARMCX1	8.570573e-02
951	ARMCX2	1
952	ARMCX3	1
953	ARMCX5	1
954	ARMCX6	1
955	ARMS2	1
956	ARNT	1
957	ARNT2	1
958	ARNTL	1
959	ARNTL2	8.338875e-02
960	ARPC1A	1
961	ARPC1B	1
962	ARPC2	1
963	ARPC3	1
964	ARPC4	1
965	ARPC5	1
966	ARPC5L	1
967	ARPM1	1.219014e-01
968	ARPP19	1
969	ARPP21	2.547615e-01
970	ARR3	1
971	ARRB1	1
972	ARRB2	1
973	ARRDC1	1
974	ARRDC2	1
975	ARRDC3	1.261526e-01
976	ARRDC4	1
977	ARRDC5	1
978	ARSA	1
979	ARSB	8.948840e-02
980	ARSD	1
981	ARSE	1
982	ARSF	1.490178e-01
983	ARSG	5.777129e-02
984	ARSH	1
985	ARSI	1
986	ARSJ	1.944123e-01
987	ARSK	1
988	ART1	1
989	ART3	1
990	ART4	1
991	ART5	1
992	ARTN	1
993	ARV1	1
994	ARVCF	5.003256e-02
995	AS3MT	1
Done

Running MutSig 2:
Scatter job 11: processing genes 906 - 995
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ARID5A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.358556e-02	ci left: 3.391561e-01	ci right 3.579322e-01	k: 3485	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: 4.359337e-02	ci left: 4.372220e-01	ci right 4.568089e-01	k: 4470	n:10000
ARID5A   10000 perm   2 sec   (5969 perm/sec)   p_kst 4.470000e-01   p_cons 3.562000e-01   p_joint 3.485000e-01

Outputting figure to mutsig2_images.part000000000011/ARID5A.2_1813_10000_0.447_0.3562_0.3485.png
                gene_name: ARID5A
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.35 
     ci_joint_bounds_left: 0.34 
    ci_joint_bounds_right: 0.36 

Current progress: 14 percent done.
ARID5B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.224432e-02	ci left: 3.506835e-01	ci right 3.695981e-01	k: 3601	n:10000
Cons ci ratio: 7.580070e-02	ci left: 2.029395e-01	ci right 2.190293e-01	k: 2109	n:10000
KS ci ratio: 2.185325e-02	ci left: 7.544383e-01	ci right 7.712083e-01	k: 7629	n:10000
ARID5B   10000 perm   2 sec   (5159 perm/sec)   p_kst 7.629000e-01   p_cons 2.109000e-01   p_joint 3.601000e-01

Outputting figure to mutsig2_images.part000000000011/ARID5B.2_3607_10000_0.7629_0.2109_0.3601.png
                gene_name: ARID5B
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.76 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.77 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 29 percent done.
ARL13B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.017006e-01	ci left: 1.409482e-02	ci right 1.919237e-02	k: 165	n:10000
Cons ci ratio: 3.902208e-02	ci left: 4.923508e-01	ci right 5.120479e-01	k: 5022	n:10000
KS ci ratio: 2.256183e-01	ci left: 2.598777e-02	ci right 3.269015e-02	k: 292	n:10000
ARL13B   10000 perm   2 sec   (5858 perm/sec)   p_kst 2.920000e-02   p_cons 5.022000e-01   p_joint 1.650000e-02

Joint ci ratio: 1.918348e-01	ci left: 1.848579e-02	ci right 2.245535e-02	k: 408	n:20000
Cons ci ratio: 2.760311e-02	ci left: 4.950957e-01	ci right 5.090037e-01	k: 10041	n:20000
KS ci ratio: 1.603879e-01	ci left: 2.666999e-02	ci right 3.136827e-02	k: 579	n:20000
ARL13B   20000 perm   4 sec   (5377 perm/sec)   p_kst 2.895000e-02   p_cons 5.020500e-01   p_joint 2.040000e-02

Joint ci ratio: 1.294329e-01	ci left: 2.774345e-02	ci right 3.161501e-02	k: 889	n:30000
Cons ci ratio: 2.261441e-02	ci left: 4.946923e-01	ci right 5.060410e-01	k: 15011	n:30000
KS ci ratio: 1.294329e-01	ci left: 2.774345e-02	ci right 3.161501e-02	k: 889	n:30000
ARL13B   30000 perm   6 sec   (5204 perm/sec)   p_kst 2.963333e-02   p_cons 5.003667e-01   p_joint 2.963333e-02

Joint ci ratio: 1.114012e-01	ci left: 2.834996e-02	ci right 3.171872e-02	k: 1200	n:40000
Cons ci ratio: 1.955131e-02	ci left: 4.963127e-01	ci right 5.061372e-01	k: 20049	n:40000
KS ci ratio: 1.114012e-01	ci left: 2.834996e-02	ci right 3.171872e-02	k: 1200	n:40000
ARL13B   40000 perm   9 sec   (4500 perm/sec)   p_kst 3.000000e-02   p_cons 5.012250e-01   p_joint 3.000000e-02

Joint ci ratio: 9.934239e-02	ci left: 2.869775e-02	ci right 3.171712e-02	k: 1509	n:50000
Cons ci ratio: 1.751343e-02	ci left: 4.960875e-01	ci right 5.048725e-01	k: 25024	n:50000
KS ci ratio: 9.934239e-02	ci left: 2.869775e-02	ci right 3.171712e-02	k: 1509	n:50000
ARL13B   50000 perm   12 sec   (4245 perm/sec)   p_kst 3.018000e-02   p_cons 5.004800e-01   p_joint 3.018000e-02

Outputting figure to mutsig2_images.part000000000011/ARL13B.2_1327_50000_0.03018_0.50048_0.03018.png
                gene_name: ARL13B
               theta_stop: 0.099 
                    nperm: 50000 
                     p_ks: 0.030 
        ci_ks_bounds_left: 0.029 
       ci_ks_bounds_right: 0.032 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.50 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.030 
     ci_joint_bounds_left: 0.029 
    ci_joint_bounds_right: 0.032 

Current progress: 43 percent done.
ARMC3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.025385e-02	ci left: 7.811735e-01	ci right 7.972577e-01	k: 7893	n:10000
Cons ci ratio: 1.424469e-02	ci left: 8.769477e-01	ci right 8.896281e-01	k: 8834	n:10000
KS ci ratio: 3.523883e-02	ci left: 5.431911e-01	ci right 5.627780e-01	k: 5530	n:10000
ARMC3   10000 perm   2 sec   (5629 perm/sec)   p_kst 5.530000e-01   p_cons 8.834000e-01   p_joint 7.893000e-01

Outputting figure to mutsig2_images.part000000000011/ARMC3.2_2691_10000_0.553_0.8834_0.7893.png
                gene_name: ARMC3
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.80 

Current progress: 57 percent done.
ARMC4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.227754e-02	ci left: 4.523904e-01	ci right 4.720316e-01	k: 4622	n:10000
Cons ci ratio: 6.483366e-02	ci left: 2.589418e-01	ci right 2.763938e-01	k: 2676	n:10000
KS ci ratio: 1.432748e-02	ci left: 8.757201e-01	ci right 8.884564e-01	k: 8822	n:10000
ARMC4   10000 perm   3 sec   (2985 perm/sec)   p_kst 8.822000e-01   p_cons 2.676000e-01   p_joint 4.622000e-01

Outputting figure to mutsig2_images.part000000000011/ARMC4.2_3211_10000_0.8822_0.2676_0.4622.png
                gene_name: ARMC4
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.88 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   p_cons: 0.27 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.28 
                  p_joint: 0.46 
     ci_joint_bounds_left: 0.45 
    ci_joint_bounds_right: 0.47 

Current progress: 71 percent done.
ARMC9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.736201e-01	ci left: 4.427577e-02	ci right 5.278970e-02	k: 484	n:10000
Cons ci ratio: 5.680355e-02	ci left: 3.133413e-01	ci right 3.317622e-01	k: 3225	n:10000
KS ci ratio: 2.413489e-01	ci left: 2.259324e-02	ci right 2.888717e-02	k: 256	n:10000
ARMC9   10000 perm   3 sec   (3370 perm/sec)   p_kst 2.560000e-02   p_cons 3.225000e-01   p_joint 4.840000e-02

Joint ci ratio: 1.350876e-01	ci left: 3.766484e-02	ci right 4.316980e-02	k: 807	n:20000
Cons ci ratio: 3.930903e-02	ci left: 3.255229e-01	ci right 3.386260e-01	k: 6641	n:20000
KS ci ratio: 1.704933e-01	ci left: 2.355113e-02	ci right 2.798821e-02	k: 514	n:20000
ARMC9   20000 perm   6 sec   (3144 perm/sec)   p_kst 2.570000e-02   p_cons 3.320500e-01   p_joint 4.035000e-02

Joint ci ratio: 6.531300e-02	ci left: 1.036879e-01	ci right 1.107217e-01	k: 3215	n:30000
Cons ci ratio: 3.216817e-02	ci left: 3.257414e-01	ci right 3.364247e-01	k: 9932	n:30000
KS ci ratio: 1.401893e-01	ci left: 2.361682e-02	ci right 2.720923e-02	k: 761	n:30000
ARMC9   30000 perm   9 sec   (3215 perm/sec)   p_kst 2.536667e-02   p_cons 3.310667e-01   p_joint 1.071667e-01

Joint ci ratio: 5.527201e-02	ci left: 1.086042e-01	ci right 1.148023e-01	k: 4467	n:40000
Cons ci ratio: 2.783803e-02	ci left: 3.267869e-01	ci right 3.360375e-01	k: 13256	n:40000
KS ci ratio: 1.226523e-01	ci left: 2.337080e-02	ci right 2.644870e-02	k: 995	n:40000
ARMC9   40000 perm   11 sec   (3484 perm/sec)   p_kst 2.487500e-02   p_cons 3.314000e-01   p_joint 1.116750e-01

Joint ci ratio: 4.890614e-02	ci left: 1.110685e-01	ci right 1.166564e-01	k: 5692	n:50000
Cons ci ratio: 2.495905e-02	ci left: 3.262173e-01	ci right 3.344824e-01	k: 16517	n:50000
KS ci ratio: 1.097491e-01	ci left: 2.351291e-02	ci right 2.626263e-02	k: 1243	n:50000
ARMC9   50000 perm   14 sec   (3648 perm/sec)   p_kst 2.486000e-02   p_cons 3.303400e-01   p_joint 1.138400e-01

Joint ci ratio: 4.252547e-02	ci left: 1.214058e-01	ci right 1.266973e-01	k: 7442	n:60000
Cons ci ratio: 2.279005e-02	ci left: 3.264702e-01	ci right 3.340129e-01	k: 19814	n:60000
KS ci ratio: 9.919641e-02	ci left: 2.410694e-02	ci right 2.663925e-02	k: 1521	n:60000
ARMC9   60000 perm   16 sec   (3749 perm/sec)   p_kst 2.535000e-02   p_cons 3.302333e-01   p_joint 1.240333e-01

Outputting figure to mutsig2_images.part000000000011/ARMC9.2_2078_60000_0.02535_0.33023_0.12403.png
                gene_name: ARMC9
               theta_stop: 0.099 
                    nperm: 60000 
                     p_ks: 0.025 
        ci_ks_bounds_left: 0.024 
       ci_ks_bounds_right: 0.027 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 86 percent done.
ARVCF
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: 4.654243e-02	ci left: 4.052191e-01	ci right 4.246305e-01	k: 4149	n:10000
KS ci ratio: 6.045373e-02	ci left: 2.869643e-01	ci right 3.049547e-01	k: 2959	n:10000
ARVCF   10000 perm   2 sec   (5828 perm/sec)   p_kst 2.959000e-01   p_cons 4.149000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000011/ARVCF.2_2957_10000_0.2959_0.4149_1.png
                gene_name: ARVCF
               theta_stop: 0.060 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.42 
                  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.165.3896/
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/181708/iteration1/scatter.0000000011
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 11 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119508: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000012> was used as the working directory.
Started at Wed Oct 10 10:41:48 2012
Results reported at Wed Oct 10 10:44:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000012.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000012.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 12  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    153.16 sec.
    Max Memory :      1438 MB
    Max Swap   :      3926 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.165.3896/
-whichjob
12
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 12: processing genes 996 - 1086
Calculating significance of each gene.
Using projection method.
996	ASAH1	1
997	ASAH2	1.448758e-02
998	ASAM	1
999	ASAP1	1
1000/18094 1000	ASAP2	1
1001	ASAP3	2.660556e-01
1002	ASB1	1
1003	ASB10	1
1004	ASB11	1
1005	ASB12	1
1006	ASB13	1
1007	ASB14	1
1008	ASB15	1
1009	ASB16	1
1010	ASB17	8.212816e-02
1011	ASB18	1
1012	ASB2	1.963628e-01
1013	ASB3	6.387312e-02
1014	ASB4	1
1015	ASB5	1
1016	ASB6	1
1017	ASB7	1
1018	ASB8	1
1019	ASB9	1
1020	ASCC1	1
1021	ASCC2	1.892943e-01
1022	ASCC3	1.234563e-01
1023	ASCL1	1
1024	ASCL3	1
1025	ASCL4	1
1026	ASF1A	1
1027	ASF1B	1
1028	ASGR1	1
1029	ASGR2	1
1030	ASH1L	2.570477e-01
1031	ASH2L	1
1032	ASIP	1
1033	ASL	1
1034	ASMT	1
1035	ASMTL	1
1036	ASNA1	1
1037	ASNS	1
1038	ASNSD1	1
1039	ASPA	3.307712e-02
1040	ASPDH	1
1041	ASPG	1.338928e-01
1042	ASPH	1
1043	ASPHD1	1
1044	ASPHD2	5.792458e-02
1045	ASPM	4.627451e-01
1046	ASPN	1
1047	ASPRV1	1
1048	ASPSCR1	1
1049	ASRGL1	1
1050	ASS1	2.117347e-01
1051	ASTE1	1
1052	ASTL	1
1053	ASTN1	4.321048e-01
1054	ASTN2	1
1055	ASXL1	1
1056	ASXL2	5.213563e-03
1057	ASXL3	1
1058	ASZ1	1
1059	ATAD1	1
1060	ATAD2	1.878430e-01
1061	ATAD2B	1
1062	ATAD3A	1
1063	ATAD3B	8.087198e-02
1064	ATAD3C	1
1065	ATAD5	1
1066	ATCAY	1
1067	ATE1	1.854013e-01
1068	ATF1	1
1069	ATF2	1
1070	ATF3	1
1071	ATF4	1
1072	ATF5	1
1073	ATF6	1
1074	ATF6B	1
1075	ATF7	1.052492e-01
1076	ATF7IP	1.745712e-01
1077	ATF7IP2	1
1078	ATG10	1
1079	ATG12	1
1080	ATG16L1	1
1081	ATG16L2	1
1082	ATG2A	6.796440e-02
1083	ATG2B	5.632391e-01
1084	ATG3	1
1085	ATG4A	1
1086	ATG4B	1.336703e-01
Done

Running MutSig 2:
Scatter job 12: processing genes 996 - 1086
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ASXL2
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: 7.555118e-02	ci left: 2.040239e-01	ci right 2.201442e-01	k: 2120	n:10000
KS ci ratio: 1.606345e-01	ci left: 5.166964e-02	ci right 6.079103e-02	k: 561	n:10000
ASXL2   10000 perm   3 sec   (3383 perm/sec)   p_kst 5.610000e-02   p_cons 2.120000e-01   p_joint 9.090000e-02

Joint ci ratio: 6.958259e-02	ci left: 1.321641e-01	ci right 1.417417e-01	k: 2738	n:20000
Cons ci ratio: 5.398102e-02	ci left: 2.029866e-01	ci right 2.142982e-01	k: 4172	n:20000
KS ci ratio: 1.130563e-01	ci left: 5.348580e-02	ci right 5.994383e-02	k: 1133	n:20000
ASXL2   20000 perm   9 sec   (2111 perm/sec)   p_kst 5.665000e-02   p_cons 2.086000e-01   p_joint 1.369000e-01

Joint ci ratio: 8.287453e-02	ci left: 6.651671e-02	ci right 7.230035e-02	k: 2081	n:30000
Cons ci ratio: 4.344259e-02	ci left: 2.088081e-01	ci right 2.181141e-01	k: 6403	n:30000
KS ci ratio: 9.236837e-02	ci left: 5.401154e-02	ci right 5.927474e-02	k: 1698	n:30000
ASXL2   30000 perm   13 sec   (2231 perm/sec)   p_kst 5.660000e-02   p_cons 2.134333e-01   p_joint 6.936667e-02

Outputting figure to mutsig2_images.part000000000012/ASXL2.6_4356_30000_0.0566_0.21343_0.069367.png
                gene_name: ASXL2
               theta_stop: 0.092 
                    nperm: 30000 
                     p_ks: 0.057 
        ci_ks_bounds_left: 0.054 
       ci_ks_bounds_right: 0.059 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.069 
     ci_joint_bounds_left: 0.067 
    ci_joint_bounds_right: 0.072 

Current progress: 17 percent done.
ASH1L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.772199e-02	ci left: 3.931666e-01	ci right 4.124900e-01	k: 4028	n:10000
Cons ci ratio: 3.658476e-02	ci left: 5.245646e-01	ci right 5.442154e-01	k: 5344	n:10000
KS ci ratio: 7.114081e-02	ci left: 2.245456e-01	ci right 2.412103e-01	k: 2328	n:10000
ASH1L   10000 perm   3 sec   (3998 perm/sec)   p_kst 2.328000e-01   p_cons 5.344000e-01   p_joint 4.028000e-01

Outputting figure to mutsig2_images.part000000000012/ASH1L.3_9003_10000_0.2328_0.5344_0.4028.png
                gene_name: ASH1L
               theta_stop: 0.071 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.40 
     ci_joint_bounds_left: 0.39 
    ci_joint_bounds_right: 0.41 

Current progress: 33 percent done.
ATG2A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.208707e-02	ci left: 1.462904e-01	ci right 1.605121e-01	k: 1533	n:10000
Cons ci ratio: 9.588261e-02	ci left: 1.362914e-01	ci right 1.501172e-01	k: 1431	n:10000
KS ci ratio: 8.355196e-02	ci left: 1.728091e-01	ci right 1.879776e-01	k: 1803	n:10000
ATG2A   10000 perm   3 sec   (3982 perm/sec)   p_kst 1.803000e-01   p_cons 1.431000e-01   p_joint 1.533000e-01

Outputting figure to mutsig2_images.part000000000012/ATG2A.3_5981_10000_0.1803_0.1431_0.1533.png
                gene_name: ATG2A
               theta_stop: 0.096 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.15 
    ci_joint_bounds_right: 0.16 

Current progress: 50 percent done.
ASCC3
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: 8.961576e-02	ci left: 1.533552e-01	ci right 1.678431e-01	k: 1605	n:10000
KS ci ratio: 1.391093e-02	ci left: 8.818604e-01	ci right 8.943125e-01	k: 8882	n:10000
ASCC3   10000 perm   2 sec   (4233 perm/sec)   p_kst 8.882000e-01   p_cons 1.605000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000012/ASCC3.2_6872_10000_0.8882_0.1605_1.png
                gene_name: ASCC3
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   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: 67 percent done.
ASPM
Processing conservation and coverage...
94% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.013812e-02	ci left: 4.782576e-01	ci right 4.979493e-01	k: 4881	n:10000
Cons ci ratio: 3.895191e-02	ci left: 4.932507e-01	ci right 5.129475e-01	k: 5031	n:10000
KS ci ratio: 3.705782e-02	ci left: 5.181586e-01	ci right 5.378251e-01	k: 5280	n:10000
ASPM   10000 perm   3 sec   (3760 perm/sec)   p_kst 5.280000e-01   p_cons 5.031000e-01   p_joint 4.881000e-01

Outputting figure to mutsig2_images.part000000000012/ASPM.2_10546_10000_0.528_0.5031_0.4881.png
                gene_name: ASPM
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 83 percent done.
ATAD2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.474170e-02	ci left: 7.061416e-01	ci right 7.239330e-01	k: 7151	n:10000
Cons ci ratio: 3.596451e-02	ci left: 5.330750e-01	ci right 5.527000e-01	k: 5429	n:10000
KS ci ratio: 5.672566e-02	ci left: 3.139366e-01	ci right 3.323665e-01	k: 3231	n:10000
ATAD2   10000 perm   2 sec   (5222 perm/sec)   p_kst 3.231000e-01   p_cons 5.429000e-01   p_joint 7.151000e-01

Outputting figure to mutsig2_images.part000000000012/ATAD2.2_4285_10000_0.3231_0.5429_0.7151.png
                gene_name: ATAD2
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.55 
                  p_joint: 0.72 
     ci_joint_bounds_left: 0.71 
    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.165.3896/
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/181708/iteration1/scatter.0000000012
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 12 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119511: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000013> was used as the working directory.
Started at Wed Oct 10 10:41:48 2012
Results reported at Wed Oct 10 10:43:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000013.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000013.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 13  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    131.22 sec.
    Max Memory :      1407 MB
    Max Swap   :      3854 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.165.3896/
-whichjob
13
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 13: processing genes 1087 - 1176
Calculating significance of each gene.
Using projection method.
1087	ATG4C	1
1088	ATG4D	2.735451e-02
1089	ATG5	1
1090	ATG7	2.244358e-01
1091	ATG9A	1
1092	ATG9B	1
1093	ATHL1	1
1094	ATIC	1
1095	ATL1	1
1096	ATL2	1
1097	ATL3	1.495378e-01
1098	ATM	1.029279e-01
1099	ATMIN	1
1100	ATN1	2.814484e-01
1101	ATOH1	1
1102	ATOH7	1
1103	ATOH8	1
1104	ATOX1	1
1105	ATP10A	5.463373e-02
1106	ATP10B	1
1107	ATP10D	1
1108	ATP11A	1
1109	ATP11B	1
1110	ATP11C	1
1111	ATP12A	1
1112	ATP13A1	1
1113	ATP13A2	2.533269e-01
1114	ATP13A3	3.722450e-01
1115	ATP13A4	1
1116	ATP13A5	1
1117	ATP1A1	9.693479e-02
1118	ATP1A2	1
1119	ATP1A3	1
1120	ATP1A4	2.916924e-01
1121	ATP1B1	1
1122	ATP1B2	1
1123	ATP1B3	1
1124	ATP1B4	1
1125	ATP2A1	7.345331e-02
1126	ATP2A2	1.454608e-01
1127	ATP2A3	3.197454e-01
1128	ATP2B1	1
1129	ATP2B2	9.248507e-02
1130	ATP2B3	1
1131	ATP2B4	3.269716e-01
1132	ATP2C1	1
1133	ATP2C2	1
1134	ATP4A	1
1135	ATP4B	1
1136	ATP5A1	2.608272e-01
1137	ATP5B	4.098356e-02
1138	ATP5C1	1
1139	ATP5D	1
1140	ATP5E	1
1141	ATP5F1	1
1142	ATP5G1	1
1143	ATP5G2	1
1144	ATP5G3	1
1145	ATP5H	1
1146	ATP5I	1
1147	ATP5J	1
1148	ATP5J2	1
1149	ATP5L	1
1150	ATP5L2	1
1151	ATP5O	1.874695e-02
1152	ATP5S	1
1153	ATP5SL	1
1154	ATP6AP1	1
1155	ATP6AP1L	1
1156	ATP6AP2	1
1157	ATP6V0A1	1.157994e-02
1158	ATP6V0A2	1
1159	ATP6V0A4	1
1160	ATP6V0B	1
1161	ATP6V0C	1
1162	ATP6V0D1	2.476195e-02
1163	ATP6V0D2	1
1164	ATP6V0E1	1
1165	ATP6V0E2	1
1166	ATP6V1A	1
1167	ATP6V1B1	1
1168	ATP6V1B2	1
1169	ATP6V1C1	8.128807e-02
1170	ATP6V1C2	1
1171	ATP6V1D	1
1172	ATP6V1E1	5.354077e-02
1173	ATP6V1E2	1
1174	ATP6V1F	1
1175	ATP6V1G1	1
1176	ATP6V1G2	1
Done

Running MutSig 2:
Scatter job 13: processing genes 1087 - 1176
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: 3.259983e-02	ci left: 5.813888e-01	ci right 6.007581e-01	k: 5911	n:10000
Cons ci ratio: 7.387413e-02	ci left: 2.115188e-01	ci right 2.278448e-01	k: 2196	n:10000
KS ci ratio: 7.507648e-03	ci left: 9.608952e-01	ci right 9.682310e-01	k: 9647	n:10000
ATM   10000 perm   3 sec   (3670 perm/sec)   p_kst 9.647000e-01   p_cons 2.196000e-01   p_joint 5.911000e-01

Outputting figure to mutsig2_images.part000000000013/ATM.3_9419_10000_0.9647_0.2196_0.5911.png
                gene_name: ATM
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.96 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.59 
     ci_joint_bounds_left: 0.58 
    ci_joint_bounds_right: 0.60 

Current progress: 14 percent done.
ATP6V0A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.332572e-02	ci left: 7.297682e-01	ci right 7.470927e-01	k: 7385	n:10000
Cons ci ratio: 8.703178e-03	ci left: 9.487722e-01	ci right 9.571614e-01	k: 9531	n:10000
KS ci ratio: 2.477206e-02	ci left: 7.056371e-01	ci right 7.234378e-01	k: 7146	n:10000
ATP6V0A1   10000 perm   2 sec   (5494 perm/sec)   p_kst 7.146000e-01   p_cons 9.531000e-01   p_joint 7.385000e-01

Outputting figure to mutsig2_images.part000000000013/ATP6V0A1.3_2619_10000_0.7146_0.9531_0.7385.png
                gene_name: ATP6V0A1
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.74 
     ci_joint_bounds_left: 0.73 
    ci_joint_bounds_right: 0.75 

Current progress: 29 percent done.
ATG4D
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.319292e-02	ci left: 7.319911e-01	ci right 7.492685e-01	k: 7407	n:10000
Cons ci ratio: 4.700555e-02	ci left: 4.004372e-01	ci right 4.198151e-01	k: 4101	n:10000
KS ci ratio: 2.398435e-02	ci left: 7.187589e-01	ci right 7.363084e-01	k: 7276	n:10000
ATG4D   10000 perm   2 sec   (6302 perm/sec)   p_kst 7.276000e-01   p_cons 4.101000e-01   p_joint 7.407000e-01

Outputting figure to mutsig2_images.part000000000013/ATG4D.2_1465_10000_0.7276_0.4101_0.7407.png
                gene_name: ATG4D
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.74 
     ci_joint_bounds_left: 0.73 
    ci_joint_bounds_right: 0.75 

Current progress: 43 percent done.
ATP10A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.627059e-03	ci left: 9.688927e-01	ci right 9.754284e-01	k: 9723	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: 1.891238e-02	ci left: 8.033895e-01	ci right 8.188289e-01	k: 8112	n:10000
ATP10A   10000 perm   2 sec   (5059 perm/sec)   p_kst 8.112000e-01   p_cons 7.917000e-01   p_joint 9.723000e-01

Outputting figure to mutsig2_images.part000000000013/ATP10A.2_4584_10000_0.8112_0.7917_0.9723.png
                gene_name: ATP10A
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.81 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.98 

Current progress: 57 percent done.
ATP2A1
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: 7.184476e-02	ci left: 2.210904e-01	ci right 2.376675e-01	k: 2293	n:10000
KS ci ratio: 1.254161e-02	ci left: 9.013439e-01	ci right 9.128177e-01	k: 9072	n:10000
ATP2A1   10000 perm   2 sec   (5606 perm/sec)   p_kst 9.072000e-01   p_cons 2.293000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000013/ATP2A1.2_3103_10000_0.9072_0.2293_1.png
                gene_name: ATP2A1
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.91 
        ci_ks_bounds_left: 0.90 
       ci_ks_bounds_right: 0.91 
                   p_cons: 0.23 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.24 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 71 percent done.
ATP2B2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.154273e-01	ci left: 9.740099e-02	ci right 1.094311e-01	k: 1033	n:10000
Cons ci ratio: 1.402025e-01	ci left: 6.739585e-02	ci right 7.765485e-02	k: 724	n:10000
KS ci ratio: 2.041810e-02	ci left: 7.784370e-01	ci right 7.945958e-01	k: 7866	n:10000
ATP2B2   10000 perm   2 sec   (5272 perm/sec)   p_kst 7.866000e-01   p_cons 7.240000e-02   p_joint 1.033000e-01

Joint ci ratio: 1.588586e-02	ci left: 7.467095e-01	ci right 7.587169e-01	k: 15055	n:20000
Cons ci ratio: 9.685466e-02	ci left: 7.202203e-02	ci right 7.940189e-02	k: 1513	n:20000
KS ci ratio: 1.441828e-02	ci left: 7.813097e-01	ci right 7.927068e-01	k: 15741	n:20000
ATP2B2   20000 perm   4 sec   (4652 perm/sec)   p_kst 7.870500e-01   p_cons 7.565000e-02   p_joint 7.527500e-01

Outputting figure to mutsig2_images.part000000000013/ATP2B2.2_3820_20000_0.78705_0.07565_0.75275.png
                gene_name: ATP2B2
               theta_stop: 0.097 
                    nperm: 20000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.79 
                   p_cons: 0.076 
      ci_cons_bounds_left: 0.072 
     ci_cons_bounds_right: 0.079 
                  p_joint: 0.75 
     ci_joint_bounds_left: 0.75 
    ci_joint_bounds_right: 0.76 

Current progress: 86 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: 4.443180e-02	ci left: 4.278462e-01	ci right 4.473902e-01	k: 4376	n:10000
KS ci ratio: 1.125544e-02	ci left: 9.185285e-01	ci right 9.290230e-01	k: 9239	n:10000
ATP2B4   10000 perm   2 sec   (5118 perm/sec)   p_kst 9.239000e-01   p_cons 4.376000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000013/ATP2B4.2_3880_10000_0.9239_0.4376_1.png
                gene_name: ATP2B4
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000013
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 13 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119515: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000014> was used as the working directory.
Started at Wed Oct 10 10:41:48 2012
Results reported at Wed Oct 10 10:49:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000014.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000014.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 14  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    461.46 sec.
    Max Memory :      1317 MB
    Max Swap   :      3829 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.165.3896/
-whichjob
14
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 14: processing genes 1177 - 1267
Calculating significance of each gene.
Using projection method.
1177	ATP6V1G3	1
1178	ATP6V1H	8.860277e-02
1179	ATP7A	4.909927e-01
1180	ATP7B	1
1181	ATP8A1	1
1182	ATP8A2	2.394610e-01
1183	ATP8B1	1
1184	ATP8B2	2.584039e-01
1185	ATP8B3	3.869757e-02
1186	ATP8B4	3.612656e-01
1187	ATP9A	4.222661e-01
1188	ATP9B	1
1189	ATPAF1	1
1190	ATPAF2	8.764008e-02
1191	ATPBD4	1
1192	ATPIF1	1
1193	ATR	2.046442e-01
1194	ATRIP	1
1195	ATRN	1
1196	ATRNL1	7.174372e-02
1197	ATRX	1.957070e-01
1198	ATXN1	1
1199	ATXN10	1
1200	ATXN2	1
1201	ATXN2L	2.182945e-01
1202	ATXN3	1
1203	ATXN3L	2.475961e-02
1204	ATXN7	3.021743e-02
1205	ATXN7L2	1
1206	ATXN7L3	1
1207	AUH	1
1208	AUP1	1
1209	AURKA	1
1210	AURKAIP1	1
1211	AURKB	3.301291e-02
1212	AURKC	1
1213	AUTS2	2.962896e-01
1214	AVEN	1
1215	AVIL	1.574031e-01
1216	AVL9	1
1217	AVP	1
1218	AVPI1	1
1219	AVPR1A	4.801147e-02
1220	AVPR1B	1
1221	AVPR2	1
1222	AWAT1	1
1223	AWAT2	1
1224	AXIN1	3.105403e-02
1225	AXIN2	2.106515e-01
1226	AXL	1
1227	AZGP1	1
1228	AZI1	3.302566e-01
1229	AZI2	1
1230	AZIN1	1
1231	AZU1	1
1232	B2M	5.230288e-02
1233	B3GALNT1	1
1234	B3GALNT2	1
1235	B3GALT1	1
1236	B3GALT2	1
1237	B3GALT4	1.018342e-02
1238	B3GALT5	9.701817e-02
1239	B3GALTL	1
1240	B3GAT1	1
1241	B3GAT2	1.498034e-02
1242	B3GAT3	1.640041e-01
1243	B3GNT1	1.305235e-01
1244	B3GNT2	1
1245	B3GNT3	1
1246	B3GNT4	1
1247	B3GNT5	1
1248	B3GNT6	1
1249	B3GNT7	1
1250	B3GNT8	1
1251	B3GNT9	1.168801e-02
1252	B3GNTL1	5.705555e-02
1253	B4GALNT1	1
1254	B4GALNT2	6.725368e-02
1255	B4GALNT3	1
1256	B4GALNT4	1
1257	B4GALT1	1
1258	B4GALT2	1
1259	B4GALT3	1
1260	B4GALT4	1
1261	B4GALT5	1
1262	B4GALT6	1
1263	B4GALT7	6.465556e-02
1264	B9D1	8.804948e-02
1265	B9D2	1
1266	BAALC	1
1267	BAAT	1
Done

Running MutSig 2:
Scatter job 14: processing genes 1177 - 1267
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ATR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.291907e-01	ci left: 7.882909e-02	ci right 8.981448e-02	k: 842	n:10000
Cons ci ratio: 6.013027e-03	ci left: 9.739755e-01	ci right 9.799422e-01	k: 9771	n:10000
KS ci ratio: 2.375804e-01	ci left: 2.334629e-02	ci right 2.973355e-02	k: 264	n:10000
ATR   10000 perm   3 sec   (2987 perm/sec)   p_kst 2.640000e-02   p_cons 9.771000e-01   p_joint 8.420000e-02

Joint ci ratio: 1.003771e-01	ci left: 6.728287e-02	ci right 7.444250e-02	k: 1416	n:20000
Cons ci ratio: 4.294775e-03	ci left: 9.744093e-01	ci right 9.786506e-01	k: 19532	n:20000
KS ci ratio: 1.711769e-01	ci left: 2.335948e-02	ci right 2.777992e-02	k: 510	n:20000
ATR   20000 perm   9 sec   (2303 perm/sec)   p_kst 2.550000e-02   p_cons 9.766000e-01   p_joint 7.080000e-02

Joint ci ratio: 7.694005e-02	ci left: 7.656125e-02	ci right 8.272045e-02	k: 2388	n:30000
Cons ci ratio: 3.412507e-03	ci left: 9.760691e-01	ci right 9.794375e-01	k: 29334	n:30000
KS ci ratio: 1.386109e-01	ci left: 2.416419e-02	ci right 2.779507e-02	k: 778	n:30000
ATR   30000 perm   12 sec   (2582 perm/sec)   p_kst 2.593333e-02   p_cons 9.778000e-01   p_joint 7.960000e-02

Joint ci ratio: 7.433623e-02	ci left: 6.257867e-02	ci right 6.743472e-02	k: 2599	n:40000
Cons ci ratio: 2.975146e-03	ci left: 9.759990e-01	ci right 9.789311e-01	k: 39100	n:40000
KS ci ratio: 1.192575e-01	ci left: 2.472946e-02	ci right 2.788981e-02	k: 1051	n:40000
ATR   40000 perm   15 sec   (2668 perm/sec)   p_kst 2.627500e-02   p_cons 9.775000e-01   p_joint 6.497500e-02

Joint ci ratio: 8.262226e-02	ci left: 4.129730e-02	ci right 4.487599e-02	k: 2153	n:50000
Cons ci ratio: 2.676454e-03	ci left: 9.758947e-01	ci right 9.785295e-01	k: 48862	n:50000
KS ci ratio: 1.064183e-01	ci left: 2.501229e-02	ci right 2.784305e-02	k: 1320	n:50000
ATR   50000 perm   18 sec   (2761 perm/sec)   p_kst 2.640000e-02   p_cons 9.772400e-01   p_joint 4.306000e-02

Joint ci ratio: 7.243990e-02	ci left: 4.484517e-02	ci right 4.823220e-02	k: 2791	n:60000
Cons ci ratio: 2.575587e-03	ci left: 9.734802e-01	ci right 9.760069e-01	k: 58486	n:60000
KS ci ratio: 9.753252e-02	ci left: 2.493654e-02	ci right 2.750956e-02	k: 1572	n:60000
ATR   60000 perm   22 sec   (2787 perm/sec)   p_kst 2.620000e-02   p_cons 9.747667e-01   p_joint 4.651667e-02

Outputting figure to mutsig2_images.part000000000014/ATR.3_8123_60000_0.0262_0.97477_0.046517.png
                gene_name: ATR
               theta_stop: 0.098 
                    nperm: 60000 
                     p_ks: 0.026 
        ci_ks_bounds_left: 0.025 
       ci_ks_bounds_right: 0.028 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.047 
     ci_joint_bounds_left: 0.045 
    ci_joint_bounds_right: 0.048 

Current progress: 12 percent done.
ATXN7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.821111e-02	ci left: 5.028508e-01	ci right 5.225418e-01	k: 5127	n:10000
Cons ci ratio: 1.064529e-01	ci left: 1.130085e-01	ci right 1.258142e-01	k: 1193	n:10000
KS ci ratio: 1.063575e-02	ci left: 9.263722e-01	ci right 9.363747e-01	k: 9315	n:10000
ATXN7   10000 perm   2 sec   (5065 perm/sec)   p_kst 9.315000e-01   p_cons 1.193000e-01   p_joint 5.127000e-01

Joint ci ratio: 2.549141e-02	ci left: 5.348140e-01	ci right 5.486738e-01	k: 10835	n:20000
Cons ci ratio: 7.458496e-02	ci left: 1.168056e-01	ci right 1.259048e-01	k: 2426	n:20000
KS ci ratio: 7.553903e-03	ci left: 9.272970e-01	ci right 9.343772e-01	k: 18618	n:20000
ATXN7   20000 perm   4 sec   (4509 perm/sec)   p_kst 9.309000e-01   p_cons 1.213000e-01   p_joint 5.417500e-01

Outputting figure to mutsig2_images.part000000000014/ATXN7.3_2954_20000_0.9309_0.1213_0.54175.png
                gene_name: ATXN7
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.93 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 25 percent done.
AZI1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.230750e-01	ci left: 9.906147e-04	ci right 2.720474e-03	k: 17	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: 3.920006e-01	ci left: 7.963073e-03	ci right 1.193024e-02	k: 98	n:10000
AZI1   10000 perm   2 sec   (5687 perm/sec)   p_kst 9.800000e-03   p_cons 8.500000e-03   p_joint 1.700000e-03

Joint ci ratio: 7.151360e-01	ci left: 9.712961e-04	ci right 2.081783e-03	k: 29	n:20000
Cons ci ratio: 2.837806e-01	ci left: 8.109344e-03	ci right 1.083612e-02	k: 188	n:20000
KS ci ratio: 3.116120e-01	ci left: 6.627764e-03	ci right 9.118513e-03	k: 156	n:20000
AZI1   20000 perm   4 sec   (5026 perm/sec)   p_kst 7.800000e-03   p_cons 9.400000e-03   p_joint 1.450000e-03

Joint ci ratio: 6.117725e-01	ci left: 9.527184e-04	ci right 1.815184e-03	k: 40	n:30000
Cons ci ratio: 2.488992e-01	ci left: 7.179429e-03	ci right 9.250843e-03	k: 245	n:30000
KS ci ratio: 2.379288e-01	ci left: 7.899689e-03	ci right 1.006368e-02	k: 268	n:30000
AZI1   30000 perm   6 sec   (4661 perm/sec)   p_kst 8.933333e-03   p_cons 8.166667e-03   p_joint 1.333333e-03

Joint ci ratio: 5.596499e-01	ci left: 8.849137e-04	ci right 1.590715e-03	k: 48	n:40000
Cons ci ratio: 2.148943e-01	ci left: 7.363245e-03	ci right 9.159242e-03	k: 329	n:40000
KS ci ratio: 2.062467e-01	ci left: 8.026618e-03	ci right 9.895715e-03	k: 357	n:40000
AZI1   40000 perm   9 sec   (4388 perm/sec)   p_kst 8.925000e-03   p_cons 8.225000e-03   p_joint 1.200000e-03

Joint ci ratio: 4.896814e-01	ci left: 9.683502e-04	ci right 1.611803e-03	k: 63	n:50000
Cons ci ratio: 1.906986e-01	ci left: 7.580572e-03	ci right 9.197284e-03	k: 418	n:50000
KS ci ratio: 1.843692e-01	ci left: 8.133555e-03	ci right 9.804203e-03	k: 447	n:50000
AZI1   50000 perm   12 sec   (4252 perm/sec)   p_kst 8.940000e-03   p_cons 8.360000e-03   p_joint 1.260000e-03

Joint ci ratio: 3.620476e-01	ci left: 1.597806e-03	ci right 2.318402e-03	k: 116	n:60000
Cons ci ratio: 1.742233e-01	ci left: 7.637419e-03	ci right 9.110728e-03	k: 501	n:60000
KS ci ratio: 1.680849e-01	ci left: 8.227880e-03	ci right 9.753516e-03	k: 538	n:60000
AZI1   60000 perm   15 sec   (4128 perm/sec)   p_kst 8.966667e-03   p_cons 8.350000e-03   p_joint 1.933333e-03

Joint ci ratio: 3.517120e-01	ci left: 1.460564e-03	ci right 2.096164e-03	k: 123	n:70000
Cons ci ratio: 1.605640e-01	ci left: 7.764634e-03	ci right 9.133724e-03	k: 590	n:70000
KS ci ratio: 1.567311e-01	ci left: 8.162601e-03	ci right 9.564280e-03	k: 619	n:70000
AZI1   70000 perm   17 sec   (4025 perm/sec)   p_kst 8.842857e-03   p_cons 8.428571e-03   p_joint 1.757143e-03

Joint ci ratio: 3.517513e-01	ci left: 1.277971e-03	ci right 1.834183e-03	k: 123	n:80000
Cons ci ratio: 1.491320e-01	ci left: 7.923621e-03	ci right 9.212399e-03	k: 684	n:80000
KS ci ratio: 1.440237e-01	ci left: 8.513843e-03	ci right 9.847116e-03	k: 733	n:80000
AZI1   80000 perm   21 sec   (3874 perm/sec)   p_kst 9.162500e-03   p_cons 8.550000e-03   p_joint 1.537500e-03

Joint ci ratio: 3.685290e-01	ci left: 1.024779e-03	ci right 1.497201e-03	k: 112	n:90000
Cons ci ratio: 1.413099e-01	ci left: 7.878396e-03	ci right 9.086939e-03	k: 762	n:90000
KS ci ratio: 1.350257e-01	ci left: 8.650978e-03	ci right 9.914288e-03	k: 834	n:90000
AZI1   90000 perm   24 sec   (3704 perm/sec)   p_kst 9.266667e-03   p_cons 8.466667e-03   p_joint 1.244444e-03

Joint ci ratio: 2.587428e-01	ci left: 1.993910e-03	ci right 2.595541e-03	k: 228	n:100000
Cons ci ratio: 1.249911e-01	ci left: 9.130864e-03	ci right 1.035782e-02	k: 973	n:100000
KS ci ratio: 1.290675e-01	ci left: 8.549761e-03	ci right 9.738972e-03	k: 913	n:100000
AZI1   100000 perm   28 sec   (3625 perm/sec)   p_kst 9.130000e-03   p_cons 9.730000e-03   p_joint 2.280000e-03

Joint ci ratio: 2.501594e-01	ci left: 1.948820e-03	ci right 2.514301e-03	k: 244	n:110000
Cons ci ratio: 1.184177e-01	ci left: 9.279211e-03	ci right 1.045594e-02	k: 1084	n:110000
KS ci ratio: 1.227167e-01	ci left: 8.626588e-03	ci right 9.763152e-03	k: 1010	n:110000
AZI1   110000 perm   31 sec   (3603 perm/sec)   p_kst 9.181818e-03   p_cons 9.854545e-03   p_joint 2.218182e-03

Joint ci ratio: 2.414515e-01	ci left: 1.927178e-03	ci right 2.464000e-03	k: 262	n:120000
Cons ci ratio: 1.127830e-01	ci left: 9.404239e-03	ci right 1.053630e-02	k: 1195	n:120000
KS ci ratio: 1.172196e-01	ci left: 8.691805e-03	ci right 9.782110e-03	k: 1107	n:120000
AZI1   120000 perm   35 sec   (3426 perm/sec)   p_kst 9.225000e-03   p_cons 9.958333e-03   p_joint 2.183333e-03

Joint ci ratio: 2.352780e-01	ci left: 1.880190e-03	ci right 2.388581e-03	k: 276	n:130000
Cons ci ratio: 1.084289e-01	ci left: 9.413832e-03	ci right 1.050050e-02	k: 1293	n:130000
KS ci ratio: 1.122128e-01	ci left: 8.777862e-03	ci right 9.828816e-03	k: 1208	n:130000
AZI1   130000 perm   39 sec   (3369 perm/sec)   p_kst 9.292308e-03   p_cons 9.946154e-03   p_joint 2.123077e-03

Joint ci ratio: 2.549542e-01	ci left: 1.470950e-03	ci right 1.907247e-03	k: 235	n:140000
Cons ci ratio: 1.048095e-01	ci left: 9.374073e-03	ci right 1.041780e-02	k: 1384	n:140000
KS ci ratio: 1.081310e-01	ci left: 8.796859e-03	ci right 9.809335e-03	k: 1301	n:140000
AZI1   140000 perm   42 sec   (3314 perm/sec)   p_kst 9.292857e-03   p_cons 9.885714e-03   p_joint 1.678571e-03

Joint ci ratio: 2.864791e-01	ci left: 1.068282e-03	ci right 1.431438e-03	k: 186	n:150000
Cons ci ratio: 1.020197e-01	ci left: 9.249161e-03	ci right 1.024993e-02	k: 1461	n:150000
KS ci ratio: 1.043890e-01	ci left: 8.826911e-03	ci right 9.805530e-03	k: 1396	n:150000
AZI1   150000 perm   46 sec   (3277 perm/sec)   p_kst 9.306667e-03   p_cons 9.740000e-03   p_joint 1.240000e-03

Joint ci ratio: 2.075277e-01	ci left: 1.994140e-03	ci right 2.461690e-03	k: 355	n:160000
Cons ci ratio: 9.841334e-02	ci left: 9.335285e-03	ci right 1.030760e-02	k: 1570	n:160000
KS ci ratio: 1.011130e-01	ci left: 8.835455e-03	ci right 9.782453e-03	k: 1488	n:160000
AZI1   160000 perm   49 sec   (3239 perm/sec)   p_kst 9.300000e-03   p_cons 9.812500e-03   p_joint 2.218750e-03

Joint ci ratio: 2.146036e-01	ci left: 1.748669e-03	ci right 2.174485e-03	k: 332	n:170000
Cons ci ratio: 9.553823e-02	ci left: 9.337161e-03	ci right 1.027967e-02	k: 1666	n:170000
KS ci ratio: 9.844206e-02	ci left: 8.786028e-03	ci right 9.701414e-03	k: 1570	n:170000
AZI1   170000 perm   53 sec   (3204 perm/sec)   p_kst 9.235294e-03   p_cons 9.800000e-03   p_joint 1.952941e-03

Joint ci ratio: 2.272731e-01	ci left: 1.462554e-03	ci right 1.842675e-03	k: 296	n:180000
Cons ci ratio: 9.271551e-02	ci left: 9.377191e-03	ci right 1.029425e-02	k: 1769	n:180000
KS ci ratio: 9.611895e-02	ci left: 8.715270e-03	ci right 9.600647e-03	k: 1647	n:180000
AZI1   180000 perm   56 sec   (3189 perm/sec)   p_kst 9.150000e-03   p_cons 9.827778e-03   p_joint 1.644444e-03

Joint ci ratio: 2.213883e-01	ci left: 1.465056e-03	ci right 1.834626e-03	k: 312	n:190000
Cons ci ratio: 9.027520e-02	ci left: 9.382500e-03	ci right 1.027466e-02	k: 1866	n:190000
KS ci ratio: 9.316574e-02	ci left: 8.801280e-03	ci right 9.666425e-03	k: 1753	n:190000
AZI1   190000 perm   60 sec   (3167 perm/sec)   p_kst 9.226316e-03   p_cons 9.821053e-03   p_joint 1.642105e-03

Joint ci ratio: 2.203424e-01	ci left: 1.405969e-03	ci right 1.758730e-03	k: 315	n:200000
Cons ci ratio: 8.774764e-02	ci left: 9.446257e-03	ci right 1.031804e-02	k: 1975	n:200000
KS ci ratio: 9.093897e-02	ci left: 8.786198e-03	ci right 9.628119e-03	k: 1840	n:200000
AZI1   200000 perm   64 sec   (3148 perm/sec)   p_kst 9.200000e-03   p_cons 9.875000e-03   p_joint 1.575000e-03

Joint ci ratio: 2.182850e-01	ci left: 1.366017e-03	ci right 1.705124e-03	k: 321	n:210000
Cons ci ratio: 8.569136e-02	ci left: 9.443663e-03	ci right 1.029376e-02	k: 2071	n:210000
KS ci ratio: 8.905124e-02	ci left: 8.735521e-03	ci right 9.554305e-03	k: 1919	n:210000
AZI1   210000 perm   67 sec   (3115 perm/sec)   p_kst 9.138095e-03   p_cons 9.861905e-03   p_joint 1.528571e-03

Joint ci ratio: 1.913216e-01	ci left: 1.722349e-03	ci right 2.090973e-03	k: 418	n:220000
Cons ci ratio: 8.361750e-02	ci left: 9.477132e-03	ci right 1.030858e-02	k: 2175	n:220000
KS ci ratio: 8.707875e-02	ci left: 8.729641e-03	ci right 9.528827e-03	k: 2007	n:220000
AZI1   220000 perm   71 sec   (3089 perm/sec)   p_kst 9.122727e-03   p_cons 9.886364e-03   p_joint 1.900000e-03

Joint ci ratio: 1.871260e-01	ci left: 1.726160e-03	ci right 2.086578e-03	k: 437	n:230000
Cons ci ratio: 8.188702e-02	ci left: 9.461060e-03	ci right 1.027310e-02	k: 2268	n:230000
KS ci ratio: 8.517029e-02	ci left: 8.737223e-03	ci right 9.518701e-03	k: 2098	n:230000
AZI1   230000 perm   75 sec   (3067 perm/sec)   p_kst 9.121739e-03   p_cons 9.860870e-03   p_joint 1.900000e-03

Joint ci ratio: 1.854444e-01	ci left: 1.686012e-03	ci right 2.034528e-03	k: 445	n:240000
Cons ci ratio: 8.020828e-02	ci left: 9.458741e-03	ci right 1.025316e-02	k: 2364	n:240000
KS ci ratio: 8.317150e-02	ci left: 8.789236e-03	ci right 9.556021e-03	k: 2200	n:240000
AZI1   240000 perm   79 sec   (3039 perm/sec)   p_kst 9.166667e-03   p_cons 9.850000e-03   p_joint 1.854167e-03

Joint ci ratio: 2.105942e-01	ci left: 1.238291e-03	ci right 1.533463e-03	k: 345	n:250000
Cons ci ratio: 7.864486e-02	ci left: 9.452842e-03	ci right 1.023058e-02	k: 2459	n:250000
KS ci ratio: 8.152176e-02	ci left: 8.790253e-03	ci right 9.541193e-03	k: 2290	n:250000
AZI1   250000 perm   83 sec   (3014 perm/sec)   p_kst 9.160000e-03   p_cons 9.836000e-03   p_joint 1.380000e-03

Joint ci ratio: 2.073255e-01	ci left: 1.230758e-03	ci right 1.519003e-03	k: 356	n:260000
Cons ci ratio: 7.694167e-02	ci left: 9.504127e-03	ci right 1.026840e-02	k: 2569	n:260000
KS ci ratio: 7.993258e-02	ci left: 8.798871e-03	ci right 9.535210e-03	k: 2382	n:260000
AZI1   260000 perm   87 sec   (2988 perm/sec)   p_kst 9.161538e-03   p_cons 9.880769e-03   p_joint 1.369231e-03

Joint ci ratio: 2.044828e-01	ci left: 1.220301e-03	ci right 1.501688e-03	k: 366	n:270000
Cons ci ratio: 7.564444e-02	ci left: 9.475458e-03	ci right 1.022401e-02	k: 2658	n:270000
KS ci ratio: 7.843285e-02	ci left: 8.806981e-03	ci right 9.529540e-03	k: 2474	n:270000
AZI1   270000 perm   93 sec   (2902 perm/sec)   p_kst 9.162963e-03   p_cons 9.844444e-03   p_joint 1.355556e-03

Joint ci ratio: 2.061824e-01	ci left: 1.156388e-03	ci right 1.425533e-03	k: 360	n:280000
Cons ci ratio: 7.421998e-02	ci left: 9.498017e-03	ci right 1.023361e-02	k: 2761	n:280000
KS ci ratio: 7.702963e-02	ci left: 8.811129e-03	ci right 9.520515e-03	k: 2565	n:280000
AZI1   280000 perm   97 sec   (2878 perm/sec)   p_kst 9.160714e-03   p_cons 9.860714e-03   p_joint 1.285714e-03

Joint ci ratio: 2.221632e-01	ci left: 9.533224e-04	ci right 1.194758e-03	k: 310	n:290000
Cons ci ratio: 7.307945e-02	ci left: 9.464968e-03	ci right 1.018626e-02	k: 2848	n:290000
KS ci ratio: 7.591570e-02	ci left: 8.764346e-03	ci right 9.459310e-03	k: 2641	n:290000
AZI1   290000 perm   101 sec   (2858 perm/sec)   p_kst 9.106897e-03   p_cons 9.820690e-03   p_joint 1.068966e-03

Joint ci ratio: 2.056218e-01	ci left: 1.085614e-03	ci right 1.337513e-03	k: 362	n:300000
Cons ci ratio: 7.205191e-02	ci left: 9.417834e-03	ci right 1.012502e-02	k: 2930	n:300000
KS ci ratio: 7.447631e-02	ci left: 8.809086e-03	ci right 9.493780e-03	k: 2744	n:300000
AZI1   300000 perm   106 sec   (2833 perm/sec)   p_kst 9.146667e-03   p_cons 9.766667e-03   p_joint 1.206667e-03

Joint ci ratio: 2.028474e-01	ci left: 1.081203e-03	ci right 1.328274e-03	k: 372	n:310000
Cons ci ratio: 7.085309e-02	ci left: 9.430851e-03	ci right 1.012675e-02	k: 3030	n:310000
KS ci ratio: 7.331090e-02	ci left: 8.803546e-03	ci right 9.476646e-03	k: 2832	n:310000
AZI1   310000 perm   111 sec   (2789 perm/sec)   p_kst 9.135484e-03   p_cons 9.774194e-03   p_joint 1.200000e-03

Joint ci ratio: 2.009720e-01	ci left: 1.068183e-03	ci right 1.309746e-03	k: 379	n:320000
Cons ci ratio: 6.982489e-02	ci left: 9.412437e-03	ci right 1.009649e-02	k: 3120	n:320000
KS ci ratio: 7.206172e-02	ci left: 8.832192e-03	ci right 9.495493e-03	k: 2931	n:320000
AZI1   320000 perm   116 sec   (2763 perm/sec)   p_kst 9.159375e-03   p_cons 9.750000e-03   p_joint 1.184375e-03

Joint ci ratio: 1.968689e-01	ci left: 1.081885e-03	ci right 1.320952e-03	k: 395	n:330000
Cons ci ratio: 6.865689e-02	ci left: 9.445845e-03	ci right 1.012038e-02	k: 3227	n:330000
KS ci ratio: 7.096888e-02	ci left: 8.835376e-03	ci right 9.488438e-03	k: 3022	n:330000
AZI1   330000 perm   120 sec   (2742 perm/sec)   p_kst 9.157576e-03   p_cons 9.778788e-03   p_joint 1.196970e-03

Joint ci ratio: 1.951531e-01	ci left: 1.069642e-03	ci right 1.303699e-03	k: 402	n:340000
Cons ci ratio: 6.775106e-02	ci left: 9.419540e-03	ci right 1.008297e-02	k: 3314	n:340000
KS ci ratio: 6.981126e-02	ci left: 8.867347e-03	ci right 9.511648e-03	k: 3123	n:340000
AZI1   340000 perm   125 sec   (2722 perm/sec)   p_kst 9.185294e-03   p_cons 9.747059e-03   p_joint 1.182353e-03

Joint ci ratio: 1.937180e-01	ci left: 1.055389e-03	ci right 1.284427e-03	k: 408	n:350000
Cons ci ratio: 6.684049e-02	ci left: 9.406033e-03	ci right 1.005927e-02	k: 3405	n:350000
KS ci ratio: 6.885951e-02	ci left: 8.858254e-03	ci right 9.492769e-03	k: 3210	n:350000
AZI1   350000 perm   130 sec   (2701 perm/sec)   p_kst 9.171429e-03   p_cons 9.728571e-03   p_joint 1.165714e-03

Joint ci ratio: 1.909371e-01	ci left: 1.057801e-03	ci right 1.283685e-03	k: 420	n:360000
Cons ci ratio: 6.583273e-02	ci left: 9.431587e-03	ci right 1.007634e-02	k: 3510	n:360000
KS ci ratio: 6.793526e-02	ci left: 8.852454e-03	ci right 9.477707e-03	k: 3298	n:360000
AZI1   360000 perm   134 sec   (2682 perm/sec)   p_kst 9.161111e-03   p_cons 9.750000e-03   p_joint 1.166667e-03

Joint ci ratio: 1.882727e-01	ci left: 1.060105e-03	ci right 1.282961e-03	k: 432	n:370000
Cons ci ratio: 6.499640e-02	ci left: 9.418600e-03	ci right 1.005398e-02	k: 3601	n:370000
KS ci ratio: 6.692770e-02	ci left: 8.878916e-03	ci right 9.496375e-03	k: 3398	n:370000
AZI1   370000 perm   139 sec   (2662 perm/sec)   p_kst 9.183784e-03   p_cons 9.732432e-03   p_joint 1.167568e-03

Joint ci ratio: 1.857167e-01	ci left: 1.062308e-03	ci right 1.282254e-03	k: 444	n:380000
Cons ci ratio: 6.410357e-02	ci left: 9.432243e-03	ci right 1.005948e-02	k: 3702	n:380000
KS ci ratio: 6.613558e-02	ci left: 8.857456e-03	ci right 9.465853e-03	k: 3480	n:380000
AZI1   380000 perm   144 sec   (2644 perm/sec)   p_kst 9.157895e-03   p_cons 9.742105e-03   p_joint 1.168421e-03

Joint ci ratio: 1.840704e-01	ci left: 1.054632e-03	ci right 1.270838e-03	k: 452	n:390000
Cons ci ratio: 6.328857e-02	ci left: 9.432624e-03	ci right 1.005162e-02	k: 3798	n:390000
KS ci ratio: 6.541727e-02	ci left: 8.824525e-03	ci right 9.423828e-03	k: 3557	n:390000
AZI1   390000 perm   149 sec   (2625 perm/sec)   p_kst 9.120513e-03   p_cons 9.738462e-03   p_joint 1.158974e-03

Joint ci ratio: 1.930248e-01	ci left: 9.305961e-04	ci right 1.131745e-03	k: 411	n:400000
Cons ci ratio: 6.240687e-02	ci left: 9.462569e-03	ci right 1.007456e-02	k: 3906	n:400000
KS ci ratio: 6.470390e-02	ci left: 8.798195e-03	ci right 9.388949e-03	k: 3636	n:400000
AZI1   400000 perm   153 sec   (2606 perm/sec)   p_kst 9.090000e-03   p_cons 9.765000e-03   p_joint 1.027500e-03

Joint ci ratio: 1.898257e-01	ci left: 9.404091e-04	ci right 1.139921e-03	k: 425	n:410000
Cons ci ratio: 6.159202e-02	ci left: 9.481504e-03	ci right 1.008643e-02	k: 4010	n:410000
KS ci ratio: 6.403945e-02	ci left: 8.765982e-03	ci right 9.348305e-03	k: 3712	n:410000
AZI1   410000 perm   159 sec   (2586 perm/sec)   p_kst 9.053659e-03   p_cons 9.780488e-03   p_joint 1.036585e-03

Joint ci ratio: 1.874212e-01	ci left: 9.429723e-04	ci right 1.140206e-03	k: 436	n:420000
Cons ci ratio: 6.095053e-02	ci left: 9.455030e-03	ci right 1.005176e-02	k: 4095	n:420000
KS ci ratio: 6.341195e-02	ci left: 8.730646e-03	ci right 9.304729e-03	k: 3786	n:420000
AZI1   420000 perm   164 sec   (2564 perm/sec)   p_kst 9.014286e-03   p_cons 9.750000e-03   p_joint 1.038095e-03

Joint ci ratio: 1.907287e-01	ci left: 8.878076e-04	ci right 1.077160e-03	k: 421	n:430000
Cons ci ratio: 6.031411e-02	ci left: 9.434400e-03	ci right 1.002340e-02	k: 4182	n:430000
KS ci ratio: 6.269610e-02	ci left: 8.726743e-03	ci right 9.293856e-03	k: 3873	n:430000
AZI1   430000 perm   169 sec   (2546 perm/sec)   p_kst 9.006977e-03   p_cons 9.725581e-03   p_joint 9.790698e-04

Joint ci ratio: 1.885083e-01	ci left: 8.892786e-04	ci right 1.076484e-03	k: 431	n:440000
Cons ci ratio: 5.953551e-02	ci left: 9.466241e-03	ci right 1.004933e-02	k: 4292	n:440000
KS ci ratio: 6.207517e-02	ci left: 8.702912e-03	ci right 9.262674e-03	k: 3951	n:440000
AZI1   440000 perm   174 sec   (2524 perm/sec)   p_kst 8.979545e-03   p_cons 9.754545e-03   p_joint 9.795455e-04

Joint ci ratio: 1.951814e-01	ci left: 8.081633e-04	ci right 9.850313e-04	k: 402	n:450000
Cons ci ratio: 5.890124e-02	ci left: 9.459485e-03	ci right 1.003574e-02	k: 4385	n:450000
KS ci ratio: 6.144925e-02	ci left: 8.686732e-03	ci right 9.239619e-03	k: 4032	n:450000
AZI1   450000 perm   180 sec   (2506 perm/sec)   p_kst 8.960000e-03   p_cons 9.744444e-03   p_joint 8.933333e-04

Joint ci ratio: 2.134575e-01	ci left: 6.544363e-04	ci right 8.128312e-04	k: 336	n:460000
Cons ci ratio: 5.825399e-02	ci left: 9.463768e-03	ci right 1.003374e-02	k: 4483	n:460000
KS ci ratio: 6.085681e-02	ci left: 8.667000e-03	ci right 9.213125e-03	k: 4111	n:460000
AZI1   460000 perm   185 sec   (2489 perm/sec)   p_kst 8.936957e-03   p_cons 9.745652e-03   p_joint 7.304348e-04

Joint ci ratio: 1.714783e-01	ci left: 1.015403e-03	ci right 1.207854e-03	k: 521	n:470000
Cons ci ratio: 6.217250e-02	ci left: 8.126386e-03	ci right 8.649914e-03	k: 3941	n:470000
KS ci ratio: 6.028844e-02	ci left: 8.646037e-03	ci right 9.185575e-03	k: 4189	n:470000
AZI1   470000 perm   191 sec   (2466 perm/sec)   p_kst 8.912766e-03   p_cons 8.385106e-03   p_joint 1.108511e-03

Joint ci ratio: 1.713160e-01	ci left: 9.962416e-04	ci right 1.184864e-03	k: 522	n:480000
Cons ci ratio: 6.150508e-02	ci left: 8.133484e-03	ci right 8.651643e-03	k: 4027	n:480000
KS ci ratio: 5.975690e-02	ci left: 8.619812e-03	ci right 9.152808e-03	k: 4264	n:480000
AZI1   480000 perm   196 sec   (2448 perm/sec)   p_kst 8.883333e-03   p_cons 8.389583e-03   p_joint 1.087500e-03

Joint ci ratio: 1.695424e-01	ci left: 9.974016e-04	ci right 1.184088e-03	k: 533	n:490000
Cons ci ratio: 6.089603e-02	ci left: 8.130270e-03	ci right 8.642915e-03	k: 4108	n:490000
KS ci ratio: 5.924605e-02	ci left: 8.592668e-03	ci right 9.119287e-03	k: 4338	n:490000
AZI1   490000 perm   202 sec   (2430 perm/sec)   p_kst 8.853061e-03   p_cons 8.383673e-03   p_joint 1.087755e-03

Joint ci ratio: 1.684426e-01	ci left: 9.908612e-04	ci right 1.174999e-03	k: 540	n:500000
Cons ci ratio: 6.031923e-02	ci left: 8.123269e-03	ci right 8.630452e-03	k: 4187	n:500000
KS ci ratio: 5.865428e-02	ci left: 8.594220e-03	ci right 9.115495e-03	k: 4426	n:500000
AZI1   500000 perm   207 sec   (2411 perm/sec)   p_kst 8.852000e-03   p_cons 8.374000e-03   p_joint 1.080000e-03

Joint ci ratio: 1.534207e-01	ci left: 1.180342e-03	ci right 1.378335e-03	k: 651	n:510000
Cons ci ratio: 5.969507e-02	ci left: 8.133951e-03	ci right 8.636364e-03	k: 4275	n:510000
KS ci ratio: 5.804100e-02	ci left: 8.607332e-03	ci right 9.123761e-03	k: 4520	n:510000
AZI1   510000 perm   213 sec   (2393 perm/sec)   p_kst 8.862745e-03   p_cons 8.382353e-03   p_joint 1.276471e-03

Joint ci ratio: 1.697068e-01	ci left: 9.380153e-04	ci right 1.113774e-03	k: 532	n:520000
Cons ci ratio: 5.915829e-02	ci left: 8.125298e-03	ci right 8.622510e-03	k: 4353	n:520000
KS ci ratio: 5.750316e-02	ci left: 8.602906e-03	ci right 9.114127e-03	k: 4605	n:520000
AZI1   520000 perm   219 sec   (2375 perm/sec)   p_kst 8.855769e-03   p_cons 8.371154e-03   p_joint 1.023077e-03

Joint ci ratio: 1.676739e-01	ci left: 9.438099e-04	ci right 1.118322e-03	k: 545	n:530000
Cons ci ratio: 5.864240e-02	ci left: 8.115133e-03	ci right 8.607245e-03	k: 4430	n:530000
KS ci ratio: 5.698000e-02	ci left: 8.598668e-03	ci right 9.104836e-03	k: 4690	n:530000
AZI1   530000 perm   225 sec   (2358 perm/sec)   p_kst 8.849057e-03   p_cons 8.358491e-03   p_joint 1.028302e-03

Joint ci ratio: 1.503410e-01	ci left: 1.162866e-03	ci right 1.353660e-03	k: 678	n:540000
Cons ci ratio: 5.813327e-02	ci left: 8.107187e-03	ci right 8.594406e-03	k: 4508	n:540000
KS ci ratio: 5.642320e-02	ci left: 8.609215e-03	ci right 9.110890e-03	k: 4783	n:540000
AZI1   540000 perm   231 sec   (2341 perm/sec)   p_kst 8.857407e-03   p_cons 8.348148e-03   p_joint 1.255556e-03

Joint ci ratio: 1.487071e-01	ci left: 1.167976e-03	ci right 1.357340e-03	k: 693	n:550000
Cons ci ratio: 5.756130e-02	ci left: 8.121055e-03	ci right 8.604145e-03	k: 4598	n:550000
KS ci ratio: 5.593452e-02	ci left: 8.603265e-03	ci right 9.100111e-03	k: 4867	n:550000
AZI1   550000 perm   237 sec   (2323 perm/sec)   p_kst 8.849091e-03   p_cons 8.360000e-03   p_joint 1.260000e-03

Joint ci ratio: 1.423784e-01	ci left: 1.255528e-03	ci right 1.449689e-03	k: 756	n:560000
Cons ci ratio: 5.714739e-02	ci left: 8.093960e-03	ci right 8.571862e-03	k: 4665	n:560000
KS ci ratio: 5.540753e-02	ci left: 8.613396e-03	ci right 9.105991e-03	k: 4960	n:560000
AZI1   560000 perm   243 sec   (2307 perm/sec)   p_kst 8.857143e-03   p_cons 8.330357e-03   p_joint 1.350000e-03

Joint ci ratio: 1.034952e-01	ci left: 2.380563e-03	ci right 2.642078e-03	k: 1430	n:570000
Cons ci ratio: 5.663980e-02	ci left: 8.097233e-03	ci right 8.570943e-03	k: 4749	n:570000
KS ci ratio: 5.502163e-02	ci left: 8.583392e-03	ci right 9.070743e-03	k: 5030	n:570000
AZI1   570000 perm   249 sec   (2289 perm/sec)   p_kst 8.824561e-03   p_cons 8.331579e-03   p_joint 2.508772e-03

Joint ci ratio: 1.025322e-01	ci left: 2.384871e-03	ci right 2.644276e-03	k: 1457	n:580000
Cons ci ratio: 5.616308e-02	ci left: 8.095311e-03	ci right 8.564793e-03	k: 4830	n:580000
KS ci ratio: 5.460049e-02	ci left: 8.568040e-03	ci right 9.050678e-03	k: 5108	n:580000
AZI1   580000 perm   255 sec   (2273 perm/sec)   p_kst 8.806897e-03   p_cons 8.327586e-03   p_joint 2.512069e-03

Joint ci ratio: 1.051704e-01	ci left: 2.225576e-03	ci right 2.474267e-03	k: 1385	n:590000
Cons ci ratio: 5.563541e-02	ci left: 8.111857e-03	ci right 8.577736e-03	k: 4922	n:590000
KS ci ratio: 5.415728e-02	ci left: 8.563256e-03	ci right 9.041586e-03	k: 5192	n:590000
AZI1   590000 perm   261 sec   (2256 perm/sec)   p_kst 8.800000e-03   p_cons 8.342373e-03   p_joint 2.347458e-03

Joint ci ratio: 9.590570e-02	ci left: 2.643466e-03	ci right 2.911371e-03	k: 1665	n:600000
Cons ci ratio: 5.518896e-02	ci left: 8.108144e-03	ci right 8.569955e-03	k: 5002	n:600000
KS ci ratio: 5.379157e-02	ci left: 8.537268e-03	ci right 9.010827e-03	k: 5263	n:600000
AZI1   600000 perm   268 sec   (2240 perm/sec)   p_kst 8.771667e-03   p_cons 8.336667e-03   p_joint 2.775000e-03

Outputting figure to mutsig2_images.part000000000014/AZI1.3_3343_600000_0.0087717_0.0083367_0.002775.png
                gene_name: AZI1
               theta_stop: 0.096 
                    nperm: 600000 
                     p_ks: 0.0088 
        ci_ks_bounds_left: 0.0085 
       ci_ks_bounds_right: 0.0090 
                   p_cons: 0.0083 
      ci_cons_bounds_left: 0.0081 
     ci_cons_bounds_right: 0.0086 
                  p_joint: 0.0028 
     ci_joint_bounds_left: 0.0026 
    ci_joint_bounds_right: 0.0029 

Current progress: 38 percent done.
ATP8B3
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: 2.955063e-02	ci left: 6.280896e-01	ci right 6.470302e-01	k: 6376	n:10000
KS ci ratio: 9.076292e-02	ci left: 1.500184e-01	ci right 1.643819e-01	k: 1571	n:10000
ATP8B3   10000 perm   2 sec   (5549 perm/sec)   p_kst 1.571000e-01   p_cons 6.376000e-01   p_joint 2.713000e-01

Outputting figure to mutsig2_images.part000000000014/ATP8B3.2_4063_10000_0.1571_0.6376_0.2713.png
                gene_name: ATP8B3
               theta_stop: 0.091 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.27 
     ci_joint_bounds_left: 0.26 
    ci_joint_bounds_right: 0.28 

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: 5.193970e-02	ci left: 3.533674e-01	ci right 3.723125e-01	k: 3628	n:10000
KS ci ratio: 1.418978e-01	ci left: 6.584842e-02	ci right 7.600325e-02	k: 708	n:10000
ATRNL1   10000 perm   2 sec   (5497 perm/sec)   p_kst 7.080000e-02   p_cons 3.628000e-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: 3.654482e-02	ci left: 3.584723e-01	ci right 3.718670e-01	k: 7303	n:20000
KS ci ratio: 1.003771e-01	ci left: 6.728287e-02	ci right 7.444250e-02	k: 1416	n:20000
ATRNL1   20000 perm   4 sec   (4905 perm/sec)   p_kst 7.080000e-02   p_cons 3.651500e-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: 2.972319e-02	ci left: 3.615091e-01	ci right 3.724500e-01	k: 11009	n:30000
KS ci ratio: 8.259776e-02	ci left: 6.694170e-02	ci right 7.274194e-02	k: 2094	n:30000
ATRNL1   30000 perm   6 sec   (4706 perm/sec)   p_kst 6.980000e-02   p_cons 3.669667e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000014/ATRNL1.2_4256_30000_0.0698_0.36697_1.png
                gene_name: ATRNL1
               theta_stop: 0.083 
                    nperm: 30000 
                     p_ks: 0.070 
        ci_ks_bounds_left: 0.067 
       ci_ks_bounds_right: 0.073 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.37 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 62 percent done.
ATRX
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.495584e-02	ci left: 1.386431e-01	ci right 1.525641e-01	k: 1455	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: 1.940616e-01	ci left: 3.538572e-02	ci right 4.308567e-02	k: 391	n:10000
ATRX   10000 perm   2 sec   (4542 perm/sec)   p_kst 3.910000e-02   p_cons 5.230000e-01   p_joint 1.455000e-01

Joint ci ratio: 7.123371e-02	ci left: 1.267960e-01	ci right 1.362115e-01	k: 2629	n:20000
Cons ci ratio: 2.765837e-02	ci left: 4.940958e-01	ci right 5.080039e-01	k: 10021	n:20000
KS ci ratio: 1.374995e-01	ci left: 3.635916e-02	ci right 4.177590e-02	k: 780	n:20000
ATRX   20000 perm   5 sec   (4127 perm/sec)   p_kst 3.900000e-02   p_cons 5.010500e-01   p_joint 1.314500e-01

Joint ci ratio: 7.467094e-02	ci left: 8.098314e-02	ci right 8.729767e-02	k: 2523	n:30000
Cons ci ratio: 2.276415e-02	ci left: 4.913927e-01	ci right 5.027412e-01	k: 14912	n:30000
KS ci ratio: 1.103944e-01	ci left: 3.810255e-02	ci right 4.258702e-02	k: 1209	n:30000
ATRX   30000 perm   8 sec   (3967 perm/sec)   p_kst 4.030000e-02   p_cons 4.970667e-01   p_joint 8.410000e-02

Joint ci ratio: 6.487081e-02	ci left: 8.092996e-02	ci right 8.638066e-02	k: 3345	n:40000
Cons ci ratio: 1.969455e-02	ci left: 4.926630e-01	ci right 5.024874e-01	k: 19903	n:40000
KS ci ratio: 9.700195e-02	ci left: 3.731916e-02	ci right 4.114810e-02	k: 1568	n:40000
ATRX   40000 perm   10 sec   (3862 perm/sec)   p_kst 3.920000e-02   p_cons 4.975750e-01   p_joint 8.362500e-02

Outputting figure to mutsig2_images.part000000000014/ATRX.2_7619_40000_0.0392_0.49757_0.083625.png
                gene_name: ATRX
               theta_stop: 0.097 
                    nperm: 40000 
                     p_ks: 0.039 
        ci_ks_bounds_left: 0.037 
       ci_ks_bounds_right: 0.041 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.084 
     ci_joint_bounds_left: 0.081 
    ci_joint_bounds_right: 0.086 

Current progress: 75 percent done.
AXIN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.099457e-02	ci left: 7.688127e-01	ci right 7.852256e-01	k: 7771	n:10000
Cons ci ratio: 5.646737e-02	ci left: 3.159213e-01	ci right 3.343806e-01	k: 3251	n:10000
KS ci ratio: 5.140488e-02	ci left: 3.581397e-01	ci right 3.771375e-01	k: 3676	n:10000
AXIN1   10000 perm   2 sec   (6146 perm/sec)   p_kst 3.676000e-01   p_cons 3.251000e-01   p_joint 7.771000e-01

Outputting figure to mutsig2_images.part000000000014/AXIN1.2_2629_10000_0.3676_0.3251_0.7771.png
                gene_name: AXIN1
               theta_stop: 0.056 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.79 

Current progress: 88 percent done.
B3GALT4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.145358e-02	ci left: 4.621749e-01	ci right 4.818414e-01	k: 4720	n:10000
Cons ci ratio: 6.404922e-02	ci left: 2.636916e-01	ci right 2.812411e-01	k: 2724	n:10000
KS ci ratio: 3.164444e-02	ci left: 5.957408e-01	ci right 6.149978e-01	k: 6054	n:10000
B3GALT4   10000 perm   1 sec   (6790 perm/sec)   p_kst 6.054000e-01   p_cons 2.724000e-01   p_joint 4.720000e-01

Outputting figure to mutsig2_images.part000000000014/B3GALT4.2_1141_10000_0.6054_0.2724_0.472.png
                gene_name: B3GALT4
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.27 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.28 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    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.165.3896/
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/181708/iteration1/scatter.0000000014
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 14 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1556>
Subject: Job 1119518: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1556>, 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/181708/iteration1/scatter.0000000015> was used as the working directory.
Started at Wed Oct 10 10:41:48 2012
Results reported at Wed Oct 10 10:44:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000015.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000015.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 15  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    135.06 sec.
    Max Memory :      1324 MB
    Max Swap   :      3877 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.165.3896/
-whichjob
15
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 15: processing genes 1268 - 1357
Calculating significance of each gene.
Using projection method.
1268	BACE1	1
1269	BACE2	1
1270	BACH1	2.492737e-01
1271	BACH2	3.369310e-01
1272	BAD	1
1273	BAG1	1
1274	BAG2	1
1275	BAG3	1
1276	BAG4	8.580324e-02
1277	BAG5	1.312189e-01
1278	BAGE	1
1279	BAGE2	1
1280	BAGE3	1
1281	BAGE4	1
1282	BAGE5	1
1283	BAHCC1	1
1284	BAHD1	2.590809e-01
1285	BAI1	1
1286	BAI2	1
1287	BAI3	1
1288	BAIAP2	1
1289	BAIAP2L1	1
1290	BAIAP2L2	1
1291	BAIAP3	9.076104e-02
1292	BAK1	1
1293	BAMBI	1
1294	BANF1	1
1295	BANF2	1
1296	BANK1	3.044810e-01
1297	BANP	1
1298	BAP1	2.162091e-02
1299	BARD1	1
1300	BARHL1	1
1301	BARHL2	1
1302	BARX1	1
1303	BARX2	1.419950e-01
1304	BASP1	1
1305	BAT1	1.518022e-02
1306	BAT2	3.203832e-01
1307	BAT2L1	1
1308	BAT2L2	7.236490e-01
1309	BAT3	1
1310	BAT4	1
1311	BAT5	1
1312	BATF	1
1313	BATF2	1
1314	BATF3	1
1315	BAX	4.826263e-02
1316	BAZ1A	4.974677e-01
1317	BAZ1B	1
1318	BAZ2A	8.608659e-02
1319	BAZ2B	4.015378e-01
1320	BBOX1	1
1321	BBS1	9.519075e-02
1322	BBS10	9.238189e-02
1323	BBS12	1
1324	BBS2	1
1325	BBS4	1
1326	BBS5	1
1327	BBS7	1
1328	BBS9	1.748016e-01
1329	BBX	1
1330	BCAM	1
1331	BCAN	1
1332	BCAP29	1.619136e-01
1333	BCAP31	1
1334	BCAR1	1
1335	BCAR3	1
1336	BCAS1	7.224202e-02
1337	BCAS2	1
1338	BCAS3	2.133838e-01
1339	BCAS4	1
1340	BCAT1	1
1341	BCAT2	1
1342	BCCIP	1
1343	BCDIN3D	1
1344	BCHE	1
1345	BCKDHA	1
1346	BCKDHB	1
1347	BCKDK	1
1348	BCL10	4.250457e-02
1349	BCL11A	1
1350	BCL11B	1
1351	BCL2	1
1352	BCL2A1	1
1353	BCL2L1	8.121013e-02
1354	BCL2L10	1
1355	BCL2L11	1
1356	BCL2L12	1
1357	BCL2L13	2.241050e-01
Done

Running MutSig 2:
Scatter job 15: processing genes 1268 - 1357
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
BAG5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.074776e-01	ci left: 1.110554e-01	ci right 1.237684e-01	k: 1173	n:10000
Cons ci ratio: 8.098835e-02	ci left: 1.820569e-01	ci right 1.975242e-01	k: 1897	n:10000
KS ci ratio: 6.587477e-02	ci left: 2.528084e-01	ci right 2.701307e-01	k: 2614	n:10000
BAG5   10000 perm   2 sec   (5586 perm/sec)   p_kst 2.614000e-01   p_cons 1.897000e-01   p_joint 1.173000e-01

Joint ci ratio: 8.445036e-02	ci left: 9.312830e-02	ci right 1.013892e-01	k: 1944	n:20000
Cons ci ratio: 5.277655e-02	ci left: 2.104619e-01	ci right 2.219207e-01	k: 4323	n:20000
KS ci ratio: 4.608554e-02	ci left: 2.594885e-01	ci right 2.717797e-01	k: 5312	n:20000
BAG5   20000 perm   8 sec   (2650 perm/sec)   p_kst 2.656000e-01   p_cons 2.161500e-01   p_joint 9.720000e-02

Outputting figure to mutsig2_images.part000000000015/BAG5.2_1475_20000_0.2656_0.21615_0.0972.png
                gene_name: BAG5
               theta_stop: 0.084 
                    nperm: 20000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.097 
     ci_joint_bounds_left: 0.093 
    ci_joint_bounds_right: 0.10 

Current progress: 20 percent done.
BAIAP3
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: 2.247489e-02	ci left: 7.440199e-01	ci right 7.610327e-01	k: 7526	n:10000
KS ci ratio: 8.751644e-03	ci left: 9.482515e-01	ci right 9.566824e-01	k: 9526	n:10000
BAIAP3   10000 perm   2 sec   (5246 perm/sec)   p_kst 9.526000e-01   p_cons 7.526000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000015/BAIAP3.2_3700_10000_0.9526_0.7526_1.png
                gene_name: BAIAP3
               theta_stop: 0.022 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.96 
                   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: 40 percent done.
BAP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.602799e-02	ci left: 8.497808e-01	ci right 8.636107e-01	k: 8568	n:10000
Cons ci ratio: 5.413272e-02	ci left: 3.345866e-01	ci right 3.533044e-01	k: 3439	n:10000
KS ci ratio: 4.511523e-02	ci left: 4.203680e-01	ci right 4.398728e-01	k: 4301	n:10000
BAP1   10000 perm   2 sec   (5145 perm/sec)   p_kst 4.301000e-01   p_cons 3.439000e-01   p_joint 8.568000e-01

Outputting figure to mutsig2_images.part000000000015/BAP1.2_2258_10000_0.4301_0.3439_0.8568.png
                gene_name: BAP1
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.35 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.86 

Current progress: 60 percent done.
BAT1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.552876e-02	ci left: 3.232663e-01	ci right 3.418313e-01	k: 3325	n:10000
Cons ci ratio: 1.451967e-02	ci left: 8.728564e-01	ci right 8.857217e-01	k: 8794	n:10000
KS ci ratio: 7.126047e-02	ci left: 2.239532e-01	ci right 2.406030e-01	k: 2322	n:10000
BAT1   10000 perm   2 sec   (5810 perm/sec)   p_kst 2.322000e-01   p_cons 8.794000e-01   p_joint 3.325000e-01

Outputting figure to mutsig2_images.part000000000015/BAT1.2_1327_10000_0.2322_0.8794_0.3325.png
                gene_name: BAT1
               theta_stop: 0.071 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 80 percent done.
BAZ2A
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: 2.695714e-02	ci left: 6.696478e-01	ci right 6.880479e-01	k: 6789	n:10000
KS ci ratio: 1.544893e-02	ci left: 8.587584e-01	ci right 8.722279e-01	k: 8656	n:10000
BAZ2A   10000 perm   3 sec   (3853 perm/sec)   p_kst 8.656000e-01   p_cons 6.789000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000015/BAZ2A.2_5834_10000_0.8656_0.6789_1.png
                gene_name: BAZ2A
               theta_stop: 0.027 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.87 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000015
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 15 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119523: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000016> was used as the working directory.
Started at Wed Oct 10 10:41:48 2012
Results reported at Wed Oct 10 10:44:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000016.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000016.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 16  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    169.28 sec.
    Max Memory :      1315 MB
    Max Swap   :      3879 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.165.3896/
-whichjob
16
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 16: processing genes 1358 - 1448
Calculating significance of each gene.
Using projection method.
1358	BCL2L14	1
1359	BCL2L15	1
1360	BCL2L2	1
1361	BCL3	1
1362	BCL6	1
1363	BCL6B	1
1364	BCL7A	1
1365	BCL7B	1
1366	BCL7C	1
1367	BCL9	1
1368	BCL9L	3.461560e-01
1369	BCLAF1	2.112810e-04
1370	BCMO1	1
1371	BCO2	1
1372	BCOR	5.824960e-01
1373	BCORL1	9.580119e-02
1374	BCR	1
1375	BCS1L	1
1376	BDH1	1
1377	BDH2	6.088042e-02
1378	BDKRB1	1.082388e-01
1379	BDKRB2	1
1380	BDNF	1
1381	BDP1	5.206669e-01
1382	BECN1	1
1383	BEGAIN	1
1384	BEND2	1
1385	BEND3	1
1386	BEND4	1
1387	BEND5	1
1388	BEND6	1
1389	BEND7	1
1390	BEST1	3.660545e-03
1391	BEST2	1
1392	BEST3	2.886738e-01
1393	BEST4	1
1394	BET1	1
1395	BET1L	1
1396	BEX1	1
1397	BEX2	1
1398	BEX4	1
1399	BEX5	1
1400	BFAR	1
1401	BFSP1	1
1402	BFSP2	2.067421e-01
1403	BGLAP	7.223510e-03
1404	BGN	1
1405	BHLHB9	1.355655e-01
1406	BHLHE22	1
1407	BHLHE23	1
1408	BHLHE40	1
1409	BHLHE41	1
1410	BHMT	1
1411	BHMT2	1.761457e-01
1412	BICC1	3.817804e-01
1413	BICD1	1
1414	BICD2	1
1415	BID	1
1416	BIK	1
1417	BIN1	1
1418	BIN2	1
1419	BIN3	1
1420	BIRC2	1
1421	BIRC3	1
1422	BIRC5	6.296700e-02
1423	BIRC6	2.889410e-01
1424	BIRC7	1
1425	BIRC8	1.010924e-01
1426	BIVM	1
1427	BLCAP	1
1428	BLID	1
1429	BLK	1
1430	BLM	3.427109e-01
1431	BLMH	1
1432	BLNK	1
1433	BLOC1S1	1
1434	BLOC1S2	1
1435	BLOC1S3	1
1436	BLVRA	1
1437	BLVRB	1
1438	BLZF1	1
1439	BMF	1
1440	BMI1	7.954606e-02
1441	BMP1	1
1442	BMP10	1
1443	BMP15	1
1444	BMP2	1
1445	BMP2K	1.197601e-01
1446	BMP3	1.868853e-01
1447	BMP4	8.231902e-02
1448	BMP5	1
Done

Running MutSig 2:
Scatter job 16: processing genes 1358 - 1448
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
BCLAF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.924285e-02	ci left: 3.782339e-01	ci right 3.974315e-01	k: 3878	n:10000
Cons ci ratio: 1.600187e-02	ci left: 8.501887e-01	ci right 8.640026e-01	k: 8572	n:10000
KS ci ratio: 6.988973e-02	ci left: 2.308658e-01	ci right 2.476864e-01	k: 2392	n:10000
BCLAF1   10000 perm   2 sec   (4487 perm/sec)   p_kst 2.392000e-01   p_cons 8.572000e-01   p_joint 3.878000e-01

Outputting figure to mutsig2_images.part000000000016/BCLAF1.5_2807_10000_0.2392_0.8572_0.3878.png
                gene_name: BCLAF1
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 25 percent done.
BIRC6
Processing conservation and coverage...
67% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.448234e-02	ci left: 3.317063e-01	ci right 3.503864e-01	k: 3410	n:10000
Cons ci ratio: 1.138976e-01	ci left: 9.983694e-02	ci right 1.119937e-01	k: 1058	n:10000
KS ci ratio: 4.954487e-02	ci left: 3.753480e-01	ci right 3.945190e-01	k: 3849	n:10000
BIRC6   10000 perm   5 sec   (2010 perm/sec)   p_kst 3.849000e-01   p_cons 1.058000e-01   p_joint 3.410000e-01

Joint ci ratio: 3.487477e-02	ci left: 3.803413e-01	ci right 3.938916e-01	k: 7742	n:20000
Cons ci ratio: 8.030626e-02	ci left: 1.021590e-01	ci right 1.107558e-01	k: 2128	n:20000
KS ci ratio: 3.487477e-02	ci left: 3.803413e-01	ci right 3.938916e-01	k: 7742	n:20000
BIRC6   20000 perm   10 sec   (1974 perm/sec)   p_kst 3.871000e-01   p_cons 1.064000e-01   p_joint 3.871000e-01

Outputting figure to mutsig2_images.part000000000016/BIRC6.3_14870_20000_0.3871_0.1064_0.3871.png
                gene_name: BIRC6
               theta_stop: 0.080 
                    nperm: 20000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.39 

Current progress: 50 percent done.
BCORL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.380712e-02	ci left: 1.719241e-01	ci right 1.870631e-01	k: 1794	n:10000
Cons ci ratio: 1.969557e-01	ci left: 3.433772e-02	ci right 4.193438e-02	k: 380	n:10000
KS ci ratio: 2.629179e-02	ci left: 6.805286e-01	ci right 6.987608e-01	k: 6897	n:10000
BCORL1   10000 perm   3 sec   (3956 perm/sec)   p_kst 6.897000e-01   p_cons 3.800000e-02   p_joint 1.794000e-01

Joint ci ratio: 6.364054e-02	ci left: 1.543517e-01	ci right 1.645475e-01	k: 3188	n:20000
Cons ci ratio: 1.379597e-01	ci left: 3.611746e-02	ci right 4.151767e-02	k: 775	n:20000
KS ci ratio: 1.880914e-02	ci left: 6.782091e-01	ci right 6.911372e-01	k: 13694	n:20000
BCORL1   20000 perm   6 sec   (3629 perm/sec)   p_kst 6.847000e-01   p_cons 3.875000e-02   p_joint 1.594000e-01

Joint ci ratio: 4.817449e-02	ci left: 1.764264e-01	ci right 1.851688e-01	k: 5423	n:30000
Cons ci ratio: 1.133043e-01	ci left: 3.618883e-02	ci right 4.056781e-02	k: 1150	n:30000
KS ci ratio: 1.529496e-02	ci left: 6.811824e-01	ci right 6.917148e-01	k: 20594	n:30000
BCORL1   30000 perm   9 sec   (3508 perm/sec)   p_kst 6.864667e-01   p_cons 3.833333e-02   p_joint 1.807667e-01

Joint ci ratio: 4.038341e-02	ci left: 1.867857e-01	ci right 1.945092e-01	k: 7625	n:40000
Cons ci ratio: 9.758604e-02	ci left: 3.687970e-02	ci right 4.068763e-02	k: 1550	n:40000
KS ci ratio: 1.331954e-02	ci left: 6.794935e-01	ci right 6.886298e-01	k: 27363	n:40000
BCORL1   40000 perm   12 sec   (3415 perm/sec)   p_kst 6.840750e-01   p_cons 3.875000e-02   p_joint 1.906250e-01

Outputting figure to mutsig2_images.part000000000016/BCORL1.2_5410_40000_0.68407_0.03875_0.19062.png
                gene_name: BCORL1
               theta_stop: 0.098 
                    nperm: 40000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.039 
      ci_cons_bounds_left: 0.037 
     ci_cons_bounds_right: 0.041 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.19 

Current progress: 75 percent done.
BEST1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.270076e-02	ci left: 3.467078e-01	ci right 3.655760e-01	k: 3561	n:10000
Cons ci ratio: 6.645966e-02	ci left: 2.494459e-01	ci right 2.666952e-01	k: 2580	n:10000
KS ci ratio: 7.090273e-02	ci left: 2.257305e-01	ci right 2.424247e-01	k: 2340	n:10000
BEST1   10000 perm   2 sec   (5467 perm/sec)   p_kst 2.340000e-01   p_cons 2.580000e-01   p_joint 3.561000e-01

Outputting figure to mutsig2_images.part000000000016/BEST1.2_2054_10000_0.234_0.258_0.3561.png
                gene_name: BEST1
               theta_stop: 0.071 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  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.165.3896/
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/181708/iteration1/scatter.0000000016
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 16 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119528: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000017> was used as the working directory.
Started at Wed Oct 10 10:41:48 2012
Results reported at Wed Oct 10 10:58:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000017.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000017.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 17  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :   1042.74 sec.
    Max Memory :      1437 MB
    Max Swap   :      3907 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.165.3896/
-whichjob
17
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 17: processing genes 1449 - 1538
Calculating significance of each gene.
Using projection method.
1449	BMP6	1
1450	BMP7	1
1451	BMP8A	1
1452	BMP8B	2.150668e-02
1453	BMPER	5.083891e-02
1454	BMPR1A	1
1455	BMPR1B	1
1456	BMPR2	1
1457	BMS1	2.987267e-01
1458	BMX	1.181498e-02
1459	BNC1	2.543957e-01
1460	BNC2	3.107269e-02
1461	BNIP1	1
1462	BNIP2	1
1463	BNIP3	1
1464	BNIP3L	1
1465	BNIPL	1
1466	BOC	2.599637e-01
1467	BOD1	1
1468	BOD1L	6.626702e-01
1469	BOK	1
1470	BOLA1	1
1471	BOLA3	1
1472	BOLL	1
1473	BPGM	1
1474	BPHL	1
1475	BPI	2.411246e-01
1476	BPIL1	7.376596e-02
1477	BPIL2	1
1478	BPIL3	1
1479	BPNT1	1
1480	BPTF	6.304256e-01
1481	BRAF	1
1482	BRAP	2.714342e-01
1483	BRCA1	3.600667e-01
1484	BRCA2	1.468292e-01
1485	BRCC3	1
1486	BRD1	1
1487	BRD2	1.316046e-01
1488	BRD3	1
1489	BRD4	4.155272e-01
1490	BRD7	3.209503e-01
1491	BRD8	4.397614e-01
1492	BRD9	1
1493	BRDT	7.754162e-02
1494	BRE	1
1495	BRF1	2.436916e-02
1496	BRF2	1
1497	BRI3	1
1498	BRI3BP	1
1499	BRIP1	8.198911e-02
1500	BRIX1	1
1501	BRMS1	1
1502	BRMS1L	1
1503	BRP44	1
1504	BRP44L	1
1505	BRPF1	1
1506	BRPF3	1
1507	BRS3	1
1508	BRSK1	1
1509	BRSK2	1
1510	BRWD1	2.789663e-01
1511	BRWD3	1
1512	BSCL2	1
1513	BSDC1	1
1514	BSG	1
1515	BSN	8.677533e-01
1516	BSND	1
1517	BSPRY	1
1518	BST1	1.004679e-01
1519	BST2	1
1520	BSX	1
1521	BTAF1	5.821414e-01
1522	BTBD1	1
1523	BTBD10	1
1524	BTBD11	1.587693e-01
1525	BTBD12	6.400389e-01
1526	BTBD16	1
1527	BTBD17	1
1528	BTBD2	1
1529	BTBD3	1
1530	BTBD6	1
1531	BTBD7	1
1532	BTBD8	1
1533	BTBD9	1
1534	BTC	1
1535	BTD	1
1536	BTF3	1
1537	BTF3L4	1
1538	BTG1	1
Done

Running MutSig 2:
Scatter job 17: processing genes 1449 - 1538
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
BRCA2
Processing conservation and coverage...
96% 
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: 1.550197e-02	ci left: 8.579419e-01	ci right 8.714449e-01	k: 8648	n:10000
KS ci ratio: 1.306013e+00	ci left: 3.454445e-04	ci right 1.575707e-03	k: 8	n:10000
BRCA2   10000 perm   3 sec   (3341 perm/sec)   p_kst 8.000000e-04   p_cons 8.648000e-01   p_joint 8.700000e-03

Joint ci ratio: 2.317754e-01	ci left: 1.246477e-02	ci right 1.577870e-02	k: 281	n:20000
Cons ci ratio: 1.087617e-02	ci left: 8.618095e-01	ci right 8.712836e-01	k: 17332	n:20000
KS ci ratio: 7.034894e-01	ci left: 1.012265e-03	ci right 2.140657e-03	k: 30	n:20000
BRCA2   20000 perm   12 sec   (1736 perm/sec)   p_kst 1.500000e-03   p_cons 8.666000e-01   p_joint 1.405000e-02

Joint ci ratio: 2.155883e-01	ci left: 9.724379e-03	ci right 1.210509e-02	k: 326	n:30000
Cons ci ratio: 8.785151e-03	ci left: 8.651971e-01	ci right 8.728646e-01	k: 26072	n:30000
KS ci ratio: 6.044355e-01	ci left: 9.809166e-04	ci right 1.853586e-03	k: 41	n:30000
BRCA2   30000 perm   17 sec   (1763 perm/sec)   p_kst 1.366667e-03   p_cons 8.690667e-01   p_joint 1.086667e-02

Joint ci ratio: 2.666190e-01	ci left: 4.658727e-03	ci right 6.114498e-03	k: 214	n:40000
Cons ci ratio: 7.592727e-03	ci left: 8.661848e-01	ci right 8.728114e-01	k: 34781	n:40000
KS ci ratio: 5.840230e-01	ci left: 7.993719e-04	ci right 1.476420e-03	k: 44	n:40000
BRCA2   40000 perm   21 sec   (1868 perm/sec)   p_kst 1.100000e-03   p_cons 8.695250e-01   p_joint 5.350000e-03

Joint ci ratio: 2.808903e-01	ci left: 3.335453e-03	ci right 4.443372e-03	k: 193	n:50000
Cons ci ratio: 6.812163e-03	ci left: 8.658295e-01	ci right 8.717676e-01	k: 43441	n:50000
KS ci ratio: 5.486243e-01	ci left: 7.423075e-04	ci right 1.318165e-03	k: 50	n:50000
BRCA2   50000 perm   26 sec   (1901 perm/sec)   p_kst 1.000000e-03   p_cons 8.688200e-01   p_joint 3.860000e-03

Joint ci ratio: 2.602608e-01	ci left: 3.276731e-03	ci right 4.272217e-03	k: 225	n:60000
Cons ci ratio: 6.235491e-03	ci left: 8.654672e-01	ci right 8.708972e-01	k: 52092	n:60000
KS ci ratio: 4.936101e-01	ci left: 7.923397e-04	ci right 1.324494e-03	k: 62	n:60000
BRCA2   60000 perm   30 sec   (1993 perm/sec)   p_kst 1.033333e-03   p_cons 8.682000e-01   p_joint 3.750000e-03

Joint ci ratio: 2.408022e-01	ci left: 3.317453e-03	ci right 4.238719e-03	k: 263	n:70000
Cons ci ratio: 5.783005e-03	ci left: 8.652685e-01	ci right 8.703010e-01	k: 60746	n:70000
KS ci ratio: 4.380157e-01	ci left: 8.935993e-04	ci right 1.406341e-03	k: 79	n:70000
BRCA2   70000 perm   34 sec   (2064 perm/sec)   p_kst 1.128571e-03   p_cons 8.678000e-01   p_joint 3.757143e-03

Joint ci ratio: 1.031720e-01	ci left: 1.680974e-02	ci right 1.865048e-02	k: 1417	n:80000
Cons ci ratio: 5.397696e-03	ci left: 8.659371e-01	ci right 8.706362e-01	k: 69464	n:80000
KS ci ratio: 3.998407e-01	ci left: 9.608614e-04	ci right 1.451465e-03	k: 95	n:80000
BRCA2   80000 perm   38 sec   (2127 perm/sec)   p_kst 1.187500e-03   p_cons 8.683000e-01   p_joint 1.771250e-02

Joint ci ratio: 1.076389e-01	ci left: 1.373996e-02	ci right 1.531378e-02	k: 1306	n:90000
Cons ci ratio: 5.396297e-03	ci left: 8.519781e-01	ci right 8.565991e-01	k: 76887	n:90000
KS ci ratio: 3.805177e-01	ci left: 9.543138e-04	ci right 1.412148e-03	k: 105	n:90000
BRCA2   90000 perm   41 sec   (2177 perm/sec)   p_kst 1.166667e-03   p_cons 8.543000e-01   p_joint 1.451111e-02

Joint ci ratio: 1.081382e-01	ci left: 1.226815e-02	ci right 1.368030e-02	k: 1296	n:100000
Cons ci ratio: 5.106614e-03	ci left: 8.527219e-01	ci right 8.570975e-01	k: 85492	n:100000
KS ci ratio: 3.561462e-01	ci left: 9.950163e-04	ci right 1.434737e-03	k: 120	n:100000
BRCA2   100000 perm   46 sec   (2197 perm/sec)   p_kst 1.200000e-03   p_cons 8.549200e-01   p_joint 1.296000e-02

Joint ci ratio: 1.059920e-01	ci left: 1.163043e-02	ci right 1.294093e-02	k: 1350	n:110000
Cons ci ratio: 4.867032e-03	ci left: 8.529236e-01	ci right 8.570940e-01	k: 94052	n:110000
KS ci ratio: 3.334817e-01	ci left: 1.045741e-03	ci right 1.472164e-03	k: 137	n:110000
BRCA2   110000 perm   50 sec   (2207 perm/sec)   p_kst 1.245455e-03   p_cons 8.550182e-01   p_joint 1.227273e-02

Joint ci ratio: 1.061662e-01	ci left: 1.063659e-02	ci right 1.183720e-02	k: 1347	n:120000
Cons ci ratio: 4.662045e-03	ci left: 8.528945e-01	ci right 8.568883e-01	k: 102588	n:120000
KS ci ratio: 3.087307e-01	ci left: 1.134846e-03	ci right 1.556512e-03	k: 160	n:120000
BRCA2   120000 perm   54 sec   (2230 perm/sec)   p_kst 1.333333e-03   p_cons 8.549000e-01   p_joint 1.122500e-02

Joint ci ratio: 1.142328e-01	ci left: 8.463856e-03	ci right 9.496686e-03	k: 1166	n:130000
Cons ci ratio: 4.470113e-03	ci left: 8.534764e-01	ci right 8.573077e-01	k: 111202	n:130000
KS ci ratio: 2.978326e-01	ci left: 1.132836e-03	ci right 1.536090e-03	k: 172	n:130000
BRCA2   130000 perm   58 sec   (2243 perm/sec)   p_kst 1.323077e-03   p_cons 8.554000e-01   p_joint 8.969231e-03

Joint ci ratio: 9.790333e-02	ci left: 1.076683e-02	ci right 1.188212e-02	k: 1584	n:140000
Cons ci ratio: 4.301036e-03	ci left: 8.539202e-01	ci right 8.576079e-01	k: 119808	n:140000
KS ci ratio: 2.864663e-01	ci left: 1.144594e-03	ci right 1.533673e-03	k: 186	n:140000
BRCA2   140000 perm   62 sec   (2255 perm/sec)   p_kst 1.328571e-03   p_cons 8.557714e-01   p_joint 1.131429e-02

Joint ci ratio: 9.659463e-02	ci left: 1.033513e-02	ci right 1.139057e-02	k: 1628	n:150000
Cons ci ratio: 4.153927e-03	ci left: 8.540589e-01	ci right 8.576206e-01	k: 128377	n:150000
KS ci ratio: 2.749429e-01	ci left: 1.167451e-03	ci right 1.545579e-03	k: 202	n:150000
BRCA2   150000 perm   66 sec   (2265 perm/sec)   p_kst 1.346667e-03   p_cons 8.558467e-01   p_joint 1.085333e-02

Joint ci ratio: 8.970623e-02	ci left: 1.126440e-02	ci right 1.232841e-02	k: 1886	n:160000
Cons ci ratio: 4.024206e-03	ci left: 8.539812e-01	ci right 8.574309e-01	k: 136914	n:160000
KS ci ratio: 2.671613e-01	ci left: 1.164390e-03	ci right 1.529065e-03	k: 214	n:160000
BRCA2   160000 perm   71 sec   (2266 perm/sec)   p_kst 1.337500e-03   p_cons 8.557125e-01   p_joint 1.178750e-02

Joint ci ratio: 9.017364e-02	ci left: 1.049810e-02	ci right 1.149516e-02	k: 1868	n:170000
Cons ci ratio: 3.904807e-03	ci left: 8.539851e-01	ci right 8.573321e-01	k: 145463	n:170000
KS ci ratio: 2.605804e-01	ci left: 1.156322e-03	ci right 1.508097e-03	k: 225	n:170000
BRCA2   170000 perm   75 sec   (2266 perm/sec)   p_kst 1.323529e-03   p_cons 8.556647e-01   p_joint 1.098824e-02

Joint ci ratio: 8.966972e-02	ci left: 1.003423e-02	ci right 1.098163e-02	k: 1890	n:180000
Cons ci ratio: 3.796039e-03	ci left: 8.539510e-01	ci right 8.572042e-01	k: 154005	n:180000
KS ci ratio: 2.544630e-01	ci left: 1.149248e-03	ci right 1.489361e-03	k: 236	n:180000
BRCA2   180000 perm   79 sec   (2267 perm/sec)   p_kst 1.311111e-03   p_cons 8.555833e-01   p_joint 1.050000e-02

Joint ci ratio: 9.464743e-02	ci left: 8.523686e-03	ci right 9.375608e-03	k: 1699	n:190000
Cons ci ratio: 3.690528e-03	ci left: 8.542811e-01	ci right 8.574449e-01	k: 162615	n:190000
KS ci ratio: 2.487571e-01	ci left: 1.143006e-03	ci right 1.472512e-03	k: 247	n:190000
BRCA2   190000 perm   84 sec   (2264 perm/sec)   p_kst 1.300000e-03   p_cons 8.558684e-01   p_joint 8.942105e-03

Joint ci ratio: 9.416729e-02	ci left: 8.185310e-03	ci right 8.999030e-03	k: 1717	n:200000
Cons ci ratio: 3.598661e-03	ci left: 8.542126e-01	ci right 8.572971e-01	k: 171152	n:200000
KS ci ratio: 2.438905e-01	ci left: 1.132768e-03	ci right 1.451968e-03	k: 257	n:200000
BRCA2   200000 perm   88 sec   (2261 perm/sec)   p_kst 1.285000e-03   p_cons 8.557600e-01   p_joint 8.585000e-03

Joint ci ratio: 8.756740e-02	ci left: 9.038270e-03	ci right 9.870593e-03	k: 1984	n:210000
Cons ci ratio: 3.507772e-03	ci left: 8.545437e-01	ci right 8.575512e-01	k: 179771	n:210000
KS ci ratio: 2.370944e-01	ci left: 1.145953e-03	ci right 1.458549e-03	k: 272	n:210000
BRCA2   210000 perm   93 sec   (2248 perm/sec)   p_kst 1.295238e-03   p_cons 8.560524e-01   p_joint 9.447619e-03

Joint ci ratio: 1.035794e-01	ci left: 6.133016e-03	ci right 6.807359e-03	k: 1422	n:220000
Cons ci ratio: 3.235001e-03	ci left: 8.682816e-01	ci right 8.710995e-01	k: 191333	n:220000
KS ci ratio: 2.304362e-01	ci left: 1.162334e-03	ci right 1.469229e-03	k: 288	n:220000
BRCA2   220000 perm   98 sec   (2243 perm/sec)   p_kst 1.309091e-03   p_cons 8.696955e-01   p_joint 6.463636e-03

Joint ci ratio: 1.018792e-01	ci left: 6.069687e-03	ci right 6.725455e-03	k: 1470	n:230000
Cons ci ratio: 3.163768e-03	ci left: 8.683218e-01	ci right 8.710776e-01	k: 200032	n:230000
KS ci ratio: 2.269319e-01	ci left: 1.148686e-03	ci right 1.446719e-03	k: 297	n:230000
BRCA2   230000 perm   103 sec   (2238 perm/sec)   p_kst 1.291304e-03   p_cons 8.697043e-01   p_joint 6.391304e-03

Joint ci ratio: 9.682332e-02	ci left: 6.454764e-03	ci right 7.115565e-03	k: 1627	n:240000
Cons ci ratio: 3.098978e-03	ci left: 8.682169e-01	ci right 8.709158e-01	k: 208697	n:240000
KS ci ratio: 2.200232e-01	ci left: 1.175562e-03	ci right 1.470027e-03	k: 316	n:240000
BRCA2   240000 perm   108 sec   (2231 perm/sec)   p_kst 1.316667e-03   p_cons 8.695708e-01   p_joint 6.779167e-03

Joint ci ratio: 9.506012e-02	ci left: 6.434715e-03	ci right 7.080800e-03	k: 1688	n:250000
Cons ci ratio: 3.038758e-03	ci left: 8.680648e-01	ci right 8.707106e-01	k: 217348	n:250000
KS ci ratio: 2.163033e-01	ci left: 1.170135e-03	ci right 1.457626e-03	k: 327	n:250000
BRCA2   250000 perm   112 sec   (2223 perm/sec)   p_kst 1.308000e-03   p_cons 8.693920e-01   p_joint 6.752000e-03

Joint ci ratio: 9.605049e-02	ci left: 6.059526e-03	ci right 6.674633e-03	k: 1654	n:260000
Cons ci ratio: 2.976664e-03	ci left: 8.683266e-01	ci right 8.709190e-01	k: 226103	n:260000
KS ci ratio: 2.124524e-01	ci left: 1.168806e-03	ci right 1.450192e-03	k: 339	n:260000
BRCA2   260000 perm   118 sec   (2213 perm/sec)   p_kst 1.303846e-03   p_cons 8.696269e-01   p_joint 6.361538e-03

Joint ci ratio: 9.446693e-02	ci left: 6.037562e-03	ci right 6.639775e-03	k: 1710	n:270000
Cons ci ratio: 2.917071e-03	ci left: 8.686587e-01	ci right 8.712000e-01	k: 234882	n:270000
KS ci ratio: 2.093966e-01	ci left: 1.160597e-03	ci right 1.435473e-03	k: 349	n:270000
BRCA2   270000 perm   122 sec   (2204 perm/sec)   p_kst 1.292593e-03   p_cons 8.699333e-01   p_joint 6.333333e-03

Joint ci ratio: 9.349314e-02	ci left: 5.947471e-03	ci right 6.534248e-03	k: 1746	n:280000
Cons ci ratio: 2.864431e-03	ci left: 8.686878e-01	ci right 8.711831e-01	k: 243583	n:280000
KS ci ratio: 2.058970e-01	ci left: 1.159776e-03	ci right 1.429288e-03	k: 361	n:280000
BRCA2   280000 perm   128 sec   (2195 perm/sec)   p_kst 1.289286e-03   p_cons 8.699393e-01   p_joint 6.235714e-03

Joint ci ratio: 9.553236e-02	ci left: 5.496550e-03	ci right 6.051328e-03	k: 1673	n:290000
Cons ci ratio: 2.814542e-03	ci left: 8.687152e-01	ci right 8.711671e-01	k: 252284	n:290000
KS ci ratio: 2.022967e-01	ci left: 1.162320e-03	ci right 1.427118e-03	k: 374	n:290000
BRCA2   290000 perm   133 sec   (2186 perm/sec)   p_kst 1.289655e-03   p_cons 8.699448e-01   p_joint 5.768966e-03

Joint ci ratio: 9.391914e-02	ci left: 5.502086e-03	ci right 6.047528e-03	k: 1731	n:300000
Cons ci ratio: 2.766764e-03	ci left: 8.687746e-01	ci right 8.711849e-01	k: 260995	n:300000
KS ci ratio: 1.991359e-01	ci left: 1.161566e-03	ci right 1.421555e-03	k: 386	n:300000
BRCA2   300000 perm   138 sec   (2176 perm/sec)   p_kst 1.286667e-03   p_cons 8.699833e-01   p_joint 5.770000e-03

Joint ci ratio: 9.607096e-02	ci left: 5.085209e-03	ci right 5.601524e-03	k: 1655	n:310000
Cons ci ratio: 2.723822e-03	ci left: 8.686233e-01	ci right 8.709956e-01	k: 269642	n:310000
KS ci ratio: 1.961188e-01	ci left: 1.160890e-03	ci right 1.416321e-03	k: 398	n:310000
BRCA2   310000 perm   143 sec   (2166 perm/sec)   p_kst 1.283871e-03   p_cons 8.698129e-01   p_joint 5.338710e-03

Joint ci ratio: 9.690599e-02	ci left: 4.840878e-03	ci right 5.336900e-03	k: 1627	n:320000
Cons ci ratio: 2.680004e-03	ci left: 8.687201e-01	ci right 8.710545e-01	k: 278365	n:320000
KS ci ratio: 1.927658e-01	ci left: 1.166233e-03	ci right 1.417938e-03	k: 412	n:320000
BRCA2   320000 perm   148 sec   (2155 perm/sec)   p_kst 1.287500e-03   p_cons 8.698906e-01   p_joint 5.084375e-03

Joint ci ratio: 8.758620e-02	ci left: 5.768985e-03	ci right 6.300352e-03	k: 1990	n:330000
Cons ci ratio: 2.639223e-03	ci left: 8.687261e-01	ci right 8.710249e-01	k: 287060	n:330000
KS ci ratio: 1.891360e-01	ci left: 1.177061e-03	ci right 1.425769e-03	k: 428	n:330000
BRCA2   330000 perm   154 sec   (2144 perm/sec)   p_kst 1.296970e-03   p_cons 8.698788e-01   p_joint 6.030303e-03

Joint ci ratio: 8.618998e-02	ci left: 5.786334e-03	ci right 6.310374e-03	k: 2055	n:340000
Cons ci ratio: 2.599573e-03	ci left: 8.687912e-01	ci right 8.710555e-01	k: 295775	n:340000
KS ci ratio: 1.867574e-01	ci left: 1.173272e-03	ci right 1.417708e-03	k: 439	n:340000
BRCA2   340000 perm   160 sec   (2129 perm/sec)   p_kst 1.291176e-03   p_cons 8.699265e-01   p_joint 6.044118e-03

Joint ci ratio: 8.118476e-02	ci left: 6.348405e-03	ci right 6.888384e-03	k: 2315	n:350000
Cons ci ratio: 2.562531e-03	ci left: 8.687753e-01	ci right 8.710072e-01	k: 304463	n:350000
KS ci ratio: 1.828497e-01	ci left: 1.191525e-03	ci right 1.433995e-03	k: 458	n:350000
BRCA2   350000 perm   165 sec   (2117 perm/sec)   p_kst 1.308571e-03   p_cons 8.698943e-01   p_joint 6.614286e-03

Joint ci ratio: 5.998141e-02	ci left: 1.137317e-02	ci right 1.207916e-02	k: 4220	n:360000
Cons ci ratio: 2.526843e-03	ci left: 8.687772e-01	ci right 8.709780e-01	k: 313157	n:360000
KS ci ratio: 1.801231e-01	ci left: 1.195550e-03	ci right 1.434815e-03	k: 472	n:360000
BRCA2   360000 perm   171 sec   (2099 perm/sec)   p_kst 1.311111e-03   p_cons 8.698806e-01   p_joint 1.172222e-02

Joint ci ratio: 6.113675e-02	ci left: 1.065309e-02	ci right 1.132757e-02	k: 4065	n:370000
Cons ci ratio: 2.493795e-03	ci left: 8.686707e-01	ci right 8.708424e-01	k: 321811	n:370000
KS ci ratio: 1.764300e-01	ci left: 1.214881e-03	ci right 1.452499e-03	k: 492	n:370000
BRCA2   370000 perm   178 sec   (2081 perm/sec)   p_kst 1.329730e-03   p_cons 8.697595e-01   p_joint 1.098649e-02

Joint ci ratio: 6.149829e-02	ci left: 1.025349e-02	ci right 1.090664e-02	k: 4019	n:380000
Cons ci ratio: 2.459008e-03	ci left: 8.688474e-01	ci right 8.709891e-01	k: 330570	n:380000
KS ci ratio: 1.743215e-01	ci left: 1.213103e-03	ci right 1.447239e-03	k: 504	n:380000
BRCA2   380000 perm   184 sec   (2069 perm/sec)   p_kst 1.326316e-03   p_cons 8.699211e-01   p_joint 1.057632e-02

Joint ci ratio: 6.240705e-02	ci left: 9.702713e-03	ci right 1.033024e-02	k: 3905	n:390000
Cons ci ratio: 2.426705e-03	ci left: 8.689148e-01	ci right 8.710285e-01	k: 339290	n:390000
KS ci ratio: 1.722869e-01	ci left: 1.211432e-03	ci right 1.442233e-03	k: 516	n:390000
BRCA2   390000 perm   190 sec   (2057 perm/sec)   p_kst 1.323077e-03   p_cons 8.699744e-01   p_joint 1.001282e-02

Joint ci ratio: 6.207877e-02	ci left: 9.563489e-03	ci right 1.017864e-02	k: 3947	n:400000
Cons ci ratio: 2.397205e-03	ci left: 8.688310e-01	ci right 8.709187e-01	k: 347951	n:400000
KS ci ratio: 1.703218e-01	ci left: 1.209860e-03	ci right 1.437462e-03	k: 528	n:400000
BRCA2   400000 perm   196 sec   (2040 perm/sec)   p_kst 1.320000e-03   p_cons 8.698775e-01   p_joint 9.867500e-03

Joint ci ratio: 6.180243e-02	ci left: 9.416656e-03	ci right 1.001957e-02	k: 3983	n:410000
Cons ci ratio: 2.368498e-03	ci left: 8.687759e-01	ci right 8.708384e-01	k: 356622	n:410000
KS ci ratio: 1.674950e-01	ci left: 1.222399e-03	ci right 1.448158e-03	k: 546	n:410000
BRCA2   410000 perm   202 sec   (2029 perm/sec)   p_kst 1.331707e-03   p_cons 8.698098e-01   p_joint 9.714634e-03

Joint ci ratio: 7.542272e-02	ci left: 6.149370e-03	ci right 6.633668e-03	k: 2683	n:420000
Cons ci ratio: 2.340823e-03	ci left: 8.687212e-01	ci right 8.707594e-01	k: 365292	n:420000
KS ci ratio: 1.652444e-01	ci left: 1.227521e-03	ci right 1.450878e-03	k: 561	n:420000
BRCA2   420000 perm   208 sec   (2017 perm/sec)   p_kst 1.335714e-03   p_cons 8.697429e-01   p_joint 6.388095e-03

Joint ci ratio: 7.605825e-02	ci left: 5.905946e-03	ci right 6.375165e-03	k: 2639	n:430000
Cons ci ratio: 2.313763e-03	ci left: 8.687018e-01	ci right 8.707164e-01	k: 373976	n:430000
KS ci ratio: 1.630820e-01	ci left: 1.232425e-03	ci right 1.453452e-03	k: 576	n:430000
BRCA2   430000 perm   215 sec   (2004 perm/sec)   p_kst 1.339535e-03   p_cons 8.697116e-01   p_joint 6.137209e-03

Joint ci ratio: 5.651533e-02	ci left: 1.051013e-02	ci right 1.112361e-02	k: 4758	n:440000
Cons ci ratio: 2.288216e-03	ci left: 8.686242e-01	ci right 8.706163e-01	k: 382634	n:440000
KS ci ratio: 1.605955e-01	ci left: 1.243668e-03	ci right 1.462982e-03	k: 594	n:440000
BRCA2   440000 perm   221 sec   (1992 perm/sec)   p_kst 1.350000e-03   p_cons 8.696227e-01   p_joint 1.081364e-02

Joint ci ratio: 5.646826e-02	ci left: 1.029626e-02	ci right 1.089674e-02	k: 4767	n:450000
Cons ci ratio: 2.263207e-03	ci left: 8.685792e-01	ci right 8.705494e-01	k: 391305	n:450000
KS ci ratio: 1.583486e-01	ci left: 1.252302e-03	ci right 1.469755e-03	k: 611	n:450000
BRCA2   450000 perm   227 sec   (1978 perm/sec)   p_kst 1.357778e-03   p_cons 8.695667e-01   p_joint 1.059333e-02

Joint ci ratio: 5.598451e-02	ci left: 1.025032e-02	ci right 1.084283e-02	k: 4850	n:460000
Cons ci ratio: 2.237392e-03	ci left: 8.686998e-01	ci right 8.706477e-01	k: 400051	n:460000
KS ci ratio: 1.568189e-01	ci left: 1.250136e-03	ci right 1.464919e-03	k: 623	n:460000
BRCA2   460000 perm   234 sec   (1966 perm/sec)   p_kst 1.354348e-03   p_cons 8.696761e-01   p_joint 1.054348e-02

Joint ci ratio: 5.699047e-02	ci left: 9.681842e-03	ci right 1.025188e-02	k: 4683	n:470000
Cons ci ratio: 2.213789e-03	ci left: 8.686766e-01	ci right 8.706039e-01	k: 408732	n:470000
KS ci ratio: 1.550888e-01	ci left: 1.252162e-03	ci right 1.464699e-03	k: 637	n:470000
BRCA2   470000 perm   240 sec   (1955 perm/sec)   p_kst 1.355319e-03   p_cons 8.696426e-01   p_joint 9.963830e-03

Joint ci ratio: 5.660719e-02	ci left: 9.611567e-03	ci right 1.017354e-02	k: 4747	n:480000
Cons ci ratio: 2.190032e-03	ci left: 8.687465e-01	ci right 8.706532e-01	k: 417457	n:480000
KS ci ratio: 1.535325e-01	ci left: 1.252113e-03	ci right 1.462313e-03	k: 650	n:480000
BRCA2   480000 perm   247 sec   (1942 perm/sec)   p_kst 1.354167e-03   p_cons 8.697021e-01   p_joint 9.889583e-03

Joint ci ratio: 6.244728e-02	ci left: 7.728350e-03	ci right 8.228514e-03	k: 3908	n:490000
Cons ci ratio: 2.168253e-03	ci left: 8.686846e-01	ci right 8.705722e-01	k: 426119	n:490000
KS ci ratio: 1.522520e-01	ci left: 1.248150e-03	ci right 1.455777e-03	k: 661	n:490000
BRCA2   490000 perm   254 sec   (1931 perm/sec)   p_kst 1.348980e-03   p_cons 8.696306e-01   p_joint 7.975510e-03

Joint ci ratio: 6.505216e-02	ci left: 6.975382e-03	ci right 7.446355e-03	k: 3604	n:500000
Cons ci ratio: 2.146183e-03	ci left: 8.687237e-01	ci right 8.705921e-01	k: 434830	n:500000
KS ci ratio: 1.505557e-01	ci left: 1.252051e-03	ci right 1.457797e-03	k: 676	n:500000
BRCA2   500000 perm   261 sec   (1919 perm/sec)   p_kst 1.352000e-03   p_cons 8.696600e-01   p_joint 7.208000e-03

Joint ci ratio: 6.529434e-02	ci left: 6.788439e-03	ci right 7.248560e-03	k: 3578	n:510000
Cons ci ratio: 2.124534e-03	ci left: 8.687868e-01	ci right 8.706365e-01	k: 443554	n:510000
KS ci ratio: 1.496747e-01	ci left: 1.242597e-03	ci right 1.445489e-03	k: 684	n:510000
BRCA2   510000 perm   267 sec   (1908 perm/sec)   p_kst 1.341176e-03   p_cons 8.697137e-01   p_joint 7.015686e-03

Joint ci ratio: 6.697750e-02	ci left: 6.324977e-03	ci right 6.765164e-03	k: 3402	n:520000
Cons ci ratio: 2.104866e-03	ci left: 8.687029e-01	ci right 8.705353e-01	k: 452203	n:520000
KS ci ratio: 1.478508e-01	ci left: 1.250177e-03	ci right 1.451599e-03	k: 701	n:520000
BRCA2   520000 perm   274 sec   (1896 perm/sec)   p_kst 1.348077e-03   p_cons 8.696212e-01   p_joint 6.542308e-03

Joint ci ratio: 5.792815e-02	ci left: 8.317821e-03	ci right 8.815876e-03	k: 4539	n:530000
Cons ci ratio: 2.085108e-03	ci left: 8.686905e-01	ci right 8.705055e-01	k: 460888	n:530000
KS ci ratio: 1.462959e-01	ci left: 1.253849e-03	ci right 1.453552e-03	k: 716	n:530000
BRCA2   530000 perm   282 sec   (1882 perm/sec)   p_kst 1.350943e-03   p_cons 8.696000e-01   p_joint 8.564151e-03

Joint ci ratio: 5.185877e-02	ci left: 1.019876e-02	ci right 1.074355e-02	k: 5653	n:540000
Cons ci ratio: 2.064919e-03	ci left: 8.687862e-01	ci right 8.705839e-01	k: 469631	n:540000
KS ci ratio: 1.443945e-01	ci left: 1.264536e-03	ci right 1.463098e-03	k: 735	n:540000
BRCA2   540000 perm   289 sec   (1870 perm/sec)   p_kst 1.361111e-03   p_cons 8.696870e-01   p_joint 1.046852e-02

Joint ci ratio: 5.307691e-02	ci left: 9.559278e-03	ci right 1.008227e-02	k: 5400	n:550000
Cons ci ratio: 2.045549e-03	ci left: 8.688512e-01	ci right 8.706321e-01	k: 478359	n:550000
KS ci ratio: 1.432318e-01	ci left: 1.262577e-03	ci right 1.459099e-03	k: 747	n:550000
BRCA2   550000 perm   296 sec   (1859 perm/sec)   p_kst 1.358182e-03   p_cons 8.697436e-01   p_joint 9.818182e-03

Joint ci ratio: 5.339192e-02	ci left: 9.279300e-03	ci right 9.790079e-03	k: 5338	n:560000
Cons ci ratio: 2.027210e-03	ci left: 8.688585e-01	ci right 8.706234e-01	k: 487056	n:560000
KS ci ratio: 1.420032e-01	ci left: 1.262417e-03	ci right 1.457086e-03	k: 760	n:560000
BRCA2   560000 perm   303 sec   (1847 perm/sec)   p_kst 1.357143e-03   p_cons 8.697429e-01   p_joint 9.532143e-03

Joint ci ratio: 5.339138e-02	ci left: 9.118217e-03	ci right 9.620122e-03	k: 5339	n:570000
Cons ci ratio: 2.010040e-03	ci left: 8.687881e-01	ci right 8.705379e-01	k: 495709	n:570000
KS ci ratio: 1.405332e-01	ci left: 1.267348e-03	ci right 1.460584e-03	k: 776	n:570000
BRCA2   570000 perm   310 sec   (1836 perm/sec)   p_kst 1.361404e-03   p_cons 8.696649e-01   p_joint 9.366667e-03

Joint ci ratio: 5.307565e-02	ci left: 9.069876e-03	ci right 9.566078e-03	k: 5403	n:580000
Cons ci ratio: 1.992631e-03	ci left: 8.687964e-01	ci right 8.705310e-01	k: 504406	n:580000
KS ci ratio: 1.393722e-01	ci left: 1.267126e-03	ci right 1.458600e-03	k: 789	n:580000
BRCA2   580000 perm   318 sec   (1825 perm/sec)   p_kst 1.360345e-03   p_cons 8.696655e-01   p_joint 9.315517e-03

Joint ci ratio: 5.286801e-02	ci left: 8.988055e-03	ci right 9.477799e-03	k: 5446	n:590000
Cons ci ratio: 1.975519e-03	ci left: 8.688214e-01	ci right 8.705411e-01	k: 513113	n:590000
KS ci ratio: 1.382395e-01	ci left: 1.266918e-03	ci right 1.456676e-03	k: 802	n:590000
BRCA2   590000 perm   325 sec   (1814 perm/sec)   p_kst 1.359322e-03   p_cons 8.696831e-01   p_joint 9.230508e-03

Joint ci ratio: 5.282320e-02	ci left: 8.854685e-03	ci right 9.336740e-03	k: 5456	n:600000
Cons ci ratio: 1.958539e-03	ci left: 8.688807e-01	ci right 8.705857e-01	k: 521841	n:600000
KS ci ratio: 1.366319e-01	ci left: 1.276381e-03	ci right 1.465153e-03	k: 821	n:600000
BRCA2   600000 perm   333 sec   (1801 perm/sec)   p_kst 1.368333e-03   p_cons 8.697350e-01   p_joint 9.093333e-03

Joint ci ratio: 5.389886e-02	ci left: 8.364948e-03	ci right 8.829901e-03	k: 5243	n:610000
Cons ci ratio: 1.942943e-03	ci left: 8.688263e-01	ci right 8.705177e-01	k: 530501	n:610000
KS ci ratio: 1.356456e-01	ci left: 1.274459e-03	ci right 1.461476e-03	k: 833	n:610000
BRCA2   610000 perm   341 sec   (1788 perm/sec)   p_kst 1.365574e-03   p_cons 8.696738e-01   p_joint 8.595082e-03

Joint ci ratio: 5.371185e-02	ci left: 8.288895e-03	ci right 8.747973e-03	k: 5280	n:620000
Cons ci ratio: 1.927070e-03	ci left: 8.688498e-01	ci right 8.705274e-01	k: 539208	n:620000
KS ci ratio: 1.342835e-01	ci left: 1.280397e-03	ci right 1.466248e-03	k: 850	n:620000
BRCA2   620000 perm   349 sec   (1778 perm/sec)   p_kst 1.370968e-03   p_cons 8.696903e-01   p_joint 8.516129e-03

Joint ci ratio: 6.032830e-02	ci left: 6.456253e-03	ci right 6.859415e-03	k: 4193	n:630000
Cons ci ratio: 1.911178e-03	ci left: 8.689204e-01	ci right 8.705842e-01	k: 547945	n:630000
KS ci ratio: 1.329617e-01	ci left: 1.286155e-03	ci right 1.470859e-03	k: 867	n:630000
BRCA2   630000 perm   356 sec   (1768 perm/sec)   p_kst 1.376190e-03   p_cons 8.697540e-01   p_joint 6.655556e-03

Joint ci ratio: 6.046220e-02	ci left: 6.327661e-03	ci right 6.723700e-03	k: 4175	n:640000
Cons ci ratio: 1.895959e-03	ci left: 8.689543e-01	ci right 8.706049e-01	k: 556660	n:640000
KS ci ratio: 1.319771e-01	ci left: 1.285699e-03	ci right 1.468863e-03	k: 880	n:640000
BRCA2   640000 perm   364 sec   (1757 perm/sec)   p_kst 1.375000e-03   p_cons 8.697812e-01   p_joint 6.523437e-03

Joint ci ratio: 6.002559e-02	ci left: 6.322745e-03	ci right 6.715519e-03	k: 4236	n:650000
Cons ci ratio: 1.881214e-03	ci left: 8.689733e-01	ci right 8.706111e-01	k: 565366	n:650000
KS ci ratio: 1.313086e-01	ci left: 1.279308e-03	ci right 1.460567e-03	k: 889	n:650000
BRCA2   650000 perm   372 sec   (1747 perm/sec)   p_kst 1.367692e-03   p_cons 8.697938e-01   p_joint 6.516923e-03

Joint ci ratio: 5.970325e-02	ci left: 6.295597e-03	ci right 6.684512e-03	k: 4282	n:660000
Cons ci ratio: 1.866607e-03	ci left: 8.690161e-01	ci right 8.706412e-01	k: 574088	n:660000
KS ci ratio: 1.308690e-01	ci left: 1.268717e-03	ci right 1.447827e-03	k: 895	n:660000
BRCA2   660000 perm   380 sec   (1737 perm/sec)   p_kst 1.356061e-03   p_cons 8.698303e-01   p_joint 6.487879e-03

Joint ci ratio: 5.916634e-02	ci left: 6.316322e-03	ci right 6.702889e-03	k: 4360	n:670000
Cons ci ratio: 1.852409e-03	ci left: 8.690487e-01	ci right 8.706615e-01	k: 582804	n:670000
KS ci ratio: 1.295735e-01	ci left: 1.275772e-03	ci right 1.453957e-03	k: 913	n:670000
BRCA2   670000 perm   388 sec   (1727 perm/sec)   p_kst 1.362687e-03   p_cons 8.698567e-01   p_joint 6.507463e-03

Joint ci ratio: 5.143578e-02	ci left: 8.251222e-03	ci right 8.688275e-03	k: 5758	n:680000
Cons ci ratio: 1.838434e-03	ci left: 8.690922e-01	ci right 8.706929e-01	k: 591528	n:680000
KS ci ratio: 1.287314e-01	ci left: 1.274087e-03	ci right 1.450793e-03	k: 925	n:680000
BRCA2   680000 perm   397 sec   (1714 perm/sec)   p_kst 1.360294e-03   p_cons 8.698941e-01   p_joint 8.467647e-03

Joint ci ratio: 5.142996e-02	ci left: 8.134488e-03	ci right 8.565307e-03	k: 5760	n:690000
Cons ci ratio: 1.824700e-03	ci left: 8.691432e-01	ci right 8.707320e-01	k: 600258	n:690000
KS ci ratio: 1.278372e-01	ci left: 1.273858e-03	ci right 1.449211e-03	k: 938	n:690000
BRCA2   690000 perm   406 sec   (1702 perm/sec)   p_kst 1.359420e-03   p_cons 8.699391e-01   p_joint 8.347826e-03

Joint ci ratio: 5.107227e-02	ci left: 8.132512e-03	ci right 8.560143e-03	k: 5841	n:700000
Cons ci ratio: 1.811967e-03	ci left: 8.691054e-01	ci right 8.706830e-01	k: 608927	n:700000
KS ci ratio: 1.270282e-01	ci left: 1.272257e-03	ci right 1.446198e-03	k: 950	n:700000
BRCA2   700000 perm   414 sec   (1690 perm/sec)   p_kst 1.357143e-03   p_cons 8.698957e-01   p_joint 8.344286e-03

Joint ci ratio: 4.979762e-02	ci left: 8.436600e-03	ci right 8.868831e-03	k: 6142	n:710000
Cons ci ratio: 1.798904e-03	ci left: 8.691435e-01	ci right 8.707098e-01	k: 617649	n:710000
KS ci ratio: 1.257126e-01	ci left: 1.281617e-03	ci right 1.454887e-03	k: 970	n:710000
BRCA2   710000 perm   423 sec   (1679 perm/sec)   p_kst 1.366197e-03   p_cons 8.699282e-01   p_joint 8.650704e-03

Joint ci ratio: 4.940869e-02	ci left: 8.452478e-03	ci right 8.882044e-03	k: 6239	n:720000
Cons ci ratio: 1.786765e-03	ci left: 8.690985e-01	ci right 8.706541e-01	k: 626312	n:720000
KS ci ratio: 1.248160e-01	ci left: 1.282652e-03	ci right 1.454734e-03	k: 984	n:720000
BRCA2   720000 perm   432 sec   (1667 perm/sec)   p_kst 1.366667e-03   p_cons 8.698778e-01   p_joint 8.665278e-03

Joint ci ratio: 5.543144e-02	ci left: 6.615455e-03	ci right 6.993954e-03	k: 4966	n:730000
Cons ci ratio: 1.774343e-03	ci left: 8.691220e-01	ci right 8.706668e-01	k: 635024	n:730000
KS ci ratio: 1.241875e-01	ci left: 1.278353e-03	ci right 1.448931e-03	k: 994	n:730000
BRCA2   730000 perm   440 sec   (1658 perm/sec)   p_kst 1.361644e-03   p_cons 8.698959e-01   p_joint 6.802740e-03

Joint ci ratio: 5.523285e-02	ci left: 6.574029e-03	ci right 6.948767e-03	k: 5002	n:740000
Cons ci ratio: 1.762029e-03	ci left: 8.691639e-01	ci right 8.706981e-01	k: 643750	n:740000
KS ci ratio: 1.237536e-01	ci left: 1.270244e-03	ci right 1.439104e-03	k: 1001	n:740000
BRCA2   740000 perm   449 sec   (1648 perm/sec)   p_kst 1.352703e-03   p_cons 8.699324e-01   p_joint 6.759459e-03

Joint ci ratio: 4.796579e-02	ci left: 8.614896e-03	ci right 9.039578e-03	k: 6619	n:750000
Cons ci ratio: 1.750411e-03	ci left: 8.691472e-01	ci right 8.706712e-01	k: 652433	n:750000
KS ci ratio: 1.232019e-01	ci left: 1.264936e-03	ci right 1.432287e-03	k: 1010	n:750000
BRCA2   750000 perm   458 sec   (1636 perm/sec)   p_kst 1.346667e-03   p_cons 8.699107e-01   p_joint 8.825333e-03

Joint ci ratio: 4.776161e-02	ci left: 8.575640e-03	ci right 8.996538e-03	k: 6676	n:760000
Cons ci ratio: 1.739565e-03	ci left: 8.690598e-01	ci right 8.705742e-01	k: 661062	n:760000
KS ci ratio: 1.225973e-01	ci left: 1.261045e-03	ci right 1.427003e-03	k: 1020	n:760000
BRCA2   760000 perm   468 sec   (1624 perm/sec)   p_kst 1.342105e-03   p_cons 8.698184e-01   p_joint 8.784211e-03

Joint ci ratio: 4.758496e-02	ci left: 8.528425e-03	ci right 8.945414e-03	k: 6726	n:770000
Cons ci ratio: 1.727709e-03	ci left: 8.691335e-01	ci right 8.706377e-01	k: 669813	n:770000
KS ci ratio: 1.217064e-01	ci left: 1.263554e-03	ci right 1.428546e-03	k: 1035	n:770000
BRCA2   770000 perm   478 sec   (1611 perm/sec)   p_kst 1.344156e-03   p_cons 8.698870e-01   p_joint 8.735065e-03

Joint ci ratio: 4.325868e-02	ci left: 1.019253e-02	ci right 1.064445e-02	k: 8125	n:780000
Cons ci ratio: 1.716383e-03	ci left: 8.691668e-01	ci right 8.706612e-01	k: 678534	n:780000
KS ci ratio: 1.202631e-01	ci left: 1.278436e-03	ci right 1.443252e-03	k: 1060	n:780000
BRCA2   780000 perm   488 sec   (1599 perm/sec)   p_kst 1.358974e-03   p_cons 8.699154e-01   p_joint 1.041667e-02

Joint ci ratio: 4.487401e-02	ci left: 9.352351e-03	ci right 9.782903e-03	k: 7557	n:790000
Cons ci ratio: 1.706364e-03	ci left: 8.690547e-01	ci right 8.705401e-01	k: 687141	n:790000
KS ci ratio: 1.195889e-01	ci left: 1.276987e-03	ci right 1.440628e-03	k: 1072	n:790000
BRCA2   790000 perm   498 sec   (1588 perm/sec)   p_kst 1.356962e-03   p_cons 8.697987e-01   p_joint 9.565823e-03

Joint ci ratio: 4.509406e-02	ci left: 9.146437e-03	ci right 9.569627e-03	k: 7485	n:800000
Cons ci ratio: 1.695600e-03	ci left: 8.690681e-01	ci right 8.705442e-01	k: 695846	n:800000
KS ci ratio: 1.189258e-01	ci left: 1.275578e-03	ci right 1.438067e-03	k: 1084	n:800000
BRCA2   800000 perm   508 sec   (1576 perm/sec)   p_kst 1.355000e-03   p_cons 8.698075e-01   p_joint 9.356250e-03

Joint ci ratio: 4.503298e-02	ci left: 9.059143e-03	ci right 9.477712e-03	k: 7506	n:810000
Cons ci ratio: 1.684900e-03	ci left: 8.690999e-01	ci right 8.705666e-01	k: 704566	n:810000
KS ci ratio: 1.183818e-01	ci left: 1.271809e-03	ci right 1.433026e-03	k: 1094	n:810000
BRCA2   810000 perm   518 sec   (1565 perm/sec)   p_kst 1.350617e-03   p_cons 8.698346e-01   p_joint 9.266667e-03

Joint ci ratio: 4.492095e-02	ci left: 8.994479e-03	ci right 9.408999e-03	k: 7544	n:820000
Cons ci ratio: 1.674715e-03	ci left: 8.690880e-01	ci right 8.705459e-01	k: 713251	n:820000
KS ci ratio: 1.179521e-01	ci left: 1.265766e-03	ci right 1.425594e-03	k: 1102	n:820000
BRCA2   820000 perm   527 sec   (1555 perm/sec)   p_kst 1.343902e-03   p_cons 8.698183e-01   p_joint 9.200000e-03

Joint ci ratio: 4.496558e-02	ci left: 8.869421e-03	ci right 9.278595e-03	k: 7530	n:830000
Cons ci ratio: 1.664154e-03	ci left: 8.691526e-01	ci right 8.706014e-01	k: 721999	n:830000
KS ci ratio: 1.173158e-01	ci left: 1.264549e-03	ci right 1.423302e-03	k: 1114	n:830000
BRCA2   830000 perm   537 sec   (1547 perm/sec)   p_kst 1.342169e-03   p_cons 8.698783e-01   p_joint 9.072289e-03

Joint ci ratio: 4.488092e-02	ci left: 8.797961e-03	ci right 9.203054e-03	k: 7559	n:840000
Cons ci ratio: 1.654295e-03	ci left: 8.691465e-01	ci right 8.705867e-01	k: 730689	n:840000
KS ci ratio: 1.167415e-01	ci left: 1.262206e-03	ci right 1.419836e-03	k: 1125	n:840000
BRCA2   840000 perm   547 sec   (1537 perm/sec)   p_kst 1.339286e-03   p_cons 8.698679e-01   p_joint 8.998810e-03

Joint ci ratio: 4.545709e-02	ci left: 8.475746e-03	ci right 8.871143e-03	k: 7371	n:850000
Cons ci ratio: 1.644780e-03	ci left: 8.691169e-01	ci right 8.705488e-01	k: 739359	n:850000
KS ci ratio: 1.160734e-01	ci left: 1.262206e-03	ci right 1.418871e-03	k: 1138	n:850000
BRCA2   850000 perm   557 sec   (1527 perm/sec)   p_kst 1.338824e-03   p_cons 8.698341e-01   p_joint 8.671765e-03

Joint ci ratio: 4.544075e-02	ci left: 8.384079e-03	ci right 8.775056e-03	k: 7377	n:860000
Cons ci ratio: 1.635209e-03	ci left: 8.691184e-01	ci right 8.705419e-01	k: 748055	n:860000
KS ci ratio: 1.153665e-01	ci left: 1.263337e-03	ci right 1.419123e-03	k: 1152	n:860000
BRCA2   860000 perm   568 sec   (1514 perm/sec)   p_kst 1.339535e-03   p_cons 8.698314e-01   p_joint 8.577907e-03

Joint ci ratio: 4.626922e-02	ci left: 7.993385e-03	ci right 8.373119e-03	k: 7118	n:870000
Cons ci ratio: 1.625779e-03	ci left: 8.691233e-01	ci right 8.705386e-01	k: 756754	n:870000
KS ci ratio: 1.146232e-01	ci left: 1.265561e-03	ci right 1.420548e-03	k: 1167	n:870000
BRCA2   870000 perm   578 sec   (1506 perm/sec)   p_kst 1.341379e-03   p_cons 8.698322e-01   p_joint 8.181609e-03

Joint ci ratio: 4.324697e-02	ci left: 9.049911e-03	ci right 9.451057e-03	k: 8139	n:880000
Cons ci ratio: 1.616655e-03	ci left: 8.691076e-01	ci right 8.705149e-01	k: 765435	n:880000
KS ci ratio: 1.141359e-01	ci left: 1.262218e-03	ci right 1.416094e-03	k: 1177	n:880000
BRCA2   880000 perm   589 sec   (1495 perm/sec)   p_kst 1.337500e-03   p_cons 8.698125e-01   p_joint 9.248864e-03

Joint ci ratio: 4.299937e-02	ci left: 9.052706e-03	ci right 9.451622e-03	k: 8233	n:890000
Cons ci ratio: 1.607453e-03	ci left: 8.691250e-01	ci right 8.705243e-01	k: 774145	n:890000
KS ci ratio: 1.133684e-01	ci left: 1.265502e-03	ci right 1.418672e-03	k: 1193	n:890000
BRCA2   890000 perm   599 sec   (1486 perm/sec)   p_kst 1.340449e-03   p_cons 8.698258e-01   p_joint 9.250562e-03

Joint ci ratio: 4.319259e-02	ci left: 8.872964e-03	ci right 9.265761e-03	k: 8161	n:900000
Cons ci ratio: 1.598421e-03	ci left: 8.691398e-01	ci right 8.705312e-01	k: 782853	n:900000
KS ci ratio: 1.126629e-01	ci left: 1.267637e-03	ci right 1.420046e-03	k: 1208	n:900000
BRCA2   900000 perm   610 sec   (1476 perm/sec)   p_kst 1.342222e-03   p_cons 8.698367e-01   p_joint 9.067778e-03

Joint ci ratio: 4.298798e-02	ci left: 8.860249e-03	ci right 9.250578e-03	k: 8239	n:910000
Cons ci ratio: 1.589725e-03	ci left: 8.691278e-01	ci right 8.705116e-01	k: 791537	n:910000
KS ci ratio: 1.121080e-01	ci left: 1.266523e-03	ci right 1.417999e-03	k: 1220	n:910000
BRCA2   910000 perm   620 sec   (1467 perm/sec)   p_kst 1.340659e-03   p_cons 8.698209e-01   p_joint 9.053846e-03

Joint ci ratio: 4.290089e-02	ci left: 8.800496e-03	ci right 9.187388e-03	k: 8273	n:920000
Cons ci ratio: 1.581010e-03	ci left: 8.691390e-01	ci right 8.705152e-01	k: 800242	n:920000
KS ci ratio: 1.116973e-01	ci left: 1.262265e-03	ci right 1.412642e-03	k: 1229	n:920000
BRCA2   920000 perm   631 sec   (1458 perm/sec)   p_kst 1.335870e-03   p_cons 8.698283e-01   p_joint 8.992391e-03

Joint ci ratio: 4.267203e-02	ci left: 8.800542e-03	ci right 9.185321e-03	k: 8362	n:930000
Cons ci ratio: 1.572549e-03	ci left: 8.691338e-01	ci right 8.705026e-01	k: 808932	n:930000
KS ci ratio: 1.112912e-01	ci left: 1.258099e-03	ci right 1.407400e-03	k: 1238	n:930000
BRCA2   930000 perm   642 sec   (1448 perm/sec)   p_kst 1.331183e-03   p_cons 8.698194e-01   p_joint 8.991398e-03

Joint ci ratio: 4.142290e-02	ci left: 9.241707e-03	ci right 9.633666e-03	k: 8870	n:940000
Cons ci ratio: 1.564141e-03	ci left: 8.691404e-01	ci right 8.705020e-01	k: 817633	n:940000
KS ci ratio: 1.105352e-01	ci left: 1.262299e-03	ci right 1.411014e-03	k: 1255	n:940000
BRCA2   940000 perm   653 sec   (1439 perm/sec)   p_kst 1.335106e-03   p_cons 8.698223e-01   p_joint 9.436170e-03

Joint ci ratio: 4.193130e-02	ci left: 8.924604e-03	ci right 9.307872e-03	k: 8659	n:950000
Cons ci ratio: 1.555961e-03	ci left: 8.691332e-01	ci right 8.704877e-01	k: 826321	n:950000
KS ci ratio: 1.096652e-01	ci left: 1.269485e-03	ci right 1.417793e-03	k: 1275	n:950000
BRCA2   950000 perm   665 sec   (1429 perm/sec)   p_kst 1.342105e-03   p_cons 8.698116e-01   p_joint 9.114737e-03

Joint ci ratio: 4.317827e-02	ci left: 8.328658e-03	ci right 8.697233e-03	k: 8171	n:960000
Cons ci ratio: 1.547936e-03	ci left: 8.691221e-01	ci right 8.704695e-01	k: 835005	n:960000
KS ci ratio: 1.091532e-01	ci left: 1.268419e-03	ci right 1.415866e-03	k: 1287	n:960000
BRCA2   960000 perm   676 sec   (1420 perm/sec)   p_kst 1.340625e-03   p_cons 8.697969e-01   p_joint 8.511458e-03

Joint ci ratio: 3.963714e-02	ci left: 9.784567e-03	ci right 1.018125e-02	k: 9682	n:970000
Cons ci ratio: 1.539943e-03	ci left: 8.691246e-01	ci right 8.704650e-01	k: 843702	n:970000
KS ci ratio: 1.086065e-01	ci left: 1.268379e-03	ci right 1.415037e-03	k: 1300	n:970000
BRCA2   970000 perm   687 sec   (1412 perm/sec)   p_kst 1.340206e-03   p_cons 8.697959e-01   p_joint 9.981443e-03

Joint ci ratio: 4.041350e-02	ci left: 9.316968e-03	ci right 9.702266e-03	k: 9318	n:980000
Cons ci ratio: 1.532018e-03	ci left: 8.691352e-01	ci right 8.704687e-01	k: 852407	n:980000
KS ci ratio: 1.079036e-01	ci left: 1.272314e-03	ci right 1.418414e-03	k: 1317	n:980000
BRCA2   980000 perm   698 sec   (1403 perm/sec)   p_kst 1.343878e-03   p_cons 8.698031e-01   p_joint 9.508163e-03

Joint ci ratio: 4.151796e-02	ci left: 8.738921e-03	ci right 9.110426e-03	k: 8834	n:990000
Cons ci ratio: 1.524016e-03	ci left: 8.691750e-01	ci right 8.705016e-01	k: 861141	n:990000
KS ci ratio: 1.073754e-01	ci left: 1.272240e-03	ci right 1.417571e-03	k: 1330	n:990000
BRCA2   990000 perm   710 sec   (1395 perm/sec)   p_kst 1.343434e-03   p_cons 8.698394e-01   p_joint 8.923232e-03

Joint ci ratio: 4.170837e-02	ci left: 8.573338e-03	ci right 8.939516e-03	k: 8755	n:1000000
Cons ci ratio: 1.516071e-03	ci left: 8.692240e-01	ci right 8.705438e-01	k: 869885	n:1000000
KS ci ratio: 1.070544e-01	ci left: 1.267303e-03	ci right 1.411610e-03	k: 1338	n:1000000
BRCA2   1000000 perm   721 sec   (1386 perm/sec)   p_kst 1.338000e-03   p_cons 8.698850e-01   p_joint 8.755000e-03

Joint ci ratio: 4.150508e-02	ci left: 8.572716e-03	ci right 8.937040e-03	k: 8841	n:1010000
Cons ci ratio: 1.508295e-03	ci left: 8.692652e-01	ci right 8.705782e-01	k: 878622	n:1010000
KS ci ratio: 1.063811e-01	ci left: 1.271138e-03	ci right 1.414914e-03	k: 1355	n:1010000
BRCA2   1010000 perm   733 sec   (1379 perm/sec)   p_kst 1.341584e-03   p_cons 8.699228e-01   p_joint 8.753465e-03

Joint ci ratio: 3.913601e-02	ci left: 9.549535e-03	ci right 9.931688e-03	k: 9934	n:1020000
Cons ci ratio: 1.500937e-03	ci left: 8.692603e-01	ci right 8.705670e-01	k: 887313	n:1020000
KS ci ratio: 1.058748e-01	ci left: 1.271083e-03	ci right 1.414126e-03	k: 1368	n:1020000
BRCA2   1020000 perm   744 sec   (1371 perm/sec)   p_kst 1.341176e-03   p_cons 8.699147e-01   p_joint 9.739216e-03

Joint ci ratio: 3.747461e-02	ci left: 1.031462e-02	ci right 1.070950e-02	k: 10826	n:1030000
Cons ci ratio: 1.493705e-03	ci left: 8.692527e-01	ci right 8.705530e-01	k: 896001	n:1030000
KS ci ratio: 1.052233e-01	ci left: 1.274811e-03	ci right 1.417337e-03	k: 1385	n:1030000
BRCA2   1030000 perm   756 sec   (1363 perm/sec)   p_kst 1.344660e-03   p_cons 8.699039e-01   p_joint 1.051068e-02

Joint ci ratio: 3.727182e-02	ci left: 1.032785e-02	ci right 1.072104e-02	k: 10944	n:1040000
Cons ci ratio: 1.486279e-03	ci left: 8.692905e-01	ci right 8.705844e-01	k: 904736	n:1040000
KS ci ratio: 1.045837e-01	ci left: 1.278471e-03	ci right 1.420483e-03	k: 1402	n:1040000
BRCA2   1040000 perm   767 sec   (1355 perm/sec)   p_kst 1.348077e-03   p_cons 8.699385e-01   p_joint 1.052308e-02

Joint ci ratio: 3.760318e-02	ci left: 1.005115e-02	ci right 1.043728e-02	k: 10755	n:1050000
Cons ci ratio: 1.479100e-03	ci left: 8.693066e-01	ci right 8.705942e-01	k: 913449	n:1050000
KS ci ratio: 1.039923e-01	ci left: 1.281136e-03	ci right 1.422590e-03	k: 1418	n:1050000
BRCA2   1050000 perm   779 sec   (1348 perm/sec)   p_kst 1.350476e-03   p_cons 8.699514e-01   p_joint 1.024286e-02

Joint ci ratio: 3.749599e-02	ci left: 1.001426e-02	ci right 1.039786e-02	k: 10817	n:1060000
Cons ci ratio: 1.471993e-03	ci left: 8.693271e-01	ci right 8.706086e-01	k: 922167	n:1060000
KS ci ratio: 1.035554e-01	ci left: 1.280077e-03	ci right 1.420784e-03	k: 1430	n:1060000
BRCA2   1060000 perm   791 sec   (1341 perm/sec)   p_kst 1.349057e-03   p_cons 8.699689e-01   p_joint 1.020472e-02

Joint ci ratio: 3.742622e-02	ci left: 9.958623e-03	ci right 1.033936e-02	k: 10858	n:1070000
Cons ci ratio: 1.465399e-03	ci left: 8.692836e-01	ci right 8.705593e-01	k: 930817	n:1070000
KS ci ratio: 1.031598e-01	ci left: 1.278128e-03	ci right 1.418052e-03	k: 1441	n:1070000
BRCA2   1070000 perm   802 sec   (1334 perm/sec)   p_kst 1.346729e-03   p_cons 8.699224e-01   p_joint 1.014766e-02

Joint ci ratio: 3.736202e-02	ci left: 9.901265e-03	ci right 1.027915e-02	k: 10896	n:1080000
Cons ci ratio: 1.458540e-03	ci left: 8.692956e-01	ci right 8.705654e-01	k: 939526	n:1080000
KS ci ratio: 1.024514e-01	ci left: 1.284336e-03	ci right 1.423916e-03	k: 1461	n:1080000
BRCA2   1080000 perm   814 sec   (1327 perm/sec)   p_kst 1.352778e-03   p_cons 8.699315e-01   p_joint 1.008889e-02

Joint ci ratio: 3.717299e-02	ci left: 9.911314e-03	ci right 1.028763e-02	k: 11007	n:1090000
Cons ci ratio: 1.451877e-03	ci left: 8.692918e-01	ci right 8.705557e-01	k: 948218	n:1090000
KS ci ratio: 1.019644e-01	ci left: 1.285069e-03	ci right 1.424025e-03	k: 1475	n:1090000
BRCA2   1090000 perm   826 sec   (1320 perm/sec)   p_kst 1.353211e-03   p_cons 8.699248e-01   p_joint 1.009817e-02

Joint ci ratio: 3.701372e-02	ci left: 9.906774e-03	ci right 1.028127e-02	k: 11102	n:1100000
Cons ci ratio: 1.445317e-03	ci left: 8.692863e-01	ci right 8.705445e-01	k: 956908	n:1100000
KS ci ratio: 1.015525e-01	ci left: 1.284018e-03	ci right 1.422266e-03	k: 1487	n:1100000
BRCA2   1100000 perm   838 sec   (1313 perm/sec)   p_kst 1.351818e-03   p_cons 8.699164e-01   p_joint 1.009273e-02

Joint ci ratio: 3.684817e-02	ci left: 9.906782e-03	ci right 1.027957e-02	k: 11202	n:1110000
Cons ci ratio: 1.438999e-03	ci left: 8.692565e-01	ci right 8.705091e-01	k: 965571	n:1110000
KS ci ratio: 1.009771e-01	ci left: 1.287377e-03	ci right 1.425155e-03	k: 1504	n:1110000
BRCA2   1110000 perm   850 sec   (1305 perm/sec)   p_kst 1.354955e-03   p_cons 8.698838e-01   p_joint 1.009189e-02

Joint ci ratio: 3.577051e-02	ci left: 1.041912e-02	ci right 1.079949e-02	k: 11881	n:1120000
Cons ci ratio: 1.432412e-03	ci left: 8.692827e-01	ci right 8.705297e-01	k: 974296	n:1120000
KS ci ratio: 1.006102e-01	ci left: 1.285457e-03	ci right 1.422500e-03	k: 1515	n:1120000
BRCA2   1120000 perm   863 sec   (1298 perm/sec)   p_kst 1.352679e-03   p_cons 8.699071e-01   p_joint 1.060804e-02

Joint ci ratio: 3.537271e-02	ci left: 1.056111e-02	ci right 1.094228e-02	k: 12148	n:1130000
Cons ci ratio: 1.426055e-03	ci left: 8.692863e-01	ci right 8.705277e-01	k: 982996	n:1130000
KS ci ratio: 1.000834e-01	ci left: 1.287885e-03	ci right 1.424426e-03	k: 1531	n:1130000
BRCA2   1130000 perm   875 sec   (1292 perm/sec)   p_kst 1.354867e-03   p_cons 8.699080e-01   p_joint 1.075044e-02

Joint ci ratio: 3.530251e-02	ci left: 1.051107e-02	ci right 1.088967e-02	k: 12197	n:1140000
Cons ci ratio: 1.420089e-03	ci left: 8.692406e-01	ci right 8.704768e-01	k: 991640	n:1140000
KS ci ratio: 9.959691e-02	ci left: 1.289417e-03	ci right 1.425417e-03	k: 1546	n:1140000
BRCA2   1140000 perm   887 sec   (1285 perm/sec)   p_kst 1.356140e-03   p_cons 8.698596e-01   p_joint 1.069912e-02

Outputting figure to mutsig2_images.part000000000017/BRCA2.3_10361_1140000_0.0013561_0.86986_0.010699.png
                gene_name: BRCA2
               theta_stop: 0.100 
                    nperm: 1140000 
                     p_ks: 0.0014 
        ci_ks_bounds_left: 0.0013 
       ci_ks_bounds_right: 0.0014 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.87 
                  p_joint: 0.011 
     ci_joint_bounds_left: 0.011 
    ci_joint_bounds_right: 0.011 

Current progress: 12 percent done.
BMPER
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.312042e-02	ci left: 4.426097e-01	ci right 4.622180e-01	k: 4524	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: 4.450408e-02	ci left: 4.270484e-01	ci right 4.465885e-01	k: 4368	n:10000
BMPER   10000 perm   2 sec   (6012 perm/sec)   p_kst 4.368000e-01   p_cons 6.952000e-01   p_joint 4.524000e-01

Outputting figure to mutsig2_images.part000000000017/BMPER.2_2118_10000_0.4368_0.6952_0.4524.png
                gene_name: BMPER
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.70 
                  p_joint: 0.45 
     ci_joint_bounds_left: 0.44 
    ci_joint_bounds_right: 0.46 

Current progress: 25 percent done.
BMX
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.838059e-03	ci left: 9.885089e-01	ci right 9.923974e-01	k: 9906	n:10000
Cons ci ratio: 3.975457e-02	ci left: 4.830544e-01	ci right 5.027497e-01	k: 4929	n:10000
KS ci ratio: 7.810253e-03	ci left: 9.579609e-01	ci right 9.655670e-01	k: 9619	n:10000
BMX   10000 perm   2 sec   (5393 perm/sec)   p_kst 9.619000e-01   p_cons 4.929000e-01   p_joint 9.906000e-01

Outputting figure to mutsig2_images.part000000000017/BMX.2_2100_10000_0.9619_0.4929_0.9906.png
                gene_name: BMX
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.96 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 38 percent done.
BNC2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.836104e-02	ci left: 8.124288e-01	ci right 8.275843e-01	k: 8201	n:10000
Cons ci ratio: 6.661620e-02	ci left: 2.485560e-01	ci right 2.657857e-01	k: 2571	n:10000
KS ci ratio: 2.351896e-02	ci left: 7.265354e-01	ci right 7.439273e-01	k: 7353	n:10000
BNC2   10000 perm   2 sec   (5069 perm/sec)   p_kst 7.353000e-01   p_cons 2.571000e-01   p_joint 8.201000e-01

Outputting figure to mutsig2_images.part000000000017/BNC2.2_3328_10000_0.7353_0.2571_0.8201.png
                gene_name: BNC2
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.83 

Current progress: 50 percent done.
BRDT
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.857317e-02	ci left: 6.435768e-01	ci right 6.623341e-01	k: 6530	n:10000
Cons ci ratio: 3.624798e-02	ci left: 5.291699e-01	ci right 5.488074e-01	k: 5390	n:10000
KS ci ratio: 7.812958e-02	ci left: 1.931834e-01	ci right 2.089911e-01	k: 2010	n:10000
BRDT   10000 perm   2 sec   (5133 perm/sec)   p_kst 2.010000e-01   p_cons 5.390000e-01   p_joint 6.530000e-01

Outputting figure to mutsig2_images.part000000000017/BRDT.2_2916_10000_0.201_0.539_0.653.png
                gene_name: BRDT
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.55 
                  p_joint: 0.65 
     ci_joint_bounds_left: 0.64 
    ci_joint_bounds_right: 0.66 

Current progress: 62 percent done.
BRF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.067756e-03	ci left: 9.649925e-01	ci right 9.719311e-01	k: 9686	n:10000
Cons ci ratio: 4.986017e-02	ci left: 3.723630e-01	ci right 3.915058e-01	k: 3819	n:10000
KS ci ratio: 3.041956e-02	ci left: 6.145218e-01	ci right 6.336059e-01	k: 6241	n:10000
BRF1   10000 perm   2 sec   (5639 perm/sec)   p_kst 6.241000e-01   p_cons 3.819000e-01   p_joint 9.686000e-01

Outputting figure to mutsig2_images.part000000000017/BRF1.2_2106_10000_0.6241_0.3819_0.9686.png
                gene_name: BRF1
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 75 percent done.
BRIP1
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: 2.571600e-02	ci left: 6.900036e-01	ci right 7.080803e-01	k: 6991	n:10000
KS ci ratio: 2.547790e-02	ci left: 6.939360e-01	ci right 7.119456e-01	k: 7030	n:10000
BRIP1   10000 perm   2 sec   (5049 perm/sec)   p_kst 7.030000e-01   p_cons 6.991000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000017/BRIP1.2_3826_10000_0.703_0.6991_1.png
                gene_name: BRIP1
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.71 
                   p_cons: 0.70 
      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: 88 percent done.
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: 2.642698e-02	ci left: 6.783117e-01	ci right 6.965790e-01	k: 6875	n:10000
KS ci ratio: 1.644997e-02	ci left: 8.431554e-01	ci right 8.572399e-01	k: 8503	n:10000
BRWD1   10000 perm   2 sec   (4076 perm/sec)   p_kst 8.503000e-01   p_cons 6.875000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000017/BRWD1.2_7384_10000_0.8503_0.6875_1.png
                gene_name: BRWD1
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.69 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.70 
                  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.165.3896/
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/181708/iteration1/scatter.0000000017
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 17 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1546>
Subject: Job 1119533: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1546>, 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/181708/iteration1/scatter.0000000018> was used as the working directory.
Started at Wed Oct 10 10:41:48 2012
Results reported at Wed Oct 10 10:44:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000018.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000018.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 18  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    125.87 sec.
    Max Memory :      1226 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.165.3896/
-whichjob
18
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 18: processing genes 1539 - 1628
Calculating significance of each gene.
Using projection method.
1539	BTG2	1
1540	BTG3	1
1541	BTG4	1
1542	BTK	2.937930e-01
1543	BTLA	1
1544	BTN1A1	1
1545	BTN2A1	3.496447e-02
1546	BTN2A2	1
1547	BTN3A1	1
1548	BTN3A2	1
1549	BTN3A3	2.720317e-01
1550	BTNL2	1
1551	BTNL3	1
1552	BTNL8	1
1553	BTNL9	1
1554	BTRC	1
1555	BUB1	1
1556	BUB1B	1.045073e-01
1557	BUB3	1
1558	BUD13	1.870367e-01
1559	BUD31	1
1560	BVES	2.247703e-02
1561	BYSL	1
1562	BZRAP1	1
1563	BZW1	1
1564	BZW2	1.953087e-01
1565	C10orf10	1
1566	C10orf107	1
1567	C10orf11	1
1568	C10orf111	1
1569	C10orf113	1
1570	C10orf114	1
1571	C10orf116	1
1572	C10orf118	1
1573	C10orf119	1
1574	C10orf12	1
1575	C10orf120	1.252054e-01
1576	C10orf125	1
1577	C10orf128	1
1578	C10orf129	1
1579	C10orf137	1
1580	C10orf140	1
1581	C10orf18	5.924340e-01
1582	C10orf2	1
1583	C10orf25	1
1584	C10orf26	1
1585	C10orf27	1
1586	C10orf28	1
1587	C10orf32	1
1588	C10orf35	1
1589	C10orf46	1
1590	C10orf47	1
1591	C10orf53	1
1592	C10orf54	6.945415e-02
1593	C10orf55	1
1594	C10orf57	1
1595	C10orf58	1
1596	C10orf62	1
1597	C10orf67	1
1598	C10orf68	1
1599	C10orf71	1
1600	C10orf72	1
1601	C10orf76	1
1602	C10orf78	1.002989e-01
1603	C10orf79	1.114450e-01
1604	C10orf81	1
1605	C10orf82	1
1606	C10orf84	1
1607	C10orf88	1
1608	C10orf90	2.144592e-01
1609	C10orf91	1
1610	C10orf93	1
1611	C10orf96	1
1612	C10orf99	1
1613	C11orf1	1
1614	C11orf10	1
1615	C11orf16	1
1616	C11orf17	1
1617	C11orf2	1
1618	C11orf20	1
1619	C11orf24	1
1620	C11orf30	3.848590e-01
1621	C11orf31	1
1622	C11orf35	1
1623	C11orf40	1
1624	C11orf41	1
1625	C11orf42	1
1626	C11orf45	1
1627	C11orf46	1
1628	C11orf48	7.074920e-02
Done

Running MutSig 2:
Scatter job 18: processing genes 1539 - 1628
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
BTN2A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.777696e-03	ci left: 9.367201e-01	ci right 9.460207e-01	k: 9415	n:10000
Cons ci ratio: 3.224372e-02	ci left: 5.867071e-01	ci right 6.060367e-01	k: 5964	n:10000
KS ci ratio: 7.507648e-03	ci left: 9.608952e-01	ci right 9.682310e-01	k: 9647	n:10000
BTN2A1   10000 perm   2 sec   (5125 perm/sec)   p_kst 9.647000e-01   p_cons 5.964000e-01   p_joint 9.415000e-01

Outputting figure to mutsig2_images.part000000000018/BTN2A1.2_1639_10000_0.9647_0.5964_0.9415.png
                gene_name: BTN2A1
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.96 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.94 
    ci_joint_bounds_right: 0.95 

Current progress: 33 percent done.
BUB1B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.159281e-01	ci left: 9.662172e-02	ci right 1.086109e-01	k: 1025	n:10000
Cons ci ratio: 3.665833e-02	ci left: 5.235635e-01	ci right 5.432170e-01	k: 5334	n:10000
KS ci ratio: 1.876749e-01	ci left: 3.786599e-02	ci right 4.580373e-02	k: 417	n:10000
BUB1B   10000 perm   2 sec   (5179 perm/sec)   p_kst 4.170000e-02   p_cons 5.334000e-01   p_joint 1.025000e-01

Joint ci ratio: 4.992055e-02	ci left: 2.297324e-01	ci right 2.415446e-01	k: 4712	n:20000
Cons ci ratio: 2.551196e-02	ci left: 5.344136e-01	ci right 5.482743e-01	k: 10827	n:20000
KS ci ratio: 1.345678e-01	ci left: 3.795510e-02	ci right 4.347944e-02	k: 813	n:20000
BUB1B   20000 perm   5 sec   (4392 perm/sec)   p_kst 4.065000e-02   p_cons 5.413500e-01   p_joint 2.356000e-01

Joint ci ratio: 5.335950e-02	ci left: 1.483831e-01	ci right 1.565510e-01	k: 4573	n:30000
Cons ci ratio: 2.081621e-02	ci left: 5.360413e-01	ci right 5.473506e-01	k: 16251	n:30000
KS ci ratio: 1.101574e-01	ci left: 3.826480e-02	ci right 4.275808e-02	k: 1214	n:30000
BUB1B   30000 perm   7 sec   (4104 perm/sec)   p_kst 4.046667e-02   p_cons 5.417000e-01   p_joint 1.524333e-01

Joint ci ratio: 3.765797e-02	ci left: 2.091203e-01	ci right 2.171714e-01	k: 8525	n:40000
Cons ci ratio: 1.802938e-02	ci left: 5.367517e-01	ci right 5.465422e-01	k: 21666	n:40000
KS ci ratio: 9.476118e-02	ci left: 3.907768e-02	ci right 4.298931e-02	k: 1640	n:40000
BUB1B   40000 perm   10 sec   (4018 perm/sec)   p_kst 4.100000e-02   p_cons 5.416500e-01   p_joint 2.131250e-01

Outputting figure to mutsig2_images.part000000000018/BUB1B.2_3245_40000_0.041_0.54165_0.21313.png
                gene_name: BUB1B
               theta_stop: 0.095 
                    nperm: 40000 
                     p_ks: 0.041 
        ci_ks_bounds_left: 0.039 
       ci_ks_bounds_right: 0.043 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.55 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 67 percent done.
C10orf79
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.135385e-02	ci left: 6.001585e-01	ci right 6.193775e-01	k: 6098	n:10000
Cons ci ratio: 5.657045e-02	ci left: 3.151274e-01	ci right 3.335750e-01	k: 3243	n:10000
KS ci ratio: 4.889213e-02	ci left: 3.816178e-01	ci right 4.008456e-01	k: 3912	n:10000
C10orf79   10000 perm   2 sec   (4156 perm/sec)   p_kst 3.912000e-01   p_cons 3.243000e-01   p_joint 6.098000e-01

Outputting figure to mutsig2_images.part000000000018/C10orf79.2_5150_10000_0.3912_0.3243_0.6098.png
                gene_name: C10orf79
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.33 
                  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.165.3896/
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/181708/iteration1/scatter.0000000018
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 18 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119538: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000019> was used as the working directory.
Started at Wed Oct 10 10:42:03 2012
Results reported at Wed Oct 10 10:44:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000019.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000019.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 19  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    142.09 sec.
    Max Memory :      1468 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.165.3896/
-whichjob
19
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 19: processing genes 1629 - 1719
Calculating significance of each gene.
Using projection method.
1629	C11orf49	1
1630	C11orf51	1
1631	C11orf52	1
1632	C11orf53	1
1633	C11orf54	1
1634	C11orf57	1
1635	C11orf58	1
1636	C11orf59	1
1637	C11orf61	1
1638	C11orf63	1
1639	C11orf65	1
1640	C11orf66	5.118912e-02
1641	C11orf67	1
1642	C11orf68	1
1643	C11orf70	1
1644	C11orf71	1
1645	C11orf73	7.849977e-02
1646	C11orf74	1
1647	C11orf75	1
1648	C11orf80	3.243093e-02
1649	C11orf82	4.047313e-01
1650	C11orf83	1
1651	C11orf84	1
1652	C11orf85	5.350923e-04
1653	C11orf87	1
1654	C11orf88	1
1655	C11orf9	1.612581e-01
1656	C11orf92	1
1657	C11orf94	1
1658	C12orf10	1
1659	C12orf11	9.830692e-02
1660	C12orf12	1
1661	C12orf23	1
1662	C12orf24	1
1663	C12orf26	1.718627e-01
1664	C12orf29	1
1665	C12orf34	1
1666	C12orf35	3.503998e-02
1667	C12orf36	1
1668	C12orf39	1
1669	C12orf4	1
1670	C12orf40	1
1671	C12orf41	1
1672	C12orf42	1
1673	C12orf43	1
1674	C12orf44	1
1675	C12orf45	1
1676	C12orf48	1
1677	C12orf49	1
1678	C12orf5	1
1679	C12orf50	2.019953e-01
1680	C12orf51	2.120970e-02
1681	C12orf52	1.277553e-01
1682	C12orf53	1
1683	C12orf54	1
1684	C12orf56	1
1685	C12orf57	1
1686	C12orf59	1
1687	C12orf60	3.242042e-02
1688	C12orf61	1
1689	C12orf62	1
1690	C12orf63	1
1691	C12orf64	1
1692	C12orf65	1
1693	C12orf66	1
1694	C12orf68	1
1695	C12orf69	1
1696	C12orf71	1
1697	C12orf72	1
1698	C12orf74	7.294784e-02
1699	C12orf76	1
1700	C12orf77	1
1701	C13orf1	1
1702	C13orf15	1
1703	C13orf16	1
1704	C13orf18	1
1705	C13orf23	1
1706	C13orf26	6.726782e-02
1707	C13orf27	5.141065e-02
1708	C13orf28	2.375044e-02
1709	C13orf30	1
1710	C13orf31	1
1711	C13orf33	1
1712	C13orf34	1
1713	C13orf35	1
1714	C13orf36	1
1715	C13orf37	1
1716	C13orf39	1
1717	C14orf1	1
1718	C14orf101	1
1719	C14orf102	1
Done

Running MutSig 2:
Scatter job 19: processing genes 1629 - 1719
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C12orf51
Processing conservation and coverage...
76% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.221543e-02	ci left: 7.483685e-01	ci right 7.652816e-01	k: 7569	n:10000
Cons ci ratio: 5.633897e-02	ci left: 3.169137e-01	ci right 3.353876e-01	k: 3261	n:10000
KS ci ratio: 3.128144e-02	ci left: 6.012631e-01	ci right 6.204723e-01	k: 6109	n:10000
C12orf51   10000 perm   4 sec   (2741 perm/sec)   p_kst 6.109000e-01   p_cons 3.261000e-01   p_joint 7.569000e-01

Outputting figure to mutsig2_images.part000000000019/C12orf51.5_13037_10000_0.6109_0.3261_0.7569.png
                gene_name: C12orf51
               theta_stop: 0.056 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.34 
                  p_joint: 0.76 
     ci_joint_bounds_left: 0.75 
    ci_joint_bounds_right: 0.77 

Current progress: 20 percent done.
C12orf35
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.361100e-02	ci left: 4.370225e-01	ci right 4.566085e-01	k: 4468	n:10000
Cons ci ratio: 2.305411e-02	ci left: 7.343154e-01	ci right 7.515429e-01	k: 7430	n:10000
KS ci ratio: 8.119962e-02	ci left: 1.812696e-01	ci right 1.967120e-01	k: 1889	n:10000
C12orf35   10000 perm   3 sec   (3198 perm/sec)   p_kst 1.889000e-01   p_cons 7.430000e-01   p_joint 4.468000e-01

Outputting figure to mutsig2_images.part000000000019/C12orf35.3_5256_10000_0.1889_0.743_0.4468.png
                gene_name: C12orf35
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.75 
                  p_joint: 0.45 
     ci_joint_bounds_left: 0.44 
    ci_joint_bounds_right: 0.46 

Current progress: 40 percent done.
C11orf85
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.862636e-02	ci left: 3.842059e-01	ci right 4.034560e-01	k: 3938	n:10000
Cons ci ratio: 1.407139e-02	ci left: 8.795059e-01	ci right 8.920683e-01	k: 8859	n:10000
KS ci ratio: 8.296339e-02	ci left: 1.748744e-01	ci right 1.901110e-01	k: 1824	n:10000
C11orf85   10000 perm   3 sec   (3723 perm/sec)   p_kst 1.824000e-01   p_cons 8.859000e-01   p_joint 3.938000e-01

Outputting figure to mutsig2_images.part000000000019/C11orf85.2_683_10000_0.1824_0.8859_0.3938.png
                gene_name: C11orf85
               theta_stop: 0.083 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 60 percent done.
C12orf11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.723193e-02	ci left: 2.450955e-01	ci right 2.622482e-01	k: 2536	n:10000
Cons ci ratio: 1.631092e-01	ci left: 5.013112e-02	ci right 5.913054e-02	k: 545	n:10000
KS ci ratio: 1.206345e-01	ci left: 8.971071e-02	ci right 1.013261e-01	k: 954	n:10000
C12orf11   10000 perm   3 sec   (3280 perm/sec)   p_kst 9.540000e-02   p_cons 5.450000e-02   p_joint 2.536000e-01

Joint ci ratio: 2.324170e-02	ci left: 5.802893e-01	ci right 5.939854e-01	k: 11743	n:20000
Cons ci ratio: 1.146183e-01	ci left: 5.207485e-02	ci right 5.845522e-02	k: 1104	n:20000
KS ci ratio: 8.582577e-02	ci left: 9.038200e-02	ci right 9.853634e-02	k: 1888	n:20000
C12orf11   20000 perm   7 sec   (2926 perm/sec)   p_kst 9.440000e-02   p_cons 5.520000e-02   p_joint 5.871500e-01

Joint ci ratio: 1.891262e-02	ci left: 5.832070e-01	ci right 5.943758e-01	k: 17664	n:30000
Cons ci ratio: 9.411313e-02	ci left: 5.208821e-02	ci right 5.726512e-02	k: 1639	n:30000
KS ci ratio: 6.927655e-02	ci left: 9.308278e-02	ci right 9.979561e-02	k: 2892	n:30000
C12orf11   30000 perm   10 sec   (3128 perm/sec)   p_kst 9.640000e-02   p_cons 5.463333e-02   p_joint 5.888000e-01

Outputting figure to mutsig2_images.part000000000019/C12orf11.2_2185_30000_0.0964_0.054633_0.5888.png
                gene_name: C12orf11
               theta_stop: 0.094 
                    nperm: 30000 
                     p_ks: 0.096 
        ci_ks_bounds_left: 0.093 
       ci_ks_bounds_right: 0.100 
                   p_cons: 0.055 
      ci_cons_bounds_left: 0.052 
     ci_cons_bounds_right: 0.057 
                  p_joint: 0.59 
     ci_joint_bounds_left: 0.58 
    ci_joint_bounds_right: 0.59 

Current progress: 80 percent done.
C12orf74
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.125218e-01	ci left: 2.939568e-02	ci right 3.647982e-02	k: 328	n:10000
Cons ci ratio: 1.687404e-01	ci left: 4.686539e-02	ci right 5.559839e-02	k: 511	n:10000
KS ci ratio: 7.321256e-02	ci left: 2.145771e-01	ci right 2.309847e-01	k: 2227	n:10000
C12orf74   10000 perm   1 sec   (7185 perm/sec)   p_kst 2.227000e-01   p_cons 5.110000e-02   p_joint 3.280000e-02

Joint ci ratio: 1.163560e-01	ci left: 5.056727e-02	ci right 5.686327e-02	k: 1073	n:20000
Cons ci ratio: 1.220452e-01	ci left: 4.604902e-02	ci right 5.208294e-02	k: 980	n:20000
KS ci ratio: 5.200999e-02	ci left: 2.154141e-01	ci right 2.269671e-01	k: 4423	n:20000
C12orf74   20000 perm   3 sec   (6270 perm/sec)   p_kst 2.211500e-01   p_cons 4.900000e-02   p_joint 5.365000e-02

Joint ci ratio: 1.184857e-01	ci left: 3.311072e-02	ci right 3.731324e-02	k: 1055	n:30000
Cons ci ratio: 9.896261e-02	ci left: 4.723528e-02	ci right 5.218573e-02	k: 1490	n:30000
KS ci ratio: 4.234734e-02	ci left: 2.174400e-01	ci right 2.268806e-01	k: 6664	n:30000
C12orf74   30000 perm   5 sec   (5936 perm/sec)   p_kst 2.221333e-01   p_cons 4.966667e-02   p_joint 3.516667e-02

Joint ci ratio: 7.590965e-02	ci left: 6.012261e-02	ci right 6.489115e-02	k: 2499	n:40000
Cons ci ratio: 8.595498e-02	ci left: 4.729664e-02	ci right 5.156908e-02	k: 1976	n:40000
KS ci ratio: 3.672885e-02	ci left: 2.175626e-01	ci right 2.257279e-01	k: 8865	n:40000
C12orf74   40000 perm   7 sec   (5716 perm/sec)   p_kst 2.216250e-01   p_cons 4.940000e-02   p_joint 6.247500e-02

Outputting figure to mutsig2_images.part000000000019/C12orf74.2_596_40000_0.22162_0.0494_0.062475.png
                gene_name: C12orf74
               theta_stop: 0.086 
                    nperm: 40000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.049 
      ci_cons_bounds_left: 0.047 
     ci_cons_bounds_right: 0.052 
                  p_joint: 0.062 
     ci_joint_bounds_left: 0.060 
    ci_joint_bounds_right: 0.065 

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.165.3896/
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/181708/iteration1/scatter.0000000019
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 19 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119541: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000020> was used as the working directory.
Started at Wed Oct 10 10:42:03 2012
Results reported at Wed Oct 10 10:44:20 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000020.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000020.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 20  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    134.56 sec.
    Max Memory :      1244 MB
    Max Swap   :      3853 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.165.3896/
-whichjob
20
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 20: processing genes 1720 - 1809
Calculating significance of each gene.
Using projection method.
1720	C14orf104	1
1721	C14orf105	1
1722	C14orf106	1
1723	C14orf109	1
1724	C14orf115	1.692742e-01
1725	C14orf118	1
1726	C14orf119	1
1727	C14orf126	1
1728	C14orf129	1
1729	C14orf135	1
1730	C14orf138	1
1731	C14orf142	1
1732	C14orf143	1
1733	C14orf145	1
1734	C14orf147	1
1735	C14orf148	1
1736	C14orf149	1
1737	C14orf153	1
1738	C14orf156	1
1739	C14orf159	1
1740	C14orf166	1
1741	C14orf166B	1
1742	C14orf169	1
1743	C14orf174	1.089355e-01
1744	C14orf177	1
1745	C14orf178	1
1746	C14orf179	1
1747	C14orf180	1
1748	C14orf181	1.793976e-02
1749	C14orf182	1
1750	C14orf183	1
1751	C14orf184	1
1752	C14orf2	1
1753	C14orf21	1
1754	C14orf28	1
1755	C14orf37	1
1756	C14orf39	2.720154e-01
1757	C14orf4	1.543577e-01
1758	C14orf43	3.879129e-01
1759	C14orf45	1.111597e-01
1760	C14orf49	1
1761	C14orf50	1
1762	C14orf68	1
1763	C14orf73	1
1764	C14orf79	1
1765	C14orf93	1.603526e-01
1766	C15orf17	1
1767	C15orf2	1
1768	C15orf23	1
1769	C15orf24	1
1770	C15orf26	1
1771	C15orf27	1
1772	C15orf29	1
1773	C15orf32	1
1774	C15orf33	8.396192e-02
1775	C15orf38	1
1776	C15orf39	1
1777	C15orf40	1
1778	C15orf41	1
1779	C15orf42	1.326015e-01
1780	C15orf43	1
1781	C15orf44	2.977297e-02
1782	C15orf48	1
1783	C15orf52	2.181028e-01
1784	C15orf53	1
1785	C15orf54	1
1786	C15orf55	1
1787	C15orf56	1
1788	C15orf57	1
1789	C15orf58	4.547583e-02
1790	C15orf59	1.247302e-01
1791	C15orf60	1
1792	C15orf63	1
1793	C16orf11	9.029717e-02
1794	C16orf13	1
1795	C16orf3	1
1796	C16orf42	1
1797	C16orf45	1
1798	C16orf46	3.836174e-02
1799	C16orf48	1
1800	C16orf5	1
1801	C16orf53	1
1802	C16orf54	1.121820e-02
1803	C16orf55	1
1804	C16orf57	1
1805	C16orf58	1
1806	C16orf59	1
1807	C16orf61	1
1808	C16orf62	6.521942e-02
1809	C16orf63	1
Done

Running MutSig 2:
Scatter job 20: processing genes 1720 - 1809
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C14orf43
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.183877e-02	ci left: 3.542622e-01	ci right 3.732173e-01	k: 3637	n:10000
Cons ci ratio: 3.864157e-02	ci left: 4.972503e-01	ci right 5.169456e-01	k: 5071	n:10000
KS ci ratio: 8.958253e-02	ci left: 1.534534e-01	ci right 1.679449e-01	k: 1606	n:10000
C14orf43   10000 perm   2 sec   (4347 perm/sec)   p_kst 1.606000e-01   p_cons 5.071000e-01   p_joint 3.637000e-01

Outputting figure to mutsig2_images.part000000000020/C14orf43.3_3182_10000_0.1606_0.5071_0.3637.png
                gene_name: C14orf43
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.50 
     ci_cons_bounds_right: 0.52 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 25 percent done.
C15orf42
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.722167e-02	ci left: 5.159569e-01	ci right 5.356281e-01	k: 5258	n:10000
Cons ci ratio: 3.699839e-02	ci left: 5.189593e-01	ci right 5.386240e-01	k: 5288	n:10000
KS ci ratio: 5.993563e-02	ci left: 2.905320e-01	ci right 3.085849e-01	k: 2995	n:10000
C15orf42   10000 perm   2 sec   (4164 perm/sec)   p_kst 2.995000e-01   p_cons 5.288000e-01   p_joint 5.258000e-01

Outputting figure to mutsig2_images.part000000000020/C15orf42.2_5821_10000_0.2995_0.5288_0.5258.png
                gene_name: C15orf42
               theta_stop: 0.060 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.53 
     ci_joint_bounds_left: 0.52 
    ci_joint_bounds_right: 0.54 

Current progress: 50 percent done.
C15orf44
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: 1.086698e-02	ci left: 9.234805e-01	ci right 9.336681e-01	k: 9287	n:10000
KS ci ratio: 1.584476e-02	ci left: 8.526363e-01	ci right 8.663535e-01	k: 8596	n:10000
C15orf44   10000 perm   2 sec   (5609 perm/sec)   p_kst 8.596000e-01   p_cons 9.287000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000020/C15orf44.2_1601_10000_0.8596_0.9287_1.png
                gene_name: C15orf44
               theta_stop: 0.016 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.87 
                   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: 75 percent done.
C16orf62
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.575280e-02	ci left: 8.540644e-01	ci right 8.677246e-01	k: 8610	n:10000
Cons ci ratio: 7.043147e-02	ci left: 2.281004e-01	ci right 2.448534e-01	k: 2364	n:10000
KS ci ratio: 2.256539e-02	ci left: 7.425032e-01	ci right 7.595503e-01	k: 7511	n:10000
C16orf62   10000 perm   2 sec   (5329 perm/sec)   p_kst 7.511000e-01   p_cons 2.364000e-01   p_joint 8.610000e-01

Outputting figure to mutsig2_images.part000000000020/C16orf62.2_3016_10000_0.7511_0.2364_0.861.png
                gene_name: C16orf62
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.87 

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.165.3896/
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/181708/iteration1/scatter.0000000020
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 20 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119543: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000021> was used as the working directory.
Started at Wed Oct 10 10:42:03 2012
Results reported at Wed Oct 10 10:45:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000021.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000021.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 21  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    182.62 sec.
    Max Memory :      1119 MB
    Max Swap   :      3940 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.165.3896/
-whichjob
21
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 21: processing genes 1810 - 1900
Calculating significance of each gene.
Using projection method.
1810	C16orf68	1
1811	C16orf7	1
1812	C16orf70	1
1813	C16orf71	1
1814	C16orf72	1
1815	C16orf73	1
1816	C16orf75	1
1817	C16orf78	1
1818	C16orf79	1
1819	C16orf80	1
1820	C16orf82	1
1821	C16orf86	1
1822	C16orf87	3.520434e-02
1823	C16orf88	1.017158e-01
1824	C16orf89	7.072195e-02
1825	C16orf90	1
1826	C16orf91	1
1827	C16orf92	1
1828	C16orf93	1
1829	C17orf100	1
1830	C17orf101	1
1831	C17orf102	1
1832	C17orf103	1
1833	C17orf104	1
1834	C17orf108	1
1835	C17orf28	3.123535e-01
1836	C17orf37	1
1837	C17orf39	1
1838	C17orf42	4.681834e-02
1839	C17orf46	1
1840	C17orf47	2.302902e-01
1841	C17orf48	1
1842	C17orf49	1
1843	C17orf50	1
1844	C17orf53	1
1845	C17orf55	1
1846	C17orf56	1
1847	C17orf57	1
1848	C17orf58	1
1849	C17orf59	3.810537e-02
1850	C17orf60	1
1851	C17orf61	1
1852	C17orf62	3.433411e-03
1853	C17orf63	1
1854	C17orf64	1
1855	C17orf65	1
1856	C17orf66	1
1857	C17orf67	1
1858	C17orf68	1
1859	C17orf70	1
1860	C17orf71	1
1861	C17orf74	1
1862	C17orf75	1
1863	C17orf76	1
1864	C17orf77	1
1865	C17orf78	1
1866	C17orf79	1
1867	C17orf80	1
1868	C17orf81	7.206187e-03
1869	C17orf82	1
1870	C17orf85	6.124307e-02
1871	C17orf87	1
1872	C17orf90	1
1873	C17orf95	1
1874	C17orf98	1
1875	C18orf1	1
1876	C18orf10	1
1877	C18orf19	1
1878	C18orf21	1
1879	C18orf22	1.560883e-01
1880	C18orf25	1
1881	C18orf26	1
1882	C18orf32	1
1883	C18orf34	1
1884	C18orf45	1
1885	C18orf54	1
1886	C18orf55	1
1887	C18orf56	1
1888	C18orf62	1
1889	C18orf8	1.068533e-01
1890	C19orf10	1
1891	C19orf12	1
1892	C19orf18	1
1893	C19orf2	1
1894	C19orf21	1
1895	C19orf22	1
1896	C19orf26	1
1897	C19orf28	6.102183e-03
1898	C19orf29	1.833499e-01
1899	C19orf33	1
1900	C19orf35	1
Done

Running MutSig 2:
Scatter job 21: processing genes 1810 - 1900
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C17orf81
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.363436e-01	ci left: 1.114735e-02	ci right 1.574255e-02	k: 133	n:10000
Cons ci ratio: 1.351440e-01	ci left: 7.233299e-02	ci right 8.291462e-02	k: 775	n:10000
KS ci ratio: 4.284655e-01	ci left: 6.526864e-03	ci right 1.016828e-02	k: 82	n:10000
C17orf81   10000 perm   3 sec   (3614 perm/sec)   p_kst 8.200000e-03   p_cons 7.750000e-02   p_joint 1.330000e-02

Joint ci ratio: 1.997038e-01	ci left: 1.701043e-02	ci right 2.083125e-02	k: 377	n:20000
Cons ci ratio: 9.467332e-02	ci left: 7.520025e-02	ci right 8.272270e-02	k: 1578	n:20000
KS ci ratio: 3.243481e-01	ci left: 6.075351e-03	ci right 8.471257e-03	k: 144	n:20000
C17orf81   20000 perm   7 sec   (2750 perm/sec)   p_kst 7.200000e-03   p_cons 7.890000e-02   p_joint 1.885000e-02

Joint ci ratio: 1.132021e-01	ci left: 3.625368e-02	ci right 4.063629e-02	k: 1152	n:30000
Cons ci ratio: 8.118995e-02	ci left: 6.916528e-02	ci right 7.505124e-02	k: 2162	n:30000
KS ci ratio: 2.558043e-01	ci left: 6.773317e-03	ci right 8.790429e-03	k: 232	n:30000
C17orf81   30000 perm   9 sec   (3208 perm/sec)   p_kst 7.733333e-03   p_cons 7.206667e-02   p_joint 3.840000e-02

Joint ci ratio: 1.089471e-01	ci left: 2.963952e-02	ci right 3.307896e-02	k: 1253	n:40000
Cons ci ratio: 6.993460e-02	ci left: 7.027251e-02	ci right 7.538972e-02	k: 2912	n:40000
KS ci ratio: 2.266127e-01	ci left: 6.583529e-03	ci right 8.289151e-03	k: 296	n:40000
C17orf81   40000 perm   11 sec   (3492 perm/sec)   p_kst 7.400000e-03   p_cons 7.280000e-02   p_joint 3.132500e-02

Joint ci ratio: 1.092547e-01	ci left: 2.372702e-02	ci right 2.648849e-02	k: 1254	n:50000
Cons ci ratio: 5.963581e-02	ci left: 7.716304e-02	ci right 8.192591e-02	k: 3976	n:50000
KS ci ratio: 2.027578e-01	ci left: 6.667492e-03	ci right 8.190535e-03	k: 370	n:50000
C17orf81   50000 perm   14 sec   (3669 perm/sec)   p_kst 7.400000e-03   p_cons 7.952000e-02   p_joint 2.508000e-02

Joint ci ratio: 1.029354e-01	ci left: 2.238388e-02	ci right 2.482917e-02	k: 1415	n:60000
Cons ci ratio: 5.434961e-02	ci left: 7.761083e-02	ci right 8.196325e-02	k: 4786	n:60000
KS ci ratio: 1.857658e-01	ci left: 6.682119e-03	ci right 8.066173e-03	k: 441	n:60000
C17orf81   60000 perm   16 sec   (3782 perm/sec)   p_kst 7.350000e-03   p_cons 7.976667e-02   p_joint 2.358333e-02

Joint ci ratio: 1.211206e-01	ci left: 1.384919e-02	ci right 1.564850e-02	k: 1031	n:70000
Cons ci ratio: 5.056356e-02	ci left: 7.706860e-02	ci right 8.108066e-02	k: 5534	n:70000
KS ci ratio: 1.731169e-01	ci left: 6.641711e-03	ci right 7.913932e-03	k: 508	n:70000
C17orf81   70000 perm   18 sec   (3829 perm/sec)   p_kst 7.257143e-03   p_cons 7.905714e-02   p_joint 1.472857e-02

Joint ci ratio: 1.147600e-01	ci left: 1.354942e-02	ci right 1.521107e-02	k: 1149	n:80000
Cons ci ratio: 4.733333e-02	ci left: 7.709042e-02	ci right 8.084018e-02	k: 6316	n:80000
KS ci ratio: 1.603764e-01	ci left: 6.817779e-03	ci right 8.018359e-03	k: 592	n:80000
C17orf81   80000 perm   21 sec   (3863 perm/sec)   p_kst 7.400000e-03   p_cons 7.895000e-02   p_joint 1.436250e-02

Joint ci ratio: 1.131702e-01	ci left: 1.241052e-02	ci right 1.390999e-02	k: 1183	n:90000
Cons ci ratio: 4.472761e-02	ci left: 7.687186e-02	ci right 8.039980e-02	k: 7076	n:90000
KS ci ratio: 1.509908e-01	ci left: 6.871830e-03	ci right 8.004710e-03	k: 668	n:90000
C17orf81   90000 perm   23 sec   (3854 perm/sec)   p_kst 7.422222e-03   p_cons 7.862222e-02   p_joint 1.314444e-02

Joint ci ratio: 1.507076e-01	ci left: 6.213353e-03	ci right 7.235573e-03	k: 671	n:100000
Cons ci ratio: 4.245971e-02	ci left: 7.686997e-02	ci right 8.021453e-02	k: 7853	n:100000
KS ci ratio: 1.410912e-01	ci left: 7.119297e-03	ci right 8.209551e-03	k: 765	n:100000
C17orf81   100000 perm   26 sec   (3863 perm/sec)   p_kst 7.650000e-03   p_cons 7.853000e-02   p_joint 6.710000e-03

Joint ci ratio: 1.162200e-01	ci left: 9.641103e-03	ci right 1.083948e-02	k: 1125	n:110000
Cons ci ratio: 4.052042e-02	ci left: 7.681811e-02	ci right 8.000416e-02	k: 8624	n:110000
KS ci ratio: 1.348157e-01	ci left: 7.112825e-03	ci right 8.149752e-03	k: 838	n:110000
C17orf81   110000 perm   29 sec   (3856 perm/sec)   p_kst 7.618182e-03   p_cons 7.840000e-02   p_joint 1.022727e-02

Joint ci ratio: 1.194710e-01	ci left: 8.360167e-03	ci right 9.430435e-03	k: 1066	n:120000
Cons ci ratio: 3.879780e-02	ci left: 7.687692e-02	ci right 7.992682e-02	k: 9407	n:120000
KS ci ratio: 1.292381e-01	ci left: 7.116393e-03	ci right 8.107625e-03	k: 912	n:120000
C17orf81   120000 perm   31 sec   (3842 perm/sec)   p_kst 7.600000e-03   p_cons 7.839167e-02   p_joint 8.883333e-03

Joint ci ratio: 1.295623e-01	ci left: 6.539078e-03	ci right 7.452352e-03	k: 908	n:130000
Cons ci ratio: 3.899609e-02	ci left: 7.071492e-02	ci right 7.353497e-02	k: 9375	n:130000
KS ci ratio: 1.237328e-01	ci left: 7.187259e-03	ci right 8.142591e-03	k: 995	n:130000
C17orf81   130000 perm   34 sec   (3820 perm/sec)   p_kst 7.653846e-03   p_cons 7.211538e-02   p_joint 6.984615e-03

Joint ci ratio: 1.430416e-01	ci left: 4.953920e-03	ci right 5.723929e-03	k: 746	n:140000
Cons ci ratio: 3.751801e-02	ci left: 7.097700e-02	ci right 7.369788e-02	k: 10126	n:140000
KS ci ratio: 1.190428e-01	ci left: 7.227973e-03	ci right 8.149736e-03	k: 1075	n:140000
C17orf81   140000 perm   37 sec   (3794 perm/sec)   p_kst 7.678571e-03   p_cons 7.232857e-02   p_joint 5.328571e-03

Joint ci ratio: 1.158116e-01	ci left: 7.140811e-03	ci right 8.025049e-03	k: 1136	n:150000
Cons ci ratio: 3.452534e-02	ci left: 7.777205e-02	ci right 8.051091e-02	k: 11870	n:150000
KS ci ratio: 1.149489e-01	ci left: 7.250897e-03	ci right 8.141624e-03	k: 1153	n:150000
C17orf81   150000 perm   40 sec   (3765 perm/sec)   p_kst 7.686667e-03   p_cons 7.913333e-02   p_joint 7.573333e-03

Joint ci ratio: 1.323853e-01	ci left: 5.089072e-03	ci right 5.816526e-03	k: 871	n:160000
Cons ci ratio: 3.340955e-02	ci left: 7.789989e-02	ci right 8.055288e-02	k: 12675	n:160000
KS ci ratio: 1.118927e-01	ci left: 7.186355e-03	ci right 8.044132e-03	k: 1217	n:160000
C17orf81   160000 perm   43 sec   (3729 perm/sec)   p_kst 7.606250e-03   p_cons 7.921875e-02   p_joint 5.443750e-03

Joint ci ratio: 1.149011e-01	ci left: 6.409116e-03	ci right 7.196080e-03	k: 1155	n:170000
Cons ci ratio: 3.237061e-02	ci left: 7.812488e-02	ci right 8.070125e-02	k: 13499	n:170000
KS ci ratio: 1.081787e-01	ci left: 7.249881e-03	ci right 8.084688e-03	k: 1302	n:170000
C17orf81   170000 perm   46 sec   (3672 perm/sec)   p_kst 7.658824e-03   p_cons 7.940588e-02   p_joint 6.794118e-03

Joint ci ratio: 1.084959e-01	ci left: 6.809191e-03	ci right 7.595695e-03	k: 1295	n:180000
Cons ci ratio: 3.144200e-02	ci left: 7.823775e-02	ci right 8.074248e-02	k: 14307	n:180000
KS ci ratio: 1.051557e-01	ci left: 7.258070e-03	ci right 8.069019e-03	k: 1378	n:180000
C17orf81   180000 perm   52 sec   (3484 perm/sec)   p_kst 7.655556e-03   p_cons 7.948333e-02   p_joint 7.194444e-03

Joint ci ratio: 1.048711e-01	ci left: 6.917001e-03	ci right 7.687620e-03	k: 1386	n:190000
Cons ci ratio: 3.051556e-02	ci left: 7.868985e-02	ci right 8.113352e-02	k: 15182	n:190000
KS ci ratio: 1.019149e-01	ci left: 7.332372e-03	ci right 8.124863e-03	k: 1467	n:190000
C17orf81   190000 perm   56 sec   (3366 perm/sec)   p_kst 7.721053e-03   p_cons 7.990526e-02   p_joint 7.294737e-03

Joint ci ratio: 1.039882e-01	ci left: 6.687975e-03	ci right 7.426421e-03	k: 1410	n:200000
Cons ci ratio: 2.970464e-02	ci left: 7.890897e-02	ci right 8.129321e-02	k: 16019	n:200000
KS ci ratio: 9.993122e-02	ci left: 7.253292e-03	ci right 8.021082e-03	k: 1526	n:200000
C17orf81   200000 perm   62 sec   (3252 perm/sec)   p_kst 7.630000e-03   p_cons 8.009500e-02   p_joint 7.050000e-03

Joint ci ratio: 1.008516e-01	ci left: 6.782471e-03	ci right 7.507424e-03	k: 1499	n:210000
Cons ci ratio: 2.901408e-02	ci left: 7.880999e-02	ci right 8.113495e-02	k: 16793	n:210000
KS ci ratio: 9.768727e-02	ci left: 7.237635e-03	ci right 7.985577e-03	k: 1597	n:210000
C17orf81   210000 perm   65 sec   (3226 perm/sec)   p_kst 7.604762e-03   p_cons 7.996667e-02   p_joint 7.138095e-03

Joint ci ratio: 9.911995e-02	ci left: 6.709049e-03	ci right 7.413124e-03	k: 1552	n:220000
Cons ci ratio: 2.832226e-02	ci left: 7.896446e-02	ci right 8.123753e-02	k: 17621	n:220000
KS ci ratio: 9.579060e-02	ci left: 7.192514e-03	ci right 7.920551e-03	k: 1661	n:220000
C17orf81   220000 perm   69 sec   (3209 perm/sec)   p_kst 7.550000e-03   p_cons 8.009545e-02   p_joint 7.054545e-03

Outputting figure to mutsig2_images.part000000000021/C17orf81.3_1088_220000_0.00755_0.080095_0.0070545.png
                gene_name: C17orf81
               theta_stop: 0.099 
                    nperm: 220000 
                     p_ks: 0.0076 
        ci_ks_bounds_left: 0.0072 
       ci_ks_bounds_right: 0.0079 
                   p_cons: 0.080 
      ci_cons_bounds_left: 0.079 
     ci_cons_bounds_right: 0.081 
                  p_joint: 0.0071 
     ci_joint_bounds_left: 0.0067 
    ci_joint_bounds_right: 0.0074 

Current progress: 33 percent done.
C17orf62
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: 3.196988e-02	ci left: 5.908220e-01	ci right 6.101194e-01	k: 6005	n:10000
KS ci ratio: 2.092792e-02	ci left: 7.699268e-01	ci right 7.863109e-01	k: 7782	n:10000
C17orf62   10000 perm   1 sec   (6807 perm/sec)   p_kst 7.782000e-01   p_cons 6.005000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000021/C17orf62.2_588_10000_0.7782_0.6005_1.png
                gene_name: C17orf62
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.79 
                   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.
C19orf28
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.700582e-02	ci left: 5.188592e-01	ci right 5.385241e-01	k: 5287	n:10000
Cons ci ratio: 1.193945e-01	ci left: 9.146191e-02	ci right 1.031739e-01	k: 972	n:10000
KS ci ratio: 1.073223e-01	ci left: 1.113483e-01	ci right 1.240753e-01	k: 1176	n:10000
C19orf28   10000 perm   2 sec   (5341 perm/sec)   p_kst 1.176000e-01   p_cons 9.720000e-02   p_joint 5.287000e-01

Joint ci ratio: 3.929574e-02	ci left: 3.256721e-01	ci right 3.387767e-01	k: 6644	n:20000
Cons ci ratio: 8.226580e-02	ci left: 9.774049e-02	ci right 1.061756e-01	k: 2038	n:20000
KS ci ratio: 7.437585e-02	ci left: 1.173959e-01	ci right 1.265143e-01	k: 2438	n:20000
C19orf28   20000 perm   4 sec   (5156 perm/sec)   p_kst 1.219000e-01   p_cons 1.019000e-01   p_joint 3.322000e-01

Outputting figure to mutsig2_images.part000000000021/C19orf28.2_1690_20000_0.1219_0.1019_0.3322.png
                gene_name: C19orf28
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.10 
      ci_cons_bounds_left: 0.098 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.33 
    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.165.3896/
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/181708/iteration1/scatter.0000000021
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 21 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119546: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000022> was used as the working directory.
Started at Wed Oct 10 10:42:03 2012
Results reported at Wed Oct 10 10:44:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000022.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000022.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 22  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    126.08 sec.
    Max Memory :       992 MB
    Max Swap   :      3755 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.165.3896/
-whichjob
22
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 22: processing genes 1901 - 1990
Calculating significance of each gene.
Using projection method.
1901	C19orf36	1
1902	C19orf39	1
1903	C19orf40	1
1904	C19orf41	1
1905	C19orf42	1
1906	C19orf43	1
1907	C19orf44	3.536021e-02
1908	C19orf45	1
1909	C19orf46	1
1910	C19orf47	9.871097e-02
1911	C19orf48	1
1912	C19orf50	1
1913	C19orf51	1
1914	C19orf52	1
1915	C19orf53	1
1916	C19orf54	1
1917	C19orf55	1
1918	C19orf56	1
1919	C19orf57	1
1920	C19orf59	1
1921	C19orf6	1
1922	C19orf60	1
1923	C19orf61	1.070798e-01
1924	C19orf62	1
1925	C19orf63	1
1926	C19orf66	1
1927	C19orf70	1
1928	C19orf73	1
1929	C19orf75	1
1930	C1D	1.223841e-02
1931	C1GALT1	1
1932	C1GALT1C1	1
1933	C1QA	1
1934	C1QB	1
1935	C1QBP	1
1936	C1QC	1
1937	C1QL1	1
1938	C1QL2	1
1939	C1QL3	1
1940	C1QL4	1
1941	C1QTNF1	1
1942	C1QTNF2	1
1943	C1QTNF3	1
1944	C1QTNF4	1
1945	C1QTNF5	1
1946	C1QTNF6	1
1947	C1QTNF7	1
1948	C1QTNF8	1
1949	C1QTNF9	1
1950	C1QTNF9B	1
1951	C1R	1
1952	C1RL	1.771577e-01
1953	C1S	1
1954	C1orf100	1
1955	C1orf101	1
1956	C1orf103	8.007101e-02
1957	C1orf104	1
1958	C1orf105	1
1959	C1orf106	1
1960	C1orf107	6.805781e-02
1961	C1orf109	1
1962	C1orf110	1
1963	C1orf111	1
1964	C1orf112	1
1965	C1orf113	1
1966	C1orf114	1
1967	C1orf115	1
1968	C1orf116	1
1969	C1orf122	1
1970	C1orf123	1
1971	C1orf124	1
1972	C1orf125	1
1973	C1orf127	1
1974	C1orf128	1
1975	C1orf129	1
1976	C1orf130	1
1977	C1orf131	1
1978	C1orf135	1
1979	C1orf14	1
1980	C1orf141	1
1981	C1orf144	9.097992e-03
1982	C1orf146	5.270451e-02
1983	C1orf150	1
1984	C1orf151	1
1985	C1orf156	1
1986	C1orf158	2.250950e-03
1987	C1orf159	1
1988	C1orf161	1
1989	C1orf162	1
1990	C1orf163	5.143132e-02
Done

Running MutSig 2:
Scatter job 22: processing genes 1901 - 1990
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C19orf44
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.580070e-02	ci left: 2.029395e-01	ci right 2.190293e-01	k: 2109	n:10000
Cons ci ratio: 7.987348e-02	ci left: 1.862897e-01	ci right 2.018889e-01	k: 1940	n:10000
KS ci ratio: 6.303106e-02	ci left: 2.700268e-01	ci right 2.877022e-01	k: 2788	n:10000
C19orf44   10000 perm   3 sec   (3380 perm/sec)   p_kst 2.788000e-01   p_cons 1.940000e-01   p_joint 2.109000e-01

Outputting figure to mutsig2_images.part000000000022/C19orf44.2_2002_10000_0.2788_0.194_0.2109.png
                gene_name: C19orf44
               theta_stop: 0.080 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.22 

Current progress: 33 percent done.
C1orf107
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.442662e-02	ci left: 5.547144e-01	ci right 5.742480e-01	k: 5645	n:10000
Cons ci ratio: 3.310124e-02	ci left: 5.739652e-01	ci right 5.933860e-01	k: 5837	n:10000
KS ci ratio: 4.010601e-02	ci left: 4.786573e-01	ci right 4.983494e-01	k: 4885	n:10000
C1orf107   10000 perm   2 sec   (6068 perm/sec)   p_kst 4.885000e-01   p_cons 5.837000e-01   p_joint 5.645000e-01

Outputting figure to mutsig2_images.part000000000022/C1orf107.2_2319_10000_0.4885_0.5837_0.5645.png
                gene_name: C1orf107
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.56 
     ci_joint_bounds_left: 0.55 
    ci_joint_bounds_right: 0.57 

Current progress: 67 percent done.
C1orf158
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.033598e-02	ci left: 1.845176e-01	ci right 2.000620e-01	k: 1922	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: 1.026335e-01	ci left: 1.207287e-01	ci right 1.338892e-01	k: 1272	n:10000
C1orf158   10000 perm   3 sec   (3570 perm/sec)   p_kst 1.272000e-01   p_cons 1.890000e-01   p_joint 1.922000e-01

Joint ci ratio: 2.915032e-02	ci left: 4.678584e-01	ci right 4.817490e-01	k: 9496	n:20000
Cons ci ratio: 5.755843e-02	ci left: 1.828035e-01	ci right 1.936873e-01	k: 3764	n:20000
KS ci ratio: 7.273787e-02	ci left: 1.221687e-01	ci right 1.314401e-01	k: 2535	n:20000
C1orf158   20000 perm   6 sec   (3292 perm/sec)   p_kst 1.267500e-01   p_cons 1.882000e-01   p_joint 4.748000e-01

Outputting figure to mutsig2_images.part000000000022/C1orf158.2_601_20000_0.12675_0.1882_0.4748.png
                gene_name: C1orf158
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.19 
                  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.165.3896/
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/181708/iteration1/scatter.0000000022
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 22 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119549: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000023> was used as the working directory.
Started at Wed Oct 10 10:42:03 2012
Results reported at Wed Oct 10 10:44:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000023.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000023.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 23  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    167.32 sec.
    Max Memory :      1098 MB
    Max Swap   :      3884 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.165.3896/
-whichjob
23
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 23: processing genes 1991 - 2081
Calculating significance of each gene.
Using projection method.
1991	C1orf168	2.455227e-01
1992	C1orf172	1
1993	C1orf173	1
1994	C1orf174	1
1995	C1orf175	1
1996	C1orf177	1
1997	C1orf182	1
1998	C1orf183	1
1999	C1orf186	1
2000/18094 2000	C1orf187	1
2001	C1orf189	1
2002	C1orf190	1
2003	C1orf192	1
2004	C1orf194	1
2005	C1orf198	8.867504e-02
2006	C1orf201	1
2007	C1orf21	1
2008	C1orf210	1
2009	C1orf213	1
2010	C1orf216	1
2011	C1orf226	1
2012	C1orf227	1
2013	C1orf25	2.332259e-01
2014	C1orf26	3.023718e-01
2015	C1orf27	1
2016	C1orf31	1
2017	C1orf35	1
2018	C1orf38	1.967996e-01
2019	C1orf43	1
2020	C1orf49	1
2021	C1orf50	1
2022	C1orf51	1.565405e-02
2023	C1orf52	1
2024	C1orf53	1
2025	C1orf54	1
2026	C1orf55	2.278646e-01
2027	C1orf56	1
2028	C1orf57	1
2029	C1orf58	1
2030	C1orf59	1
2031	C1orf61	1
2032	C1orf63	1
2033	C1orf64	1
2034	C1orf65	1
2035	C1orf66	1
2036	C1orf69	1
2037	C1orf74	1
2038	C1orf77	1
2039	C1orf83	1
2040	C1orf84	1
2041	C1orf85	1
2042	C1orf86	2.681613e-02
2043	C1orf87	1
2044	C1orf88	1
2045	C1orf89	1
2046	C1orf9	2.229803e-01
2047	C1orf91	1
2048	C1orf92	1
2049	C1orf93	1
2050	C1orf94	1
2051	C1orf95	1
2052	C1orf96	1
2053	C2	3.620698e-01
2054	C20orf103	1
2055	C20orf106	1
2056	C20orf107	1
2057	C20orf108	1
2058	C20orf11	1
2059	C20orf111	1
2060	C20orf112	1
2061	C20orf114	1
2062	C20orf117	8.973248e-02
2063	C20orf118	1
2064	C20orf12	1
2065	C20orf132	1
2066	C20orf134	1
2067	C20orf135	1
2068	C20orf141	1
2069	C20orf151	1
2070	C20orf152	1
2071	C20orf160	1
2072	C20orf165	1
2073	C20orf166	1
2074	C20orf177	1.908412e-01
2075	C20orf185	1
2076	C20orf186	1
2077	C20orf194	1
2078	C20orf195	1
2079	C20orf196	1
2080	C20orf197	1
2081	C20orf20	1.494967e-03
Done

Running MutSig 2:
Scatter job 23: processing genes 1991 - 2081
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C1orf168
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.512569e-01	ci left: 1.014137e-02	ci right 1.454954e-02	k: 122	n:10000
Cons ci ratio: 1.079470e-01	ci left: 1.101767e-01	ci right 1.228477e-01	k: 1164	n:10000
KS ci ratio: 3.389164e-01	ci left: 1.096414e-02	ci right 1.552595e-02	k: 131	n:10000
C1orf168   10000 perm   3 sec   (3926 perm/sec)   p_kst 1.310000e-02   p_cons 1.164000e-01   p_joint 1.220000e-02

Joint ci ratio: 2.640385e-01	ci left: 9.460703e-03	ci right 1.238410e-02	k: 217	n:20000
Cons ci ratio: 7.073902e-02	ci left: 1.283717e-01	ci right 1.378353e-01	k: 2661	n:20000
KS ci ratio: 2.443899e-01	ci left: 1.114729e-02	ci right 1.429674e-02	k: 253	n:20000
C1orf168   20000 perm   8 sec   (2418 perm/sec)   p_kst 1.265000e-02   p_cons 1.330500e-01   p_joint 1.085000e-02

Joint ci ratio: 2.621136e-01	ci left: 6.430299e-03	ci right 8.400236e-03	k: 221	n:30000
Cons ci ratio: 6.213373e-02	ci left: 1.134820e-01	ci right 1.207923e-01	k: 3513	n:30000
KS ci ratio: 2.003455e-01	ci left: 1.133685e-02	ci right 1.389217e-02	k: 377	n:30000
C1orf168   30000 perm   12 sec   (2448 perm/sec)   p_kst 1.256667e-02   p_cons 1.171000e-01   p_joint 7.366667e-03

Joint ci ratio: 1.650836e-01	ci left: 1.275159e-02	ci right 1.506977e-02	k: 555	n:40000
Cons ci ratio: 5.363681e-02	ci left: 1.146314e-01	ci right 1.209742e-01	k: 4711	n:40000
KS ci ratio: 1.749164e-01	ci left: 1.131462e-02	ci right 1.350702e-02	k: 495	n:40000
C1orf168   40000 perm   15 sec   (2637 perm/sec)   p_kst 1.237500e-02   p_cons 1.177750e-01   p_joint 1.387500e-02

Joint ci ratio: 1.632506e-01	ci left: 1.046874e-02	ci right 1.234863e-02	k: 569	n:50000
Cons ci ratio: 4.814589e-02	ci left: 1.142345e-01	ci right 1.198900e-01	k: 5852	n:50000
KS ci ratio: 1.527509e-01	ci left: 1.200623e-02	ci right 1.401090e-02	k: 649	n:50000
C1orf168   50000 perm   18 sec   (2831 perm/sec)   p_kst 1.298000e-02   p_cons 1.170400e-01   p_joint 1.138000e-02

Joint ci ratio: 1.505937e-01	ci left: 1.032519e-02	ci right 1.202259e-02	k: 669	n:60000
Cons ci ratio: 4.407408e-02	ci left: 1.139102e-01	ci right 1.190603e-01	k: 6988	n:60000
KS ci ratio: 1.397145e-01	ci left: 1.204455e-02	ci right 1.386968e-02	k: 776	n:60000
C1orf168   60000 perm   20 sec   (3004 perm/sec)   p_kst 1.293333e-02   p_cons 1.164667e-01   p_joint 1.115000e-02

Joint ci ratio: 1.393027e-01	ci left: 1.040600e-02	ci right 1.197777e-02	k: 782	n:70000
Cons ci ratio: 4.070260e-02	ci left: 1.146135e-01	ci right 1.193897e-01	k: 8189	n:70000
KS ci ratio: 1.305598e-01	ci left: 1.188359e-02	ci right 1.355717e-02	k: 889	n:70000
C1orf168   70000 perm   22 sec   (3126 perm/sec)   p_kst 1.270000e-02   p_cons 1.169857e-01   p_joint 1.117143e-02

Joint ci ratio: 1.293486e-01	ci left: 1.061537e-02	ci right 1.209539e-02	k: 907	n:80000
Cons ci ratio: 3.802324e-02	ci left: 1.150407e-01	ci right 1.195121e-01	k: 9381	n:80000
KS ci ratio: 1.223192e-01	ci left: 1.189915e-02	ci right 1.346149e-02	k: 1013	n:80000
C1orf168   80000 perm   26 sec   (3101 perm/sec)   p_kst 1.266250e-02   p_cons 1.172625e-01   p_joint 1.133750e-02

Joint ci ratio: 1.209668e-01	ci left: 1.083521e-02	ci right 1.224098e-02	k: 1037	n:90000
Cons ci ratio: 3.583088e-02	ci left: 1.152707e-01	ci right 1.194873e-01	k: 10563	n:90000
KS ci ratio: 1.153109e-01	ci left: 1.194623e-02	ci right 1.341876e-02	k: 1140	n:90000
C1orf168   90000 perm   29 sec   (3132 perm/sec)   p_kst 1.266667e-02   p_cons 1.173667e-01   p_joint 1.152222e-02

Joint ci ratio: 1.158480e-01	ci left: 1.066380e-02	ci right 1.198477e-02	k: 1131	n:100000
Cons ci ratio: 3.181952e-02	ci left: 1.296694e-01	ci right 1.338720e-01	k: 13176	n:100000
KS ci ratio: 1.092095e-01	ci left: 1.202487e-02	ci right 1.342361e-02	k: 1271	n:100000
C1orf168   100000 perm   31 sec   (3189 perm/sec)   p_kst 1.271000e-02   p_cons 1.317600e-01   p_joint 1.131000e-02

Joint ci ratio: 1.893327e-01	ci left: 3.514271e-03	ci right 4.257717e-03	k: 426	n:110000
Cons ci ratio: 3.039394e-02	ci left: 1.293545e-01	ci right 1.333558e-01	k: 14448	n:110000
KS ci ratio: 1.046665e-01	ci left: 1.193147e-02	ci right 1.325805e-02	k: 1384	n:110000
C1orf168   110000 perm   34 sec   (3224 perm/sec)   p_kst 1.258182e-02   p_cons 1.313455e-01   p_joint 3.872727e-03

Joint ci ratio: 1.059280e-01	ci left: 1.068528e-02	ci right 1.188851e-02	k: 1353	n:120000
Cons ci ratio: 2.912824e-02	ci left: 1.292200e-01	ci right 1.330478e-01	k: 15735	n:120000
KS ci ratio: 1.000067e-01	ci left: 1.200905e-02	ci right 1.328133e-02	k: 1516	n:120000
C1orf168   120000 perm   37 sec   (3249 perm/sec)   p_kst 1.263333e-02   p_cons 1.311250e-01   p_joint 1.127500e-02

Joint ci ratio: 1.012789e-01	ci left: 1.081499e-02	ci right 1.197619e-02	k: 1480	n:130000
Cons ci ratio: 2.797544e-02	ci left: 1.293768e-01	ci right 1.330551e-01	k: 17057	n:130000
KS ci ratio: 9.562518e-02	ci left: 1.215091e-02	ci right 1.337865e-02	k: 1658	n:130000
C1orf168   130000 perm   40 sec   (3269 perm/sec)   p_kst 1.275385e-02   p_cons 1.312077e-01   p_joint 1.138462e-02

Joint ci ratio: 6.314998e-02	ci left: 2.593918e-02	ci right 2.763764e-02	k: 3749	n:140000
Cons ci ratio: 2.694528e-02	ci left: 1.295492e-01	ci right 1.330947e-01	k: 18384	n:140000
KS ci ratio: 9.172168e-02	ci left: 1.228751e-02	ci right 1.347565e-02	k: 1802	n:140000
C1orf168   140000 perm   43 sec   (3279 perm/sec)   p_kst 1.287143e-02   p_cons 1.313143e-01   p_joint 2.677857e-02

Outputting figure to mutsig2_images.part000000000023/C1orf168.2_2267_140000_0.012871_0.13131_0.026779.png
                gene_name: C1orf168
               theta_stop: 0.092 
                    nperm: 140000 
                     p_ks: 0.013 
        ci_ks_bounds_left: 0.012 
       ci_ks_bounds_right: 0.013 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.027 
     ci_joint_bounds_left: 0.026 
    ci_joint_bounds_right: 0.028 

Current progress: 33 percent done.
C1orf51
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.961818e-02	ci left: 3.746515e-01	ci right 3.938160e-01	k: 3842	n:10000
Cons ci ratio: 8.098835e-02	ci left: 1.820569e-01	ci right 1.975242e-01	k: 1897	n:10000
KS ci ratio: 2.187136e-02	ci left: 7.541348e-01	ci right 7.709120e-01	k: 7626	n:10000
C1orf51   10000 perm   2 sec   (4588 perm/sec)   p_kst 7.626000e-01   p_cons 1.897000e-01   p_joint 3.842000e-01

Outputting figure to mutsig2_images.part000000000023/C1orf51.2_1178_10000_0.7626_0.1897_0.3842.png
                gene_name: C1orf51
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.76 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.77 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 67 percent done.
C20orf20
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.337364e-02	ci left: 4.397162e-01	ci right 4.593132e-01	k: 4495	n:10000
Cons ci ratio: 1.725017e-01	ci left: 4.485094e-02	ci right 5.341415e-02	k: 490	n:10000
KS ci ratio: 8.773547e-02	ci left: 1.590500e-01	ci right 1.737448e-01	k: 1663	n:10000
C20orf20   10000 perm   2 sec   (4628 perm/sec)   p_kst 1.663000e-01   p_cons 4.900000e-02   p_joint 4.495000e-01

Joint ci ratio: 3.768713e-02	ci left: 3.443824e-01	ci right 3.576610e-01	k: 7020	n:20000
Cons ci ratio: 1.202513e-01	ci left: 4.740861e-02	ci right 5.352292e-02	k: 1008	n:20000
KS ci ratio: 6.091195e-02	ci left: 1.662989e-01	ci right 1.767967e-01	k: 3430	n:20000
C20orf20   20000 perm   4 sec   (4788 perm/sec)   p_kst 1.715000e-01   p_cons 5.040000e-02   p_joint 3.510000e-01

Joint ci ratio: 6.062895e-02	ci left: 1.185797e-01	ci right 1.260269e-01	k: 3668	n:30000
Cons ci ratio: 9.793022e-02	ci left: 4.821186e-02	ci right 5.320894e-02	k: 1520	n:30000
KS ci ratio: 5.017955e-02	ci left: 1.647749e-01	ci right 1.732893e-01	k: 5070	n:30000
C20orf20   30000 perm   6 sec   (4827 perm/sec)   p_kst 1.690000e-01   p_cons 5.066667e-02   p_joint 1.222667e-01

Outputting figure to mutsig2_images.part000000000023/C20orf20.2_635_30000_0.169_0.050667_0.12227.png
                gene_name: C20orf20
               theta_stop: 0.098 
                    nperm: 30000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.051 
      ci_cons_bounds_left: 0.048 
     ci_cons_bounds_right: 0.053 
                  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.165.3896/
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/181708/iteration1/scatter.0000000023
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 23 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1534>
Subject: Job 1119600: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1534>, 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/181708/iteration1/scatter.0000000024> was used as the working directory.
Started at Wed Oct 10 10:42:03 2012
Results reported at Wed Oct 10 10:43:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000024.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000024.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 24  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    111.61 sec.
    Max Memory :       627 MB
    Max Swap   :      3430 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.165.3896/
-whichjob
24
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 24: processing genes 2082 - 2171
Calculating significance of each gene.
Using projection method.
2082	C20orf24	1
2083	C20orf26	1
2084	C20orf27	1
2085	C20orf29	1
2086	C20orf3	1
2087	C20orf30	1
2088	C20orf4	1
2089	C20orf43	1
2090	C20orf46	1
2091	C20orf54	1
2092	C20orf7	1
2093	C20orf70	1
2094	C20orf71	1.341375e-01
2095	C20orf72	1
2096	C20orf79	1
2097	C20orf85	1
2098	C20orf94	1
2099	C20orf96	1
2100	C21orf2	1
2101	C21orf29	1
2102	C21orf33	1
2103	C21orf45	1
2104	C21orf56	1
2105	C21orf57	1
2106	C21orf58	1
2107	C21orf59	1
2108	C21orf63	1
2109	C21orf7	1
2110	C21orf70	1
2111	C21orf91	1
2112	C22orf13	1
2113	C22orf15	1
2114	C22orf23	1
2115	C22orf24	2.692894e-03
2116	C22orf25	1
2117	C22orf28	2.128632e-01
2118	C22orf29	1
2119	C22orf31	1
2120	C22orf32	1
2121	C22orf33	1
2122	C22orf36	1
2123	C22orf39	1
2124	C22orf40	1
2125	C22orf42	1
2126	C22orf43	1
2127	C22orf9	1.724846e-01
2128	C2CD2	1
2129	C2CD2L	1
2130	C2CD3	1
2131	C2orf15	1
2132	C2orf16	6.876211e-01
2133	C2orf18	1
2134	C2orf24	1
2135	C2orf28	1
2136	C2orf29	1
2137	C2orf3	1
2138	C2orf34	1
2139	C2orf39	1
2140	C2orf40	3.443298e-02
2141	C2orf42	6.303780e-02
2142	C2orf43	1
2143	C2orf44	1.765129e-01
2144	C2orf47	1
2145	C2orf48	1
2146	C2orf49	1
2147	C2orf50	1
2148	C2orf51	1
2149	C2orf53	1
2150	C2orf54	1
2151	C2orf55	1
2152	C2orf56	1
2153	C2orf57	1
2154	C2orf60	1
2155	C2orf61	1
2156	C2orf62	1
2157	C2orf63	1.965154e-01
2158	C2orf64	1
2159	C2orf65	1
2160	C2orf66	1
2161	C2orf67	1
2162	C2orf68	1
2163	C2orf69	1.205132e-01
2164	C2orf7	1
2165	C2orf70	1
2166	C2orf71	1
2167	C2orf73	1
2168	C2orf76	1
2169	C2orf77	1.924549e-01
2170	C2orf78	1
2171	C2orf79	1
Done

Running MutSig 2:
Scatter job 24: processing genes 2082 - 2171
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.165.3896/
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/181708/iteration1/scatter.0000000024
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 24 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1699>
Subject: Job 1119609: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, 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/181708/iteration1/scatter.0000000025> was used as the working directory.
Started at Wed Oct 10 10:42:03 2012
Results reported at Wed Oct 10 10:43:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000025.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000025.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 25  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    111.54 sec.
    Max Memory :      1110 MB
    Max Swap   :      3820 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.165.3896/
-whichjob
25
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 25: processing genes 2172 - 2262
Calculating significance of each gene.
Using projection method.
2172	C2orf80	1
2173	C2orf83	1
2174	C2orf84	1
2175	C2orf85	1
2176	C2orf86	1
2177	C2orf88	1
2178	C2orf89	1
2179	C3	1
2180	C3AR1	1
2181	C3orf1	1.047634e-01
2182	C3orf10	1
2183	C3orf14	1
2184	C3orf15	1
2185	C3orf17	1
2186	C3orf18	1
2187	C3orf19	1
2188	C3orf20	1
2189	C3orf21	9.045657e-02
2190	C3orf22	1
2191	C3orf23	1
2192	C3orf24	1
2193	C3orf26	8.784130e-03
2194	C3orf27	1
2195	C3orf30	9.789306e-02
2196	C3orf31	1
2197	C3orf32	1
2198	C3orf33	1
2199	C3orf34	1
2200	C3orf35	7.248934e-02
2201	C3orf36	1
2202	C3orf37	9.886397e-02
2203	C3orf38	1.485591e-01
2204	C3orf39	1
2205	C3orf43	1
2206	C3orf45	1
2207	C3orf52	5.502418e-02
2208	C3orf54	1
2209	C3orf55	1
2210	C3orf57	1
2211	C3orf58	1.435468e-01
2212	C3orf59	1
2213	C3orf62	1
2214	C3orf63	1
2215	C3orf64	1
2216	C3orf67	1
2217	C3orf70	1.369641e-01
2218	C3orf71	7.368795e-02
2219	C3orf72	1
2220	C3orf75	1
2221	C3orf79	1
2222	C4BPA	6.617530e-02
2223	C4BPB	1
2224	C4orf14	2.325110e-01
2225	C4orf17	1.335770e-01
2226	C4orf19	1
2227	C4orf21	4.777016e-01
2228	C4orf22	1
2229	C4orf23	1
2230	C4orf26	1
2231	C4orf27	1
2232	C4orf29	1
2233	C4orf3	1
2234	C4orf31	1.728114e-01
2235	C4orf32	1
2236	C4orf33	1
2237	C4orf34	1
2238	C4orf35	7.295757e-02
2239	C4orf36	1
2240	C4orf37	1
2241	C4orf39	1
2242	C4orf40	1
2243	C4orf41	4.102286e-01
2244	C4orf43	1
2245	C4orf44	1
2246	C4orf45	1
2247	C4orf46	1
2248	C4orf49	1
2249	C4orf50	1
2250	C4orf51	1
2251	C4orf6	1
2252	C4orf7	1
2253	C5	3.592537e-01
2254	C5AR1	1
2255	C5orf13	1
2256	C5orf15	1
2257	C5orf20	1
2258	C5orf22	1
2259	C5orf23	1
2260	C5orf24	1
2261	C5orf25	1.546424e-01
2262	C5orf28	1
Done

Running MutSig 2:
Scatter job 25: processing genes 2172 - 2262
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C3orf26
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.357525e-03	ci left: 9.524213e-01	ci right 9.605100e-01	k: 9566	n:10000
Cons ci ratio: 2.862992e-02	ci left: 6.426714e-01	ci right 6.614400e-01	k: 6521	n:10000
KS ci ratio: 1.839835e-02	ci left: 8.118192e-01	ci right 8.269942e-01	k: 8195	n:10000
C3orf26   10000 perm   2 sec   (5502 perm/sec)   p_kst 8.195000e-01   p_cons 6.521000e-01   p_joint 9.566000e-01

Outputting figure to mutsig2_images.part000000000025/C3orf26.2_894_10000_0.8195_0.6521_0.9566.png
                gene_name: C3orf26
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.96 

Current progress: 50 percent done.
C3orf37
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.277544e-02	ci left: 5.787803e-01	ci right 5.981681e-01	k: 5885	n:10000
Cons ci ratio: 3.523883e-02	ci left: 5.431911e-01	ci right 5.627780e-01	k: 5530	n:10000
KS ci ratio: 6.973651e-02	ci left: 2.316560e-01	ci right 2.484957e-01	k: 2400	n:10000
C3orf37   10000 perm   2 sec   (6035 perm/sec)   p_kst 2.400000e-01   p_cons 5.530000e-01   p_joint 5.885000e-01

Outputting figure to mutsig2_images.part000000000025/C3orf37.2_1089_10000_0.24_0.553_0.5885.png
                gene_name: C3orf37
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.55 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.56 
                  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.165.3896/
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/181708/iteration1/scatter.0000000025
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 25 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119619: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000026> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:44:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000026.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000026.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 26  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    119.86 sec.
    Max Memory :      1273 MB
    Max Swap   :      3887 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.165.3896/
-whichjob
26
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 26: processing genes 2263 - 2352
Calculating significance of each gene.
Using projection method.
2263	C5orf30	1
2264	C5orf32	1
2265	C5orf33	1
2266	C5orf34	1
2267	C5orf35	1
2268	C5orf36	1
2269	C5orf38	1
2270	C5orf39	1
2271	C5orf4	1
2272	C5orf40	1.210640e-01
2273	C5orf41	1
2274	C5orf42	8.553572e-02
2275	C5orf43	1
2276	C5orf44	1
2277	C5orf45	1
2278	C5orf46	1
2279	C5orf48	1
2280	C5orf49	1
2281	C5orf51	1
2282	C5orf53	7.349255e-03
2283	C5orf54	2.592174e-01
2284	C5orf55	1
2285	C5orf56	1
2286	C5orf58	3.266665e-02
2287	C5orf62	1
2288	C6	1
2289	C6orf1	1
2290	C6orf10	1
2291	C6orf105	1
2292	C6orf106	1
2293	C6orf108	1
2294	C6orf114	1
2295	C6orf115	1
2296	C6orf118	1
2297	C6orf120	1
2298	C6orf125	1
2299	C6orf126	1
2300	C6orf127	1
2301	C6orf129	1
2302	C6orf130	1
2303	C6orf134	1
2304	C6orf136	1
2305	C6orf138	1
2306	C6orf142	1
2307	C6orf145	1
2308	C6orf146	1
2309	C6orf15	1
2310	C6orf150	1
2311	C6orf153	1
2312	C6orf154	1
2313	C6orf162	1
2314	C6orf165	1.963519e-01
2315	C6orf167	1
2316	C6orf168	1
2317	C6orf170	1
2318	C6orf174	6.282953e-02
2319	C6orf182	1
2320	C6orf186	1
2321	C6orf191	1
2322	C6orf192	1
2323	C6orf195	1
2324	C6orf201	1
2325	C6orf203	5.944742e-02
2326	C6orf204	2.941267e-01
2327	C6orf211	1
2328	C6orf221	1
2329	C6orf222	4.643369e-02
2330	C6orf223	2.011279e-03
2331	C6orf225	1
2332	C6orf226	1
2333	C6orf25	1
2334	C6orf26	1
2335	C6orf27	8.330196e-02
2336	C6orf35	1
2337	C6orf47	1
2338	C6orf48	1
2339	C6orf57	1
2340	C6orf58	1
2341	C6orf62	1
2342	C6orf64	1
2343	C6orf70	1
2344	C6orf72	6.798948e-02
2345	C6orf81	1
2346	C6orf89	1
2347	C6orf97	1.529024e-01
2348	C7	1
2349	C7orf10	1
2350	C7orf11	1
2351	C7orf16	1
2352	C7orf23	1
Done

Running MutSig 2:
Scatter job 26: processing genes 2263 - 2352
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C5orf42
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.243893e-02	ci left: 1.767434e-01	ci right 1.920409e-01	k: 1843	n:10000
Cons ci ratio: 5.371559e-02	ci left: 3.380633e-01	ci right 3.568256e-01	k: 3474	n:10000
KS ci ratio: 8.122612e-02	ci left: 1.811711e-01	ci right 1.966105e-01	k: 1888	n:10000
C5orf42   10000 perm   4 sec   (2690 perm/sec)   p_kst 1.888000e-01   p_cons 3.474000e-01   p_joint 1.843000e-01

Outputting figure to mutsig2_images.part000000000026/C5orf42.2_9798_10000_0.1888_0.3474_0.1843.png
                gene_name: C5orf42
               theta_stop: 0.082 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.19 

Current progress: 25 percent done.
C6orf174
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: 2.471135e-02	ci left: 7.066461e-01	ci right 7.244281e-01	k: 7156	n:10000
KS ci ratio: 4.854499e-02	ci left: 3.850022e-01	ci right 4.042592e-01	k: 3946	n:10000
C6orf174   10000 perm   2 sec   (5769 perm/sec)   p_kst 3.946000e-01   p_cons 7.156000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000026/C6orf174.2_2868_10000_0.3946_0.7156_1.png
                gene_name: C6orf174
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.72 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
C6orf222
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: 4.623708e-02	ci left: 4.084076e-01	ci right 4.278402e-01	k: 4181	n:10000
KS ci ratio: 1.684847e-02	ci left: 8.368400e-01	ci right 8.511590e-01	k: 8441	n:10000
C6orf222   10000 perm   2 sec   (6215 perm/sec)   p_kst 8.441000e-01   p_cons 4.181000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000026/C6orf222.2_2003_10000_0.8441_0.4181_1.png
                gene_name: C6orf222
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.85 
                   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: 75 percent done.
C6orf223
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: 3.797060e-03	ci left: 9.887288e-01	ci right 9.925772e-01	k: 9908	n:10000
KS ci ratio: 2.704991e-02	ci left: 6.681371e-01	ci right 6.865595e-01	k: 6774	n:10000
C6orf223   10000 perm   2 sec   (6489 perm/sec)   p_kst 6.774000e-01   p_cons 9.908000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000026/C6orf223.2_788_10000_0.6774_0.9908_1.png
                gene_name: C6orf223
               theta_stop: 0.027 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.99 
      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: 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.165.3896/
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/181708/iteration1/scatter.0000000026
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 26 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1645>
Subject: Job 1119625: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1645>, 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/181708/iteration1/scatter.0000000027> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:43:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000027.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000027.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 27  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     99.47 sec.
    Max Memory :       800 MB
    Max Swap   :      3631 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.165.3896/
-whichjob
27
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 27: processing genes 2353 - 2443
Calculating significance of each gene.
Using projection method.
2353	C7orf25	1
2354	C7orf26	1
2355	C7orf27	8.693657e-02
2356	C7orf28A	1
2357	C7orf28B	1
2358	C7orf29	1
2359	C7orf30	1
2360	C7orf31	1
2361	C7orf33	1
2362	C7orf34	1
2363	C7orf36	9.995166e-04
2364	C7orf41	1
2365	C7orf42	1
2366	C7orf43	1
2367	C7orf44	1
2368	C7orf45	1
2369	C7orf46	1.219102e-01
2370	C7orf47	1
2371	C7orf49	1
2372	C7orf50	1
2373	C7orf51	1
2374	C7orf52	2.740440e-02
2375	C7orf53	1
2376	C7orf55	1
2377	C7orf57	1
2378	C7orf58	1
2379	C7orf59	1
2380	C7orf60	1.823256e-01
2381	C7orf61	1
2382	C7orf63	1
2383	C7orf64	1
2384	C7orf65	1
2385	C7orf66	1
2386	C7orf68	1
2387	C7orf69	1
2388	C7orf70	1
2389	C8A	1
2390	C8B	1
2391	C8G	1
2392	C8orf22	1
2393	C8orf31	1
2394	C8orf33	6.727285e-02
2395	C8orf34	1
2396	C8orf37	1
2397	C8orf38	1
2398	C8orf4	1
2399	C8orf40	1
2400	C8orf41	1
2401	C8orf42	2.975082e-02
2402	C8orf44	1
2403	C8orf45	1
2404	C8orf46	1
2405	C8orf47	1
2406	C8orf58	1
2407	C8orf59	1
2408	C8orf73	1
2409	C8orf74	1
2410	C8orf76	7.977687e-02
2411	C8orf79	1
2412	C8orf80	1
2413	C8orf84	1
2414	C8orf85	1
2415	C8orf86	1
2416	C9	1
2417	C9orf100	1
2418	C9orf102	1
2419	C9orf103	1
2420	C9orf106	1
2421	C9orf11	1
2422	C9orf114	1
2423	C9orf116	1
2424	C9orf117	1
2425	C9orf119	1
2426	C9orf123	1
2427	C9orf125	1
2428	C9orf128	1
2429	C9orf129	1
2430	C9orf131	1
2431	C9orf135	1
2432	C9orf139	1
2433	C9orf140	1
2434	C9orf142	1
2435	C9orf150	3.270803e-02
2436	C9orf152	1
2437	C9orf153	1
2438	C9orf156	1
2439	C9orf16	1
2440	C9orf163	1
2441	C9orf167	1
2442	C9orf170	1
2443	C9orf171	1
Done

Running MutSig 2:
Scatter job 27: processing genes 2353 - 2443
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
C7orf36
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.811802e-02	ci left: 8.163920e-01	ci right 8.314188e-01	k: 8240	n:10000
Cons ci ratio: 2.578935e-02	ci left: 6.887938e-01	ci right 7.068908e-01	k: 6979	n:10000
KS ci ratio: 4.360219e-02	ci left: 4.371223e-01	ci right 4.567087e-01	k: 4469	n:10000
C7orf36   10000 perm   1 sec   (6826 perm/sec)   p_kst 4.469000e-01   p_cons 6.979000e-01   p_joint 8.240000e-01

Outputting figure to mutsig2_images.part000000000027/C7orf36.2_693_10000_0.4469_0.6979_0.824.png
                gene_name: C7orf36
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.82 
    ci_joint_bounds_right: 0.83 

Current progress: 50 percent done.
C8orf42
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.329722e-02	ci left: 2.141824e-01	ci right 2.305796e-01	k: 2223	n:10000
Cons ci ratio: 1.528606e-01	ci left: 5.696592e-02	ci right 6.649137e-02	k: 616	n:10000
KS ci ratio: 1.178575e-01	ci left: 9.370045e-02	ci right 1.055340e-01	k: 995	n:10000
C8orf42   10000 perm   2 sec   (5849 perm/sec)   p_kst 9.950000e-02   p_cons 6.160000e-02   p_joint 2.223000e-01

Joint ci ratio: 5.102617e-02	ci left: 2.220022e-01	ci right 2.336770e-01	k: 4556	n:20000
Cons ci ratio: 1.057364e-01	ci left: 6.089032e-02	ci right 6.773701e-02	k: 1285	n:20000
KS ci ratio: 8.454669e-02	ci left: 9.293210e-02	ci right 1.011855e-01	k: 1940	n:20000
C8orf42   20000 perm   4 sec   (5694 perm/sec)   p_kst 9.700000e-02   p_cons 6.425000e-02   p_joint 2.278000e-01

Joint ci ratio: 4.185119e-02	ci left: 2.215089e-01	ci right 2.310108e-01	k: 6787	n:30000
Cons ci ratio: 8.602466e-02	ci left: 6.194193e-02	ci right 6.754272e-02	k: 1941	n:30000
KS ci ratio: 6.913119e-02	ci left: 9.344374e-02	ci right 1.001679e-01	k: 2903	n:30000
C8orf42   30000 perm   5 sec   (5579 perm/sec)   p_kst 9.676667e-02   p_cons 6.470000e-02   p_joint 2.262333e-01

Outputting figure to mutsig2_images.part000000000027/C8orf42.2_570_30000_0.096767_0.0647_0.22623.png
                gene_name: C8orf42
               theta_stop: 0.086 
                    nperm: 30000 
                     p_ks: 0.097 
        ci_ks_bounds_left: 0.093 
       ci_ks_bounds_right: 0.10 
                   p_cons: 0.065 
      ci_cons_bounds_left: 0.062 
     ci_cons_bounds_right: 0.068 
                  p_joint: 0.23 
     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.165.3896/
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/181708/iteration1/scatter.0000000027
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 27 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1726>
Subject: Job 1119631: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1726>, 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/181708/iteration1/scatter.0000000028> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 11:12:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000028.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000028.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 28  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :   1847.05 sec.
    Max Memory :      1386 MB
    Max Swap   :      3992 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.165.3896/
-whichjob
28
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 28: processing genes 2444 - 2533
Calculating significance of each gene.
Using projection method.
2444	C9orf172	1
2445	C9orf173	1
2446	C9orf21	1
2447	C9orf23	1
2448	C9orf24	1
2449	C9orf25	1
2450	C9orf3	2.188945e-01
2451	C9orf30	1
2452	C9orf37	1
2453	C9orf4	1
2454	C9orf40	1
2455	C9orf41	2.496495e-02
2456	C9orf43	1
2457	C9orf46	1
2458	C9orf47	1
2459	C9orf5	1
2460	C9orf50	3.575686e-02
2461	C9orf6	1
2462	C9orf64	1
2463	C9orf66	1
2464	C9orf68	1
2465	C9orf69	1
2466	C9orf7	1
2467	C9orf71	1
2468	C9orf72	1
2469	C9orf78	1
2470	C9orf79	1
2471	C9orf80	1
2472	C9orf82	1
2473	C9orf84	1
2474	C9orf85	1
2475	C9orf86	1
2476	C9orf89	1
2477	C9orf9	1
2478	C9orf91	4.018901e-02
2479	C9orf93	1
2480	C9orf95	1
2481	C9orf96	3.112454e-01
2482	C9orf98	6.800577e-02
2483	CA1	1
2484	CA10	3.761232e-02
2485	CA11	1
2486	CA12	1
2487	CA13	1
2488	CA14	1
2489	CA2	1
2490	CA3	1
2491	CA4	1
2492	CA5A	1
2493	CA5B	1
2494	CA6	1
2495	CA7	1
2496	CA8	1
2497	CA9	1
2498	CAB39	1
2499	CAB39L	1
2500	CABC1	3.605308e-02
2501	CABIN1	1
2502	CABLES1	1
2503	CABLES2	1
2504	CABP1	1
2505	CABP2	1
2506	CABP4	1
2507	CABP5	1
2508	CABP7	1
2509	CABYR	1
2510	CACHD1	1
2511	CACNA1A	6.515916e-01
2512	CACNA1B	1.393392e-01
2513	CACNA1C	1
2514	CACNA1D	5.787123e-01
2515	CACNA1E	5.332116e-01
2516	CACNA1F	1.058736e-01
2517	CACNA1G	1
2518	CACNA1H	1
2519	CACNA1I	1
2520	CACNA1S	1
2521	CACNA2D1	3.897862e-01
2522	CACNA2D2	2.432414e-01
2523	CACNA2D3	7.638567e-03
2524	CACNA2D4	1
2525	CACNB1	1
2526	CACNB2	1
2527	CACNB3	1
2528	CACNB4	1
2529	CACNG1	1
2530	CACNG2	1
2531	CACNG3	1
2532	CACNG4	1
2533	CACNG5	1
Done

Running MutSig 2:
Scatter job 28: processing genes 2444 - 2533
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CACNA2D3
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: 1.824276e-02	ci left: 8.143595e-01	ci right 8.294525e-01	k: 8220	n:10000
KS ci ratio: 1.247453e-02	ci left: 9.022685e-01	ci right 9.136926e-01	k: 9081	n:10000
CACNA2D3   10000 perm   2 sec   (5267 perm/sec)   p_kst 9.081000e-01   p_cons 8.220000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000028/CACNA2D3.3_3428_10000_0.9081_0.822_1.png
                gene_name: CACNA2D3
               theta_stop: 0.018 
                    nperm: 10000 
                     p_ks: 0.91 
        ci_ks_bounds_left: 0.90 
       ci_ks_bounds_right: 0.91 
                   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.
C9orf41
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.481028e+00	ci left: 2.202202e-04	ci right 1.305486e-03	k: 6	n:10000
Cons ci ratio: 2.925084e-02	ci left: 6.328151e-01	ci right 6.517020e-01	k: 6423	n:10000
KS ci ratio: 1.481028e+00	ci left: 2.202202e-04	ci right 1.305486e-03	k: 6	n:10000
C9orf41   10000 perm   2 sec   (6599 perm/sec)   p_kst 6.000000e-04   p_cons 6.423000e-01   p_joint 6.000000e-04

Joint ci ratio: 9.503118e-01	ci left: 4.573361e-04	ci right 1.298826e-03	k: 16	n:20000
Cons ci ratio: 2.144222e-02	ci left: 6.188498e-01	ci right 6.323137e-01	k: 12512	n:20000
KS ci ratio: 9.503118e-01	ci left: 4.573361e-04	ci right 1.298826e-03	k: 16	n:20000
C9orf41   20000 perm   3 sec   (5781 perm/sec)   p_kst 8.000000e-04   p_cons 6.256000e-01   p_joint 8.000000e-04

Joint ci ratio: 8.170495e-01	ci left: 4.596314e-04	ci right 1.110066e-03	k: 22	n:30000
Cons ci ratio: 1.746669e-02	ci left: 6.211980e-01	ci right 6.321774e-01	k: 18801	n:30000
KS ci ratio: 8.170495e-01	ci left: 4.596314e-04	ci right 1.110066e-03	k: 22	n:30000
C9orf41   30000 perm   5 sec   (5500 perm/sec)   p_kst 7.333333e-04   p_cons 6.267000e-01   p_joint 7.333333e-04

Joint ci ratio: 7.276527e-01	ci left: 4.651937e-04	ci right 1.011537e-03	k: 28	n:40000
Cons ci ratio: 1.506859e-02	ci left: 6.237430e-01	ci right 6.332384e-01	k: 25140	n:40000
KS ci ratio: 7.276527e-01	ci left: 4.651937e-04	ci right 1.011537e-03	k: 28	n:40000
C9orf41   40000 perm   8 sec   (5295 perm/sec)   p_kst 7.000000e-04   p_cons 6.285000e-01   p_joint 7.000000e-04

Joint ci ratio: 6.530916e-01	ci left: 4.876226e-04	ci right 9.733974e-04	k: 35	n:50000
Cons ci ratio: 1.347724e-02	ci left: 6.242673e-01	ci right 6.327578e-01	k: 31426	n:50000
KS ci ratio: 6.530916e-01	ci left: 4.876226e-04	ci right 9.733974e-04	k: 35	n:50000
C9orf41   50000 perm   10 sec   (5145 perm/sec)   p_kst 7.000000e-04   p_cons 6.285200e-01   p_joint 7.000000e-04

Joint ci ratio: 5.777461e-01	ci left: 5.471061e-04	ci right 1.003432e-03	k: 45	n:60000
Cons ci ratio: 1.231716e-02	ci left: 6.241014e-01	ci right 6.318529e-01	k: 37679	n:60000
KS ci ratio: 5.777461e-01	ci left: 5.471061e-04	ci right 1.003432e-03	k: 45	n:60000
C9orf41   60000 perm   12 sec   (5014 perm/sec)   p_kst 7.500000e-04   p_cons 6.279833e-01   p_joint 7.500000e-04

Joint ci ratio: 5.541697e-01	ci left: 5.179073e-04	ci right 9.253328e-04	k: 49	n:70000
Cons ci ratio: 1.141007e-02	ci left: 6.241208e-01	ci right 6.312972e-01	k: 43940	n:70000
KS ci ratio: 5.541697e-01	ci left: 5.179073e-04	ci right 9.253328e-04	k: 49	n:70000
C9orf41   70000 perm   14 sec   (4896 perm/sec)   p_kst 7.000000e-04   p_cons 6.277143e-01   p_joint 7.000000e-04

Joint ci ratio: 5.017101e-01	ci left: 5.723763e-04	ci right 9.652947e-04	k: 60	n:80000
Cons ci ratio: 1.068805e-02	ci left: 6.237007e-01	ci right 6.304151e-01	k: 50165	n:80000
KS ci ratio: 5.017101e-01	ci left: 5.723763e-04	ci right 9.652947e-04	k: 60	n:80000
C9orf41   80000 perm   17 sec   (4783 perm/sec)   p_kst 7.500000e-04   p_cons 6.270625e-01   p_joint 7.500000e-04

Joint ci ratio: 4.555008e-01	ci left: 6.358338e-04	ci right 1.019744e-03	k: 73	n:90000
Cons ci ratio: 1.005925e-02	ci left: 6.247102e-01	ci right 6.310371e-01	k: 56509	n:90000
KS ci ratio: 4.555008e-01	ci left: 6.358338e-04	ci right 1.019744e-03	k: 73	n:90000
C9orf41   90000 perm   19 sec   (4682 perm/sec)   p_kst 8.111111e-04   p_cons 6.278778e-01   p_joint 8.111111e-04

Joint ci ratio: 4.176874e-01	ci left: 6.968912e-04	ci right 1.073033e-03	k: 87	n:100000
Cons ci ratio: 9.538920e-03	ci left: 6.250757e-01	ci right 6.310768e-01	k: 62808	n:100000
KS ci ratio: 4.176874e-01	ci left: 6.968912e-04	ci right 1.073033e-03	k: 87	n:100000
C9orf41   100000 perm   22 sec   (4581 perm/sec)   p_kst 8.700000e-04   p_cons 6.280800e-01   p_joint 8.700000e-04

Joint ci ratio: 3.978384e-01	ci left: 7.069673e-04	ci right 1.065647e-03	k: 96	n:110000
Cons ci ratio: 9.090552e-03	ci left: 6.254454e-01	ci right 6.311660e-01	k: 69114	n:110000
KS ci ratio: 3.978384e-01	ci left: 7.069673e-04	ci right 1.065647e-03	k: 96	n:110000
C9orf41   110000 perm   24 sec   (4491 perm/sec)   p_kst 8.727273e-04   p_cons 6.283091e-01   p_joint 8.727273e-04

Joint ci ratio: 3.770308e-01	ci left: 7.307981e-04	ci right 1.077388e-03	k: 107	n:120000
Cons ci ratio: 8.713502e-03	ci left: 6.250327e-01	ci right 6.305111e-01	k: 75333	n:120000
KS ci ratio: 3.770308e-01	ci left: 7.307981e-04	ci right 1.077388e-03	k: 107	n:120000
C9orf41   120000 perm   27 sec   (4401 perm/sec)   p_kst 8.916667e-04   p_cons 6.277750e-01   p_joint 8.916667e-04

Joint ci ratio: 3.591799e-01	ci left: 7.513768e-04	ci right 1.086914e-03	k: 118	n:130000
Cons ci ratio: 8.362128e-03	ci left: 6.256740e-01	ci right 6.309356e-01	k: 81680	n:130000
KS ci ratio: 3.591799e-01	ci left: 7.513768e-04	ci right 1.086914e-03	k: 118	n:130000
C9orf41   130000 perm   30 sec   (4315 perm/sec)   p_kst 9.076923e-04   p_cons 6.283077e-01   p_joint 9.076923e-04

Joint ci ratio: 3.532979e-01	ci left: 7.237197e-04	ci right 1.040399e-03	k: 122	n:140000
Cons ci ratio: 8.060427e-03	ci left: 6.256265e-01	ci right 6.306968e-01	k: 87943	n:140000
KS ci ratio: 3.532979e-01	ci left: 7.237197e-04	ci right 1.040399e-03	k: 122	n:140000
C9orf41   140000 perm   33 sec   (4232 perm/sec)   p_kst 8.714286e-04   p_cons 6.281643e-01   p_joint 8.714286e-04

Joint ci ratio: 3.463333e-01	ci left: 7.058752e-04	ci right 1.007292e-03	k: 127	n:150000
Cons ci ratio: 7.781965e-03	ci left: 6.260222e-01	ci right 6.309195e-01	k: 94271	n:150000
KS ci ratio: 3.463333e-01	ci left: 7.058752e-04	ci right 1.007292e-03	k: 127	n:150000
C9orf41   150000 perm   36 sec   (4156 perm/sec)   p_kst 8.466667e-04   p_cons 6.284733e-01   p_joint 8.466667e-04

Joint ci ratio: 3.359933e-01	ci left: 7.074754e-04	ci right 9.986029e-04	k: 135	n:160000
Cons ci ratio: 7.536545e-03	ci left: 6.259955e-01	ci right 6.307374e-01	k: 100539	n:160000
KS ci ratio: 3.359933e-01	ci left: 7.074754e-04	ci right 9.986029e-04	k: 135	n:160000
C9orf41   160000 perm   39 sec   (4083 perm/sec)   p_kst 8.437500e-04   p_cons 6.283688e-01   p_joint 8.437500e-04

Joint ci ratio: 3.231754e-01	ci left: 7.252144e-04	ci right 1.009899e-03	k: 146	n:170000
Cons ci ratio: 7.312141e-03	ci left: 6.260271e-01	ci right 6.306273e-01	k: 106816	n:170000
KS ci ratio: 3.231754e-01	ci left: 7.252144e-04	ci right 1.009899e-03	k: 146	n:170000
C9orf41   170000 perm   42 sec   (4013 perm/sec)   p_kst 8.588235e-04   p_cons 6.283294e-01   p_joint 8.588235e-04

Joint ci ratio: 3.199324e-01	ci left: 7.002447e-04	ci right 9.718035e-04	k: 149	n:180000
Cons ci ratio: 7.107166e-03	ci left: 6.260237e-01	ci right 6.304944e-01	k: 113087	n:180000
KS ci ratio: 3.199324e-01	ci left: 7.002447e-04	ci right 9.718035e-04	k: 149	n:180000
C9orf41   180000 perm   46 sec   (3943 perm/sec)   p_kst 8.277778e-04   p_cons 6.282611e-01   p_joint 8.277778e-04

Joint ci ratio: 3.137215e-01	ci left: 6.924575e-04	ci right 9.547384e-04	k: 155	n:190000
Cons ci ratio: 6.915864e-03	ci left: 6.262015e-01	ci right 6.305525e-01	k: 119392	n:190000
KS ci ratio: 3.137215e-01	ci left: 6.924575e-04	ci right 9.547384e-04	k: 155	n:190000
C9orf41   190000 perm   49 sec   (3875 perm/sec)   p_kst 8.157895e-04   p_cons 6.283789e-01   p_joint 8.157895e-04

Joint ci ratio: 3.069122e-01	ci left: 6.901094e-04	ci right 9.447185e-04	k: 162	n:200000
Cons ci ratio: 6.742902e-03	ci left: 6.261076e-01	ci right 6.303486e-01	k: 125646	n:200000
KS ci ratio: 3.069122e-01	ci left: 6.901094e-04	ci right 9.447185e-04	k: 162	n:200000
C9orf41   200000 perm   52 sec   (3813 perm/sec)   p_kst 8.100000e-04   p_cons 6.282300e-01   p_joint 8.100000e-04

Joint ci ratio: 3.005278e-01	ci left: 6.880406e-04	ci right 9.355977e-04	k: 169	n:210000
Cons ci ratio: 6.580420e-03	ci left: 6.261575e-01	ci right 6.302961e-01	k: 131928	n:210000
KS ci ratio: 3.005278e-01	ci left: 6.880406e-04	ci right 9.355977e-04	k: 169	n:210000
C9orf41   210000 perm   56 sec   (3753 perm/sec)   p_kst 8.047619e-04   p_cons 6.282286e-01   p_joint 8.047619e-04

Joint ci ratio: 2.920593e-01	ci left: 6.988435e-04	ci right 9.418925e-04	k: 179	n:220000
Cons ci ratio: 6.433212e-03	ci left: 6.259081e-01	ci right 6.299522e-01	k: 138145	n:220000
KS ci ratio: 2.920593e-01	ci left: 6.988435e-04	ci right 9.418925e-04	k: 179	n:220000
C9orf41   220000 perm   60 sec   (3695 perm/sec)   p_kst 8.136364e-04   p_cons 6.279318e-01   p_joint 8.136364e-04

Joint ci ratio: 2.857779e-01	ci left: 7.007215e-04	ci right 9.382366e-04	k: 187	n:230000
Cons ci ratio: 6.290128e-03	ci left: 6.260775e-01	ci right 6.300323e-01	k: 144453	n:230000
KS ci ratio: 2.857779e-01	ci left: 7.007215e-04	ci right 9.382366e-04	k: 187	n:230000
C9orf41   230000 perm   63 sec   (3639 perm/sec)   p_kst 8.130435e-04   p_cons 6.280565e-01   p_joint 8.130435e-04

Joint ci ratio: 2.806024e-01	ci left: 6.986202e-04	ci right 9.303761e-04	k: 194	n:240000
Cons ci ratio: 6.154866e-03	ci left: 6.263338e-01	ci right 6.302048e-01	k: 150785	n:240000
KS ci ratio: 2.806024e-01	ci left: 6.986202e-04	ci right 9.303761e-04	k: 194	n:240000
C9orf41   240000 perm   67 sec   (3581 perm/sec)   p_kst 8.083333e-04   p_cons 6.282708e-01   p_joint 8.083333e-04

Joint ci ratio: 2.716895e-01	ci left: 7.190769e-04	ci right 9.487503e-04	k: 207	n:250000
Cons ci ratio: 6.029465e-03	ci left: 6.264542e-01	ci right 6.302468e-01	k: 157088	n:250000
KS ci ratio: 2.716895e-01	ci left: 7.190769e-04	ci right 9.487503e-04	k: 207	n:250000
C9orf41   250000 perm   71 sec   (3525 perm/sec)   p_kst 8.280000e-04   p_cons 6.283520e-01   p_joint 8.280000e-04

Joint ci ratio: 2.653841e-01	ci left: 7.272931e-04	ci right 9.533039e-04	k: 217	n:260000
Cons ci ratio: 5.913767e-03	ci left: 6.263814e-01	ci right 6.301004e-01	k: 163343	n:260000
KS ci ratio: 2.653841e-01	ci left: 7.272931e-04	ci right 9.533039e-04	k: 217	n:260000
C9orf41   260000 perm   75 sec   (3470 perm/sec)   p_kst 8.346154e-04   p_cons 6.282423e-01   p_joint 8.346154e-04

Joint ci ratio: 2.578062e-01	ci left: 7.453489e-04	ci right 9.692928e-04	k: 230	n:270000
Cons ci ratio: 5.801307e-03	ci left: 6.265703e-01	ci right 6.302195e-01	k: 169667	n:270000
KS ci ratio: 2.578062e-01	ci left: 7.453489e-04	ci right 9.692928e-04	k: 230	n:270000
C9orf41   270000 perm   79 sec   (3420 perm/sec)   p_kst 8.518519e-04   p_cons 6.283963e-01   p_joint 8.518519e-04

Joint ci ratio: 2.550623e-01	ci left: 7.354383e-04	ci right 9.536783e-04	k: 235	n:280000
Cons ci ratio: 5.696116e-03	ci left: 6.266571e-01	ci right 6.302403e-01	k: 175966	n:280000
KS ci ratio: 2.550623e-01	ci left: 7.354383e-04	ci right 9.536783e-04	k: 235	n:280000
C9orf41   280000 perm   83 sec   (3368 perm/sec)   p_kst 8.392857e-04   p_cons 6.284500e-01   p_joint 8.392857e-04

Joint ci ratio: 2.508463e-01	ci left: 7.359159e-04	ci right 9.501242e-04	k: 243	n:290000
Cons ci ratio: 5.597935e-03	ci left: 6.266141e-01	ci right 6.301351e-01	k: 182229	n:290000
KS ci ratio: 2.508463e-01	ci left: 7.359159e-04	ci right 9.501242e-04	k: 243	n:290000
C9orf41   290000 perm   87 sec   (3318 perm/sec)   p_kst 8.379310e-04   p_cons 6.283759e-01   p_joint 8.379310e-04

Joint ci ratio: 2.468326e-01	ci left: 7.363892e-04	ci right 9.467796e-04	k: 251	n:300000
Cons ci ratio: 5.504426e-03	ci left: 6.265945e-01	ci right 6.300563e-01	k: 188498	n:300000
KS ci ratio: 2.468326e-01	ci left: 7.363892e-04	ci right 9.467796e-04	k: 251	n:300000
C9orf41   300000 perm   92 sec   (3270 perm/sec)   p_kst 8.366667e-04   p_cons 6.283267e-01   p_joint 8.366667e-04

Joint ci ratio: 2.430057e-01	ci left: 7.368575e-04	ci right 9.436254e-04	k: 259	n:310000
Cons ci ratio: 5.412908e-03	ci left: 6.267962e-01	ci right 6.302014e-01	k: 194835	n:310000
KS ci ratio: 2.430057e-01	ci left: 7.368575e-04	ci right 9.436254e-04	k: 259	n:310000
C9orf41   310000 perm   96 sec   (3222 perm/sec)   p_kst 8.354839e-04   p_cons 6.285000e-01   p_joint 8.354839e-04

Joint ci ratio: 2.397996e-01	ci left: 7.343825e-04	ci right 9.373329e-04	k: 266	n:320000
Cons ci ratio: 5.325450e-03	ci left: 6.270170e-01	ci right 6.303682e-01	k: 201182	n:320000
KS ci ratio: 2.397996e-01	ci left: 7.343825e-04	ci right 9.373329e-04	k: 266	n:320000
C9orf41   320000 perm   101 sec   (3177 perm/sec)   p_kst 8.312500e-04   p_cons 6.286938e-01   p_joint 8.312500e-04

Joint ci ratio: 2.362860e-01	ci left: 7.349252e-04	ci right 9.346145e-04	k: 274	n:330000
Cons ci ratio: 5.246931e-03	ci left: 6.267941e-01	ci right 6.300945e-01	k: 207387	n:330000
KS ci ratio: 2.362860e-01	ci left: 7.349252e-04	ci right 9.346145e-04	k: 274	n:330000
C9orf41   330000 perm   105 sec   (3133 perm/sec)   p_kst 8.303030e-04   p_cons 6.284455e-01   p_joint 8.303030e-04

Joint ci ratio: 2.337506e-01	ci left: 7.299175e-04	ci right 9.258104e-04	k: 280	n:340000
Cons ci ratio: 5.170740e-03	ci left: 6.266789e-01	ci right 6.299306e-01	k: 213624	n:340000
KS ci ratio: 2.337506e-01	ci left: 7.299175e-04	ci right 9.258104e-04	k: 280	n:340000
C9orf41   340000 perm   110 sec   (3092 perm/sec)   p_kst 8.235294e-04   p_cons 6.283059e-01   p_joint 8.235294e-04

Joint ci ratio: 2.304927e-01	ci left: 7.305908e-04	ci right 9.235426e-04	k: 288	n:350000
Cons ci ratio: 5.095092e-03	ci left: 6.268166e-01	ci right 6.300213e-01	k: 219947	n:350000
KS ci ratio: 2.304927e-01	ci left: 7.305908e-04	ci right 9.235426e-04	k: 288	n:350000
C9orf41   350000 perm   115 sec   (3053 perm/sec)   p_kst 8.228571e-04   p_cons 6.284200e-01   p_joint 8.228571e-04

Joint ci ratio: 2.281374e-01	ci left: 7.260057e-04	ci right 9.155114e-04	k: 294	n:360000
Cons ci ratio: 5.023118e-03	ci left: 6.269052e-01	ci right 6.300649e-01	k: 226255	n:360000
KS ci ratio: 2.281374e-01	ci left: 7.260057e-04	ci right 9.155114e-04	k: 294	n:360000
C9orf41   360000 perm   119 sec   (3013 perm/sec)   p_kst 8.166667e-04   p_cons 6.284861e-01   p_joint 8.166667e-04

Joint ci ratio: 2.247347e-01	ci left: 7.293288e-04	ci right 9.164694e-04	k: 303	n:370000
Cons ci ratio: 4.954138e-03	ci left: 6.269867e-01	ci right 6.301032e-01	k: 232562	n:370000
KS ci ratio: 2.247347e-01	ci left: 7.293288e-04	ci right 9.164694e-04	k: 303	n:370000
C9orf41   370000 perm   124 sec   (2974 perm/sec)   p_kst 8.189189e-04   p_cons 6.285459e-01   p_joint 8.189189e-04

Joint ci ratio: 2.218349e-01	ci left: 7.300112e-04	ci right 9.145799e-04	k: 311	n:380000
Cons ci ratio: 4.888283e-03	ci left: 6.270298e-01	ci right 6.301050e-01	k: 238856	n:380000
KS ci ratio: 2.218349e-01	ci left: 7.300112e-04	ci right 9.145799e-04	k: 311	n:380000
C9orf41   380000 perm   129 sec   (2935 perm/sec)   p_kst 8.184211e-04   p_cons 6.285684e-01   p_joint 8.184211e-04

Joint ci ratio: 2.190445e-01	ci left: 7.306732e-04	ci right 9.127727e-04	k: 319	n:390000
Cons ci ratio: 4.826072e-03	ci left: 6.269659e-01	ci right 6.300015e-01	k: 245109	n:390000
KS ci ratio: 2.190445e-01	ci left: 7.306732e-04	ci right 9.127727e-04	k: 319	n:390000
C9orf41   390000 perm   135 sec   (2898 perm/sec)   p_kst 8.179487e-04   p_cons 6.284846e-01   p_joint 8.179487e-04

Joint ci ratio: 2.156996e-01	ci left: 7.360456e-04	ci right 9.163120e-04	k: 329	n:400000
Cons ci ratio: 4.767172e-03	ci left: 6.268077e-01	ci right 6.298054e-01	k: 251323	n:400000
KS ci ratio: 2.156996e-01	ci left: 7.360456e-04	ci right 9.163120e-04	k: 329	n:400000
C9orf41   400000 perm   140 sec   (2863 perm/sec)   p_kst 8.225000e-04   p_cons 6.283075e-01   p_joint 8.225000e-04

Joint ci ratio: 2.118806e-01	ci left: 7.457951e-04	ci right 9.247953e-04	k: 341	n:410000
Cons ci ratio: 4.707179e-03	ci left: 6.269749e-01	ci right 6.299355e-01	k: 257667	n:410000
KS ci ratio: 2.118806e-01	ci left: 7.457951e-04	ci right 9.247953e-04	k: 341	n:410000
C9orf41   410000 perm   145 sec   (2827 perm/sec)   p_kst 8.317073e-04   p_cons 6.284561e-01   p_joint 8.317073e-04

Joint ci ratio: 2.097453e-01	ci left: 7.438247e-04	ci right 9.203218e-04	k: 348	n:420000
Cons ci ratio: 4.651315e-03	ci left: 6.269413e-01	ci right 6.298665e-01	k: 263930	n:420000
KS ci ratio: 2.097453e-01	ci left: 7.438247e-04	ci right 9.203218e-04	k: 348	n:420000
C9orf41   420000 perm   150 sec   (2793 perm/sec)   p_kst 8.285714e-04   p_cons 6.284048e-01   p_joint 8.285714e-04

Joint ci ratio: 2.068031e-01	ci left: 7.485696e-04	ci right 9.233857e-04	k: 358	n:430000
Cons ci ratio: 4.595334e-03	ci left: 6.271189e-01	ci right 6.300096e-01	k: 270283	n:430000
KS ci ratio: 2.068031e-01	ci left: 7.485696e-04	ci right 9.233857e-04	k: 358	n:430000
C9orf41   430000 perm   156 sec   (2760 perm/sec)   p_kst 8.325581e-04   p_cons 6.285651e-01   p_joint 8.325581e-04

Joint ci ratio: 2.053786e-01	ci left: 7.423336e-04	ci right 9.143493e-04	k: 363	n:440000
Cons ci ratio: 4.545239e-03	ci left: 6.268860e-01	ci right 6.297441e-01	k: 276459	n:440000
KS ci ratio: 2.053786e-01	ci left: 7.423336e-04	ci right 9.143493e-04	k: 363	n:440000
C9orf41   440000 perm   161 sec   (2727 perm/sec)   p_kst 8.250000e-04   p_cons 6.283159e-01   p_joint 8.250000e-04

Joint ci ratio: 2.023433e-01	ci left: 7.490343e-04	ci right 9.197206e-04	k: 374	n:450000
Cons ci ratio: 4.495055e-03	ci left: 6.268394e-01	ci right 6.296656e-01	k: 282714	n:450000
KS ci ratio: 2.023433e-01	ci left: 7.490343e-04	ci right 9.197206e-04	k: 374	n:450000
C9orf41   450000 perm   167 sec   (2697 perm/sec)   p_kst 8.311111e-04   p_cons 6.282533e-01   p_joint 8.311111e-04

Joint ci ratio: 2.002190e-01	ci left: 7.492658e-04	ci right 9.179934e-04	k: 382	n:460000
Cons ci ratio: 4.446270e-03	ci left: 6.268189e-01	ci right 6.296143e-01	k: 288980	n:460000
KS ci ratio: 2.002190e-01	ci left: 7.492658e-04	ci right 9.179934e-04	k: 382	n:460000
C9orf41   460000 perm   172 sec   (2667 perm/sec)   p_kst 8.304348e-04   p_cons 6.282174e-01   p_joint 8.304348e-04

Joint ci ratio: 1.981602e-01	ci left: 7.494963e-04	ci right 9.163307e-04	k: 390	n:470000
Cons ci ratio: 4.397356e-03	ci left: 6.269783e-01	ci right 6.297435e-01	k: 295330	n:470000
KS ci ratio: 1.981602e-01	ci left: 7.494963e-04	ci right 9.163307e-04	k: 390	n:470000
C9orf41   470000 perm   178 sec   (2638 perm/sec)   p_kst 8.297872e-04   p_cons 6.283617e-01   p_joint 8.297872e-04

Joint ci ratio: 1.954297e-01	ci left: 7.556696e-04	ci right 9.212845e-04	k: 401	n:480000
Cons ci ratio: 4.351050e-03	ci left: 6.270207e-01	ci right 6.297569e-01	k: 301627	n:480000
KS ci ratio: 1.954297e-01	ci left: 7.556696e-04	ci right 9.212845e-04	k: 401	n:480000
C9orf41   480000 perm   184 sec   (2608 perm/sec)   p_kst 8.354167e-04   p_cons 6.283896e-01   p_joint 8.354167e-04

Joint ci ratio: 1.937504e-01	ci left: 7.538375e-04	ci right 9.174637e-04	k: 408	n:490000
Cons ci ratio: 4.304821e-03	ci left: 6.272086e-01	ci right 6.299164e-01	k: 307996	n:490000
KS ci ratio: 1.937504e-01	ci left: 7.538375e-04	ci right 9.174637e-04	k: 408	n:490000
C9orf41   490000 perm   190 sec   (2580 perm/sec)   p_kst 8.326531e-04   p_cons 6.285633e-01   p_joint 8.326531e-04

Joint ci ratio: 1.916531e-01	ci left: 7.558924e-04	ci right 9.179817e-04	k: 417	n:500000
Cons ci ratio: 4.262005e-03	ci left: 6.271729e-01	ci right 6.298536e-01	k: 314257	n:500000
KS ci ratio: 1.916531e-01	ci left: 7.558924e-04	ci right 9.179817e-04	k: 417	n:500000
C9orf41   500000 perm   196 sec   (2551 perm/sec)   p_kst 8.340000e-04   p_cons 6.285140e-01   p_joint 8.340000e-04

Joint ci ratio: 1.902927e-01	ci left: 7.522731e-04	ci right 9.123088e-04	k: 423	n:510000
Cons ci ratio: 4.219609e-03	ci left: 6.272310e-01	ci right 6.298852e-01	k: 320565	n:510000
KS ci ratio: 1.902927e-01	ci left: 7.522731e-04	ci right 9.123088e-04	k: 423	n:510000
C9orf41   510000 perm   202 sec   (2524 perm/sec)   p_kst 8.294118e-04   p_cons 6.285588e-01   p_joint 8.294118e-04

Joint ci ratio: 1.885225e-01	ci left: 7.524614e-04	ci right 9.108776e-04	k: 431	n:520000
Cons ci ratio: 4.180829e-03	ci left: 6.270214e-01	ci right 6.296502e-01	k: 326735	n:520000
KS ci ratio: 1.885225e-01	ci left: 7.524614e-04	ci right 9.108776e-04	k: 431	n:520000
C9orf41   520000 perm   208 sec   (2496 perm/sec)   p_kst 8.288462e-04   p_cons 6.283365e-01   p_joint 8.288462e-04

Joint ci ratio: 1.872273e-01	ci left: 7.490522e-04	ci right 9.055440e-04	k: 437	n:530000
Cons ci ratio: 4.142627e-03	ci left: 6.268727e-01	ci right 6.294768e-01	k: 332933	n:530000
KS ci ratio: 1.872273e-01	ci left: 7.490522e-04	ci right 9.055440e-04	k: 437	n:530000
C9orf41   530000 perm   215 sec   (2470 perm/sec)   p_kst 8.245283e-04   p_cons 6.281755e-01   p_joint 8.245283e-04

Joint ci ratio: 1.863789e-01	ci left: 7.422417e-04	ci right 8.965284e-04	k: 441	n:540000
Cons ci ratio: 4.102086e-03	ci left: 6.271132e-01	ci right 6.296928e-01	k: 339338	n:540000
KS ci ratio: 1.863789e-01	ci left: 7.422417e-04	ci right 8.965284e-04	k: 441	n:540000
C9orf41   540000 perm   221 sec   (2445 perm/sec)   p_kst 8.166667e-04   p_cons 6.284037e-01   p_joint 8.166667e-04

Joint ci ratio: 1.838986e-01	ci left: 7.495537e-04	ci right 9.030558e-04	k: 453	n:550000
Cons ci ratio: 4.064830e-03	ci left: 6.271013e-01	ci right 6.296573e-01	k: 345609	n:550000
KS ci ratio: 1.838986e-01	ci left: 7.495537e-04	ci right 9.030558e-04	k: 453	n:550000
C9orf41   550000 perm   227 sec   (2421 perm/sec)   p_kst 8.236364e-04   p_cons 6.283800e-01   p_joint 8.236364e-04

Joint ci ratio: 1.824973e-01	ci left: 7.480955e-04	ci right 9.000025e-04	k: 460	n:560000
Cons ci ratio: 4.029078e-03	ci left: 6.270310e-01	ci right 6.295642e-01	k: 351847	n:560000
KS ci ratio: 1.824973e-01	ci left: 7.480955e-04	ci right 9.000025e-04	k: 460	n:560000
C9orf41   560000 perm   234 sec   (2396 perm/sec)   p_kst 8.214286e-04   p_cons 6.282982e-01   p_joint 8.214286e-04

Joint ci ratio: 1.805493e-01	ci left: 7.517178e-04	ci right 9.025530e-04	k: 470	n:570000
Cons ci ratio: 3.995724e-03	ci left: 6.267911e-01	ci right 6.293023e-01	k: 357987	n:570000
KS ci ratio: 1.805493e-01	ci left: 7.517178e-04	ci right 9.025530e-04	k: 470	n:570000
C9orf41   570000 perm   240 sec   (2372 perm/sec)   p_kst 8.245614e-04   p_cons 6.280474e-01   p_joint 8.245614e-04

Joint ci ratio: 1.786623e-01	ci left: 7.552236e-04	ci right 9.050073e-04	k: 480	n:580000
Cons ci ratio: 3.961399e-03	ci left: 6.267701e-01	ci right 6.292596e-01	k: 364249	n:580000
KS ci ratio: 1.786623e-01	ci left: 7.552236e-04	ci right 9.050073e-04	k: 480	n:580000
C9orf41   580000 perm   247 sec   (2349 perm/sec)   p_kst 8.275862e-04   p_cons 6.280155e-01   p_joint 8.275862e-04

Joint ci ratio: 1.777414e-01	ci left: 7.505196e-04	ci right 8.985206e-04	k: 485	n:590000
Cons ci ratio: 3.927615e-03	ci left: 6.267890e-01	ci right 6.292572e-01	k: 370534	n:590000
KS ci ratio: 1.777414e-01	ci left: 7.505196e-04	ci right 8.985206e-04	k: 485	n:590000
C9orf41   590000 perm   254 sec   (2327 perm/sec)   p_kst 8.220339e-04   p_cons 6.280237e-01   p_joint 8.220339e-04

Joint ci ratio: 1.766546e-01	ci left: 7.475673e-04	ci right 8.939884e-04	k: 491	n:600000
Cons ci ratio: 3.894848e-03	ci left: 6.267872e-01	ci right 6.292349e-01	k: 376807	n:600000
KS ci ratio: 1.766546e-01	ci left: 7.475673e-04	ci right 8.939884e-04	k: 491	n:600000
C9orf41   600000 perm   261 sec   (2303 perm/sec)   p_kst 8.183333e-04   p_cons 6.280117e-01   p_joint 8.183333e-04

Joint ci ratio: 1.761193e-01	ci left: 7.400127e-04	ci right 8.844682e-04	k: 494	n:610000
Cons ci ratio: 3.862102e-03	ci left: 6.268808e-01	ci right 6.293082e-01	k: 383138	n:610000
KS ci ratio: 1.761193e-01	ci left: 7.400127e-04	ci right 8.844682e-04	k: 494	n:610000
C9orf41   610000 perm   267 sec   (2281 perm/sec)   p_kst 8.098361e-04   p_cons 6.280951e-01   p_joint 8.098361e-04

Joint ci ratio: 1.740220e-01	ci left: 7.465840e-04	ci right 8.904044e-04	k: 506	n:620000
Cons ci ratio: 3.830683e-03	ci left: 6.269085e-01	ci right 6.293161e-01	k: 389430	n:620000
KS ci ratio: 1.740220e-01	ci left: 7.465840e-04	ci right 8.904044e-04	k: 506	n:620000
C9orf41   620000 perm   275 sec   (2258 perm/sec)   p_kst 8.161290e-04   p_cons 6.281129e-01   p_joint 8.161290e-04

Joint ci ratio: 1.733401e-01	ci left: 7.408065e-04	ci right 8.828962e-04	k: 510	n:630000
Cons ci ratio: 3.799709e-03	ci left: 6.269735e-01	ci right 6.293619e-01	k: 395746	n:630000
KS ci ratio: 1.733401e-01	ci left: 7.408065e-04	ci right 8.828962e-04	k: 510	n:630000
C9orf41   630000 perm   282 sec   (2237 perm/sec)   p_kst 8.095238e-04   p_cons 6.281683e-01   p_joint 8.095238e-04

Joint ci ratio: 1.710125e-01	ci left: 7.501641e-04	ci right 8.919173e-04	k: 524	n:640000
Cons ci ratio: 3.769979e-03	ci left: 6.269740e-01	ci right 6.293436e-01	k: 402022	n:640000
KS ci ratio: 1.710125e-01	ci left: 7.501641e-04	ci right 8.919173e-04	k: 524	n:640000
C9orf41   640000 perm   289 sec   (2216 perm/sec)   p_kst 8.187500e-04   p_cons 6.281594e-01   p_joint 8.187500e-04

Joint ci ratio: 1.687762e-01	ci left: 7.592460e-04	ci right 9.006485e-04	k: 538	n:650000
Cons ci ratio: 3.740098e-03	ci left: 6.270792e-01	ci right 6.294304e-01	k: 408366	n:650000
KS ci ratio: 1.687762e-01	ci left: 7.592460e-04	ci right 9.006485e-04	k: 538	n:650000
C9orf41   650000 perm   296 sec   (2196 perm/sec)   p_kst 8.276923e-04   p_cons 6.282554e-01   p_joint 8.276923e-04

Joint ci ratio: 1.672318e-01	ci left: 7.622569e-04	ci right 9.027902e-04	k: 548	n:660000
Cons ci ratio: 3.711169e-03	ci left: 6.271495e-01	ci right 6.294827e-01	k: 414689	n:660000
KS ci ratio: 1.672318e-01	ci left: 7.622569e-04	ci right 9.027902e-04	k: 548	n:660000
C9orf41   660000 perm   303 sec   (2176 perm/sec)   p_kst 8.303030e-04   p_cons 6.283167e-01   p_joint 8.303030e-04

Joint ci ratio: 1.657290e-01	ci left: 7.651835e-04	ci right 9.048622e-04	k: 558	n:670000
Cons ci ratio: 3.683525e-03	ci left: 6.271386e-01	ci right 6.294544e-01	k: 420959	n:670000
KS ci ratio: 1.657290e-01	ci left: 7.651835e-04	ci right 9.048622e-04	k: 558	n:670000
C9orf41   670000 perm   311 sec   (2156 perm/sec)   p_kst 8.328358e-04   p_cons 6.282970e-01   p_joint 8.328358e-04

Joint ci ratio: 1.642661e-01	ci left: 7.680296e-04	ci right 9.068679e-04	k: 568	n:680000
Cons ci ratio: 3.656915e-03	ci left: 6.270736e-01	ci right 6.293724e-01	k: 427192	n:680000
KS ci ratio: 1.642661e-01	ci left: 7.680296e-04	ci right 9.068679e-04	k: 568	n:680000
C9orf41   680000 perm   318 sec   (2136 perm/sec)   p_kst 8.352941e-04   p_cons 6.282235e-01   p_joint 8.352941e-04

Joint ci ratio: 1.618648e-01	ci left: 7.805314e-04	ci right 9.193666e-04	k: 585	n:690000
Cons ci ratio: 3.629195e-03	ci left: 6.272266e-01	ci right 6.295085e-01	k: 433574	n:690000
KS ci ratio: 1.618648e-01	ci left: 7.805314e-04	ci right 9.193666e-04	k: 585	n:690000
C9orf41   690000 perm   326 sec   (2116 perm/sec)   p_kst 8.478261e-04   p_cons 6.283681e-01   p_joint 8.478261e-04

Joint ci ratio: 1.600982e-01	ci left: 7.872045e-04	ci right 9.255514e-04	k: 598	n:700000
Cons ci ratio: 3.602393e-03	ci left: 6.273368e-01	ci right 6.296022e-01	k: 439929	n:700000
KS ci ratio: 1.600982e-01	ci left: 7.872045e-04	ci right 9.255514e-04	k: 598	n:700000
C9orf41   700000 perm   334 sec   (2098 perm/sec)   p_kst 8.542857e-04   p_cons 6.284700e-01   p_joint 8.542857e-04

Joint ci ratio: 1.586479e-01	ci left: 7.909923e-04	ci right 9.286257e-04	k: 609	n:710000
Cons ci ratio: 3.577665e-03	ci left: 6.272494e-01	ci right 6.294989e-01	k: 446146	n:710000
KS ci ratio: 1.586479e-01	ci left: 7.909923e-04	ci right 9.286257e-04	k: 609	n:710000
C9orf41   710000 perm   341 sec   (2080 perm/sec)   p_kst 8.577465e-04   p_cons 6.283746e-01   p_joint 8.577465e-04

Joint ci ratio: 1.580020e-01	ci left: 7.866755e-04	ci right 9.229476e-04	k: 614	n:720000
Cons ci ratio: 3.553745e-03	ci left: 6.271242e-01	ci right 6.293581e-01	k: 452334	n:720000
KS ci ratio: 1.580020e-01	ci left: 7.866755e-04	ci right 9.229476e-04	k: 614	n:720000
C9orf41   720000 perm   349 sec   (2061 perm/sec)   p_kst 8.527778e-04   p_cons 6.282417e-01   p_joint 8.527778e-04

Joint ci ratio: 1.572372e-01	ci left: 7.837940e-04	ci right 9.188478e-04	k: 620	n:730000
Cons ci ratio: 3.528279e-03	ci left: 6.272697e-01	ci right 6.294882e-01	k: 458717	n:730000
KS ci ratio: 1.572372e-01	ci left: 7.837940e-04	ci right 9.188478e-04	k: 620	n:730000
C9orf41   730000 perm   357 sec   (2043 perm/sec)   p_kst 8.493151e-04   p_cons 6.283795e-01   p_joint 8.493151e-04

Joint ci ratio: 1.563585e-01	ci left: 7.822904e-04	ci right 9.162613e-04	k: 627	n:740000
Cons ci ratio: 3.504427e-03	ci left: 6.272681e-01	ci right 6.294715e-01	k: 464994	n:740000
KS ci ratio: 1.563585e-01	ci left: 7.822904e-04	ci right 9.162613e-04	k: 627	n:740000
C9orf41   740000 perm   365 sec   (2026 perm/sec)   p_kst 8.472973e-04   p_cons 6.283703e-01   p_joint 8.472973e-04

Joint ci ratio: 1.540445e-01	ci left: 7.962098e-04	ci right 9.303603e-04	k: 646	n:750000
Cons ci ratio: 3.480665e-03	ci left: 6.273185e-01	ci right 6.295071e-01	k: 471310	n:750000
KS ci ratio: 1.540445e-01	ci left: 7.962098e-04	ci right 9.303603e-04	k: 646	n:750000
C9orf41   750000 perm   373 sec   (2009 perm/sec)   p_kst 8.613333e-04   p_cons 6.284133e-01   p_joint 8.613333e-04

Joint ci ratio: 1.533354e-01	ci left: 7.933244e-04	ci right 9.263169e-04	k: 652	n:760000
Cons ci ratio: 3.457370e-03	ci left: 6.273690e-01	ci right 6.295431e-01	k: 477627	n:760000
KS ci ratio: 1.533354e-01	ci left: 7.933244e-04	ci right 9.263169e-04	k: 652	n:760000
C9orf41   760000 perm   381 sec   (1992 perm/sec)   p_kst 8.578947e-04   p_cons 6.284566e-01   p_joint 8.578947e-04

Joint ci ratio: 1.513768e-01	ci left: 8.042581e-04	ci right 9.372054e-04	k: 669	n:770000
Cons ci ratio: 3.434718e-03	ci left: 6.273936e-01	ci right 6.295535e-01	k: 483925	n:770000
KS ci ratio: 1.513768e-01	ci left: 8.042581e-04	ci right 9.372054e-04	k: 669	n:770000
C9orf41   770000 perm   390 sec   (1975 perm/sec)   p_kst 8.688312e-04   p_cons 6.284740e-01   p_joint 8.688312e-04

Joint ci ratio: 1.501490e-01	ci left: 8.075178e-04	ci right 9.398240e-04	k: 680	n:780000
Cons ci ratio: 3.411934e-03	ci left: 6.274958e-01	ci right 6.296417e-01	k: 490284	n:780000
KS ci ratio: 1.501490e-01	ci left: 8.075178e-04	ci right 9.398240e-04	k: 680	n:780000
C9orf41   780000 perm   398 sec   (1960 perm/sec)   p_kst 8.717949e-04   p_cons 6.285692e-01   p_joint 8.717949e-04

Joint ci ratio: 1.489507e-01	ci left: 8.106992e-04	ci right 9.423720e-04	k: 691	n:790000
Cons ci ratio: 3.389864e-03	ci left: 6.275588e-01	ci right 6.296909e-01	k: 496614	n:790000
KS ci ratio: 1.489507e-01	ci left: 8.106992e-04	ci right 9.423720e-04	k: 691	n:790000
C9orf41   790000 perm   406 sec   (1944 perm/sec)   p_kst 8.746835e-04   p_cons 6.286253e-01   p_joint 8.746835e-04

Joint ci ratio: 1.477805e-01	ci left: 8.138051e-04	ci right 9.448523e-04	k: 702	n:800000
Cons ci ratio: 3.368703e-03	ci left: 6.275526e-01	ci right 6.296714e-01	k: 502890	n:800000
KS ci ratio: 1.477805e-01	ci left: 8.138051e-04	ci right 9.448523e-04	k: 702	n:800000
C9orf41   800000 perm   415 sec   (1929 perm/sec)   p_kst 8.775000e-04   p_cons 6.286125e-01   p_joint 8.775000e-04

Joint ci ratio: 1.469469e-01	ci left: 8.132705e-04	ci right 9.434280e-04	k: 710	n:810000
Cons ci ratio: 3.348358e-03	ci left: 6.274874e-01	ci right 6.295932e-01	k: 509118	n:810000
KS ci ratio: 1.469469e-01	ci left: 8.132705e-04	ci right 9.434280e-04	k: 710	n:810000
C9orf41   810000 perm   423 sec   (1914 perm/sec)   p_kst 8.765432e-04   p_cons 6.285407e-01   p_joint 8.765432e-04

Joint ci ratio: 1.461271e-01	ci left: 8.127509e-04	ci right 9.420363e-04	k: 718	n:820000
Cons ci ratio: 3.327613e-03	ci left: 6.275312e-01	ci right 6.296240e-01	k: 515434	n:820000
KS ci ratio: 1.461271e-01	ci left: 8.127509e-04	ci right 9.420363e-04	k: 718	n:820000
C9orf41   820000 perm   432 sec   (1899 perm/sec)   p_kst 8.756098e-04   p_cons 6.285780e-01   p_joint 8.756098e-04

Joint ci ratio: 1.444290e-01	ci left: 8.226965e-04	ci right 9.519120e-04	k: 735	n:830000
Cons ci ratio: 3.307496e-03	ci left: 6.275390e-01	ci right 6.296192e-01	k: 521721	n:830000
KS ci ratio: 1.444290e-01	ci left: 8.226965e-04	ci right 9.519120e-04	k: 735	n:830000
C9orf41   830000 perm   441 sec   (1884 perm/sec)   p_kst 8.855422e-04   p_cons 6.285795e-01   p_joint 8.855422e-04

Joint ci ratio: 1.429788e-01	ci left: 8.301178e-04	ci right 9.590782e-04	k: 750	n:840000
Cons ci ratio: 3.287673e-03	ci left: 6.275562e-01	ci right 6.296239e-01	k: 528016	n:840000
KS ci ratio: 1.429788e-01	ci left: 8.301178e-04	ci right 9.590782e-04	k: 750	n:840000
C9orf41   840000 perm   449 sec   (1870 perm/sec)   p_kst 8.928571e-04   p_cons 6.285905e-01   p_joint 8.928571e-04

Joint ci ratio: 1.421297e-01	ci left: 8.305624e-04	ci right 9.587605e-04	k: 759	n:850000
Cons ci ratio: 3.268020e-03	ci left: 6.275989e-01	ci right 6.296544e-01	k: 534333	n:850000
KS ci ratio: 1.421297e-01	ci left: 8.305624e-04	ci right 9.587605e-04	k: 759	n:850000
C9orf41   850000 perm   458 sec   (1855 perm/sec)   p_kst 8.929412e-04   p_cons 6.286271e-01   p_joint 8.929412e-04

Joint ci ratio: 1.413876e-01	ci left: 8.298770e-04	ci right 9.572442e-04	k: 767	n:860000
Cons ci ratio: 3.249112e-03	ci left: 6.275836e-01	ci right 6.296271e-01	k: 540601	n:860000
KS ci ratio: 1.413876e-01	ci left: 8.298770e-04	ci right 9.572442e-04	k: 767	n:860000
C9orf41   860000 perm   467 sec   (1841 perm/sec)   p_kst 8.918605e-04   p_cons 6.286058e-01   p_joint 8.918605e-04

Joint ci ratio: 1.408387e-01	ci left: 8.269912e-04	ci right 9.533814e-04	k: 773	n:870000
Cons ci ratio: 3.230529e-03	ci left: 6.275687e-01	ci right 6.296005e-01	k: 546869	n:870000
KS ci ratio: 1.408387e-01	ci left: 8.269912e-04	ci right 9.533814e-04	k: 773	n:870000
C9orf41   870000 perm   476 sec   (1827 perm/sec)   p_kst 8.885057e-04   p_cons 6.285851e-01   p_joint 8.885057e-04

Joint ci ratio: 1.396703e-01	ci left: 8.318481e-04	ci right 9.578381e-04	k: 786	n:880000
Cons ci ratio: 3.212433e-03	ci left: 6.275292e-01	ci right 6.295495e-01	k: 553115	n:880000
KS ci ratio: 1.396703e-01	ci left: 8.318481e-04	ci right 9.578381e-04	k: 786	n:880000
C9orf41   880000 perm   485 sec   (1813 perm/sec)   p_kst 8.931818e-04   p_cons 6.285398e-01   p_joint 8.931818e-04

Joint ci ratio: 1.393171e-01	ci left: 8.268388e-04	ci right 9.517272e-04	k: 790	n:890000
Cons ci ratio: 3.193892e-03	ci left: 6.275997e-01	ci right 6.296085e-01	k: 559458	n:890000
KS ci ratio: 1.393171e-01	ci left: 8.268388e-04	ci right 9.517272e-04	k: 790	n:890000
C9orf41   890000 perm   495 sec   (1799 perm/sec)   p_kst 8.876404e-04   p_cons 6.286045e-01   p_joint 8.876404e-04

Joint ci ratio: 1.387920e-01	ci left: 8.240864e-04	ci right 9.480510e-04	k: 796	n:900000
Cons ci ratio: 3.176250e-03	ci left: 6.275830e-01	ci right 6.295806e-01	k: 565724	n:900000
KS ci ratio: 1.387920e-01	ci left: 8.240864e-04	ci right 9.480510e-04	k: 796	n:900000
C9orf41   900000 perm   504 sec   (1786 perm/sec)   p_kst 8.844444e-04   p_cons 6.285822e-01   p_joint 8.844444e-04

Joint ci ratio: 1.384453e-01	ci left: 8.192735e-04	ci right 9.421810e-04	k: 800	n:910000
Cons ci ratio: 3.158540e-03	ci left: 6.276195e-01	ci right 6.296061e-01	k: 572038	n:910000
KS ci ratio: 1.384453e-01	ci left: 8.192735e-04	ci right 9.421810e-04	k: 800	n:910000
C9orf41   910000 perm   513 sec   (1772 perm/sec)   p_kst 8.791209e-04   p_cons 6.286132e-01   p_joint 8.791209e-04

Joint ci ratio: 1.379299e-01	ci left: 8.166646e-04	ci right 9.386871e-04	k: 806	n:920000
Cons ci ratio: 3.141160e-03	ci left: 6.276498e-01	ci right 6.296255e-01	k: 578347	n:920000
KS ci ratio: 1.379299e-01	ci left: 8.166646e-04	ci right 9.386871e-04	k: 806	n:920000
C9orf41   920000 perm   523 sec   (1760 perm/sec)   p_kst 8.760870e-04   p_cons 6.286380e-01   p_joint 8.760870e-04

Joint ci ratio: 1.371672e-01	ci left: 8.172276e-04	ci right 9.386039e-04	k: 815	n:930000
Cons ci ratio: 3.124467e-03	ci left: 6.276192e-01	ci right 6.295843e-01	k: 584600	n:930000
KS ci ratio: 1.371672e-01	ci left: 8.172276e-04	ci right 9.386039e-04	k: 815	n:930000
C9orf41   930000 perm   532 sec   (1747 perm/sec)   p_kst 8.763441e-04   p_cons 6.286022e-01   p_joint 8.763441e-04

Joint ci ratio: 1.364997e-01	ci left: 8.167530e-04	ci right 9.374206e-04	k: 823	n:940000
Cons ci ratio: 3.107484e-03	ci left: 6.276723e-01	ci right 6.296269e-01	k: 590931	n:940000
KS ci ratio: 1.364997e-01	ci left: 8.167530e-04	ci right 9.374206e-04	k: 823	n:940000
C9orf41   940000 perm   542 sec   (1734 perm/sec)   p_kst 8.755319e-04   p_cons 6.286500e-01   p_joint 8.755319e-04

Joint ci ratio: 1.357603e-01	ci left: 8.173067e-04	ci right 9.373491e-04	k: 832	n:950000
Cons ci ratio: 3.091076e-03	ci left: 6.276791e-01	ci right 6.296233e-01	k: 597219	n:950000
KS ci ratio: 1.357603e-01	ci left: 8.173067e-04	ci right 9.373491e-04	k: 832	n:950000
C9orf41   950000 perm   552 sec   (1721 perm/sec)   p_kst 8.757895e-04   p_cons 6.286516e-01   p_joint 8.757895e-04

Joint ci ratio: 1.349526e-01	ci left: 8.188570e-04	ci right 9.383542e-04	k: 842	n:960000
Cons ci ratio: 3.075061e-03	ci left: 6.276649e-01	ci right 6.295989e-01	k: 603487	n:960000
KS ci ratio: 1.349526e-01	ci left: 8.188570e-04	ci right 9.383542e-04	k: 842	n:960000
C9orf41   960000 perm   562 sec   (1708 perm/sec)   p_kst 8.770833e-04   p_cons 6.286323e-01   p_joint 8.770833e-04

Joint ci ratio: 1.339236e-01	ci left: 8.233666e-04	ci right 9.425328e-04	k: 855	n:970000
Cons ci ratio: 3.059455e-03	ci left: 6.276262e-01	ci right 6.295503e-01	k: 609731	n:970000
KS ci ratio: 1.339236e-01	ci left: 8.233666e-04	ci right 9.425328e-04	k: 855	n:970000
C9orf41   970000 perm   572 sec   (1695 perm/sec)   p_kst 8.814433e-04   p_cons 6.285887e-01   p_joint 8.814433e-04

Joint ci ratio: 1.333022e-01	ci left: 8.228553e-04	ci right 9.413512e-04	k: 863	n:980000
Cons ci ratio: 3.043306e-03	ci left: 6.277078e-01	ci right 6.296220e-01	k: 616092	n:980000
KS ci ratio: 1.333022e-01	ci left: 8.228553e-04	ci right 9.413512e-04	k: 863	n:980000
C9orf41   980000 perm   583 sec   (1682 perm/sec)   p_kst 8.806122e-04   p_cons 6.286653e-01   p_joint 8.806122e-04

Joint ci ratio: 1.330718e-01	ci left: 8.174728e-04	ci right 9.349740e-04	k: 866	n:990000
Cons ci ratio: 3.027652e-03	ci left: 6.277504e-01	ci right 6.296549e-01	k: 622416	n:990000
KS ci ratio: 1.330718e-01	ci left: 8.174728e-04	ci right 9.349740e-04	k: 866	n:990000
C9orf41   990000 perm   593 sec   (1670 perm/sec)   p_kst 8.747475e-04   p_cons 6.287030e-01   p_joint 8.747475e-04

Joint ci ratio: 1.326900e-01	ci left: 8.141318e-04	ci right 9.307905e-04	k: 871	n:1000000
Cons ci ratio: 3.011857e-03	ci left: 6.278512e-01	ci right 6.297460e-01	k: 628799	n:1000000
KS ci ratio: 1.326900e-01	ci left: 8.141318e-04	ci right 9.307905e-04	k: 871	n:1000000
C9orf41   1000000 perm   603 sec   (1658 perm/sec)   p_kst 8.710000e-04   p_cons 6.287990e-01   p_joint 8.710000e-04

Joint ci ratio: 1.320855e-01	ci left: 8.137295e-04	ci right 9.297577e-04	k: 879	n:1010000
Cons ci ratio: 2.996820e-03	ci left: 6.278698e-01	ci right 6.297552e-01	k: 635101	n:1010000
KS ci ratio: 1.320855e-01	ci left: 8.137295e-04	ci right 9.297577e-04	k: 879	n:1010000
C9orf41   1010000 perm   614 sec   (1646 perm/sec)   p_kst 8.702970e-04   p_cons 6.288129e-01   p_joint 8.702970e-04

Joint ci ratio: 1.311203e-01	ci left: 8.180774e-04	ci right 9.338067e-04	k: 892	n:1020000
Cons ci ratio: 2.981901e-03	ci left: 6.279047e-01	ci right 6.297808e-01	k: 641420	n:1020000
KS ci ratio: 1.311203e-01	ci left: 8.180774e-04	ci right 9.338067e-04	k: 892	n:1020000
C9orf41   1020000 perm   624 sec   (1634 perm/sec)   p_kst 8.745098e-04   p_cons 6.288431e-01   p_joint 8.745098e-04

Joint ci ratio: 1.304645e-01	ci left: 8.185869e-04	ci right 9.337642e-04	k: 901	n:1030000
Cons ci ratio: 2.967171e-03	ci left: 6.279438e-01	ci right 6.298108e-01	k: 647744	n:1030000
KS ci ratio: 1.304645e-01	ci left: 8.185869e-04	ci right 9.337642e-04	k: 901	n:1030000
C9orf41   1030000 perm   635 sec   (1623 perm/sec)   p_kst 8.747573e-04   p_cons 6.288777e-01   p_joint 8.747573e-04

Joint ci ratio: 1.301046e-01	ci left: 8.153668e-04	ci right 9.297502e-04	k: 906	n:1040000
Cons ci ratio: 2.952584e-03	ci left: 6.279938e-01	ci right 6.298517e-01	k: 654080	n:1040000
KS ci ratio: 1.301046e-01	ci left: 8.153668e-04	ci right 9.297502e-04	k: 906	n:1040000
C9orf41   1040000 perm   645 sec   (1612 perm/sec)   p_kst 8.711538e-04   p_cons 6.289231e-01   p_joint 8.711538e-04

Joint ci ratio: 1.293226e-01	ci left: 8.177377e-04	ci right 9.317113e-04	k: 917	n:1050000
Cons ci ratio: 2.938258e-03	ci left: 6.280352e-01	ci right 6.298841e-01	k: 660408	n:1050000
KS ci ratio: 1.293226e-01	ci left: 8.177377e-04	ci right 9.317113e-04	k: 917	n:1050000
C9orf41   1050000 perm   656 sec   (1601 perm/sec)   p_kst 8.733333e-04   p_cons 6.289600e-01   p_joint 8.733333e-04

Joint ci ratio: 1.284854e-01	ci left: 8.209790e-04	ci right 9.346070e-04	k: 929	n:1060000
Cons ci ratio: 2.924741e-03	ci left: 6.279795e-01	ci right 6.298198e-01	k: 666634	n:1060000
KS ci ratio: 1.284854e-01	ci left: 8.209790e-04	ci right 9.346070e-04	k: 929	n:1060000
C9orf41   1060000 perm   667 sec   (1590 perm/sec)   p_kst 8.764151e-04   p_cons 6.289000e-01   p_joint 8.764151e-04

Joint ci ratio: 1.277321e-01	ci left: 8.232573e-04	ci right 9.364820e-04	k: 940	n:1070000
Cons ci ratio: 2.911240e-03	ci left: 6.279520e-01	ci right 6.297837e-01	k: 672889	n:1070000
KS ci ratio: 1.277321e-01	ci left: 8.232573e-04	ci right 9.364820e-04	k: 940	n:1070000
C9orf41   1070000 perm   677 sec   (1579 perm/sec)   p_kst 8.785047e-04   p_cons 6.288682e-01   p_joint 8.785047e-04

Joint ci ratio: 1.270587e-01	ci left: 8.245987e-04	ci right 9.373650e-04	k: 950	n:1080000
Cons ci ratio: 2.897591e-03	ci left: 6.279788e-01	ci right 6.298020e-01	k: 679202	n:1080000
KS ci ratio: 1.270587e-01	ci left: 8.245987e-04	ci right 9.373650e-04	k: 950	n:1080000
C9orf41   1080000 perm   689 sec   (1568 perm/sec)   p_kst 8.796296e-04   p_cons 6.288907e-01   p_joint 8.796296e-04

Joint ci ratio: 1.266599e-01	ci left: 8.223634e-04	ci right 9.344446e-04	k: 956	n:1090000
Cons ci ratio: 2.884467e-03	ci left: 6.279510e-01	ci right 6.297658e-01	k: 685456	n:1090000
KS ci ratio: 1.266599e-01	ci left: 8.223634e-04	ci right 9.344446e-04	k: 956	n:1090000
C9orf41   1090000 perm   700 sec   (1558 perm/sec)   p_kst 8.770642e-04   p_cons 6.288587e-01   p_joint 8.770642e-04

Joint ci ratio: 1.263963e-01	ci left: 8.184086e-04	ci right 9.297012e-04	k: 960	n:1100000
Cons ci ratio: 2.871010e-03	ci left: 6.280064e-01	ci right 6.298129e-01	k: 691801	n:1100000
KS ci ratio: 1.263963e-01	ci left: 8.184086e-04	ci right 9.297012e-04	k: 960	n:1100000
C9orf41   1100000 perm   711 sec   (1548 perm/sec)   p_kst 8.727273e-04   p_cons 6.289100e-01   p_joint 8.727273e-04

Joint ci ratio: 1.257437e-01	ci left: 8.197604e-04	ci right 9.306184e-04	k: 970	n:1110000
Cons ci ratio: 2.858054e-03	ci left: 6.280095e-01	ci right 6.298078e-01	k: 698089	n:1110000
KS ci ratio: 1.257437e-01	ci left: 8.197604e-04	ci right 9.306184e-04	k: 970	n:1110000
C9orf41   1110000 perm   722 sec   (1538 perm/sec)   p_kst 8.738739e-04   p_cons 6.289090e-01   p_joint 8.738739e-04

Joint ci ratio: 1.251650e-01	ci left: 8.202247e-04	ci right 9.305971e-04	k: 979	n:1120000
Cons ci ratio: 2.844859e-03	ci left: 6.280805e-01	ci right 6.298707e-01	k: 704453	n:1120000
KS ci ratio: 1.251650e-01	ci left: 8.202247e-04	ci right 9.305971e-04	k: 979	n:1120000
C9orf41   1120000 perm   733 sec   (1527 perm/sec)   p_kst 8.741071e-04   p_cons 6.289759e-01   p_joint 8.741071e-04

Joint ci ratio: 1.246572e-01	ci left: 8.198245e-04	ci right 9.296625e-04	k: 987	n:1130000
Cons ci ratio: 2.831952e-03	ci left: 6.281325e-01	ci right 6.299147e-01	k: 710797	n:1130000
KS ci ratio: 1.246572e-01	ci left: 8.198245e-04	ci right 9.296625e-04	k: 987	n:1130000
C9orf41   1130000 perm   745 sec   (1517 perm/sec)   p_kst 8.734513e-04   p_cons 6.290239e-01   p_joint 8.734513e-04

Joint ci ratio: 1.241556e-01	ci left: 8.194322e-04	ci right 9.287434e-04	k: 995	n:1140000
Cons ci ratio: 2.819500e-03	ci left: 6.281370e-01	ci right 6.299114e-01	k: 717088	n:1140000
KS ci ratio: 1.241556e-01	ci left: 8.194322e-04	ci right 9.287434e-04	k: 995	n:1140000
C9orf41   1140000 perm   756 sec   (1507 perm/sec)   p_kst 8.728070e-04   p_cons 6.290246e-01   p_joint 8.728070e-04

Joint ci ratio: 1.240315e-01	ci left: 8.139917e-04	ci right 9.224606e-04	k: 997	n:1150000
Cons ci ratio: 2.807582e-03	ci left: 6.280798e-01	ci right 6.298465e-01	k: 723308	n:1150000
KS ci ratio: 1.240315e-01	ci left: 8.139917e-04	ci right 9.224606e-04	k: 997	n:1150000
C9orf41   1150000 perm   768 sec   (1497 perm/sec)   p_kst 8.669565e-04   p_cons 6.289635e-01   p_joint 8.669565e-04

Joint ci ratio: 1.233535e-01	ci left: 8.161639e-04	ci right 9.242843e-04	k: 1008	n:1160000
Cons ci ratio: 2.795447e-03	ci left: 6.280848e-01	ci right 6.298439e-01	k: 729599	n:1160000
KS ci ratio: 1.233535e-01	ci left: 8.161639e-04	ci right 9.242843e-04	k: 1008	n:1160000
C9orf41   1160000 perm   780 sec   (1488 perm/sec)   p_kst 8.689655e-04   p_cons 6.289647e-01   p_joint 8.689655e-04

Joint ci ratio: 1.228070e-01	ci left: 8.166437e-04	ci right 9.243134e-04	k: 1017	n:1170000
Cons ci ratio: 2.783738e-03	ci left: 6.280444e-01	ci right 6.297960e-01	k: 735837	n:1170000
KS ci ratio: 1.228070e-01	ci left: 8.166437e-04	ci right 9.243134e-04	k: 1017	n:1170000
C9orf41   1170000 perm   791 sec   (1479 perm/sec)   p_kst 8.692308e-04   p_cons 6.289205e-01   p_joint 8.692308e-04

Joint ci ratio: 1.222677e-01	ci left: 8.171163e-04	ci right 9.243411e-04	k: 1026	n:1180000
Cons ci ratio: 2.772105e-03	ci left: 6.280166e-01	ci right 6.297607e-01	k: 742089	n:1180000
KS ci ratio: 1.222677e-01	ci left: 8.171163e-04	ci right 9.243411e-04	k: 1026	n:1180000
C9orf41   1180000 perm   803 sec   (1469 perm/sec)   p_kst 8.694915e-04   p_cons 6.288890e-01   p_joint 8.694915e-04

Joint ci ratio: 1.218532e-01	ci left: 8.159525e-04	ci right 9.226354e-04	k: 1033	n:1190000
Cons ci ratio: 2.760064e-03	ci left: 6.280826e-01	ci right 6.298193e-01	k: 748452	n:1190000
KS ci ratio: 1.218532e-01	ci left: 8.159525e-04	ci right 9.226354e-04	k: 1033	n:1190000
C9orf41   1190000 perm   815 sec   (1461 perm/sec)   p_kst 8.680672e-04   p_cons 6.289513e-01   p_joint 8.680672e-04

Joint ci ratio: 1.215013e-01	ci left: 8.140007e-04	ci right 9.200989e-04	k: 1039	n:1200000
Cons ci ratio: 2.748327e-03	ci left: 6.281225e-01	ci right 6.298519e-01	k: 754785	n:1200000
KS ci ratio: 1.215013e-01	ci left: 8.140007e-04	ci right 9.200989e-04	k: 1039	n:1200000
C9orf41   1200000 perm   827 sec   (1452 perm/sec)   p_kst 8.658333e-04   p_cons 6.289875e-01   p_joint 8.658333e-04

Joint ci ratio: 1.207488e-01	ci left: 8.176918e-04	ci right 9.235639e-04	k: 1052	n:1210000
Cons ci ratio: 2.736951e-03	ci left: 6.281253e-01	ci right 6.298476e-01	k: 761074	n:1210000
KS ci ratio: 1.207488e-01	ci left: 8.176918e-04	ci right 9.235639e-04	k: 1052	n:1210000
C9orf41   1210000 perm   839 sec   (1443 perm/sec)   p_kst 8.694215e-04   p_cons 6.289868e-01   p_joint 8.694215e-04

Joint ci ratio: 1.202360e-01	ci left: 8.181441e-04	ci right 9.235929e-04	k: 1061	n:1220000
Cons ci ratio: 2.725715e-03	ci left: 6.281281e-01	ci right 6.298434e-01	k: 767363	n:1220000
KS ci ratio: 1.202360e-01	ci left: 8.181441e-04	ci right 9.235929e-04	k: 1061	n:1220000
C9orf41   1220000 perm   851 sec   (1434 perm/sec)   p_kst 8.696721e-04   p_cons 6.289861e-01   p_joint 8.696721e-04

Joint ci ratio: 1.198418e-01	ci left: 8.170127e-04	ci right 9.219460e-04	k: 1068	n:1230000
Cons ci ratio: 2.714564e-03	ci left: 6.281399e-01	ci right 6.298481e-01	k: 773663	n:1230000
KS ci ratio: 1.198418e-01	ci left: 8.170127e-04	ci right 9.219460e-04	k: 1068	n:1230000
C9orf41   1230000 perm   863 sec   (1425 perm/sec)   p_kst 8.682927e-04   p_cons 6.289943e-01   p_joint 8.682927e-04

Joint ci ratio: 1.195070e-01	ci left: 8.151177e-04	ci right 9.194945e-04	k: 1074	n:1240000
Cons ci ratio: 2.703717e-03	ci left: 6.281224e-01	ci right 6.298238e-01	k: 779927	n:1240000
KS ci ratio: 1.195070e-01	ci left: 8.151177e-04	ci right 9.194945e-04	k: 1074	n:1240000
C9orf41   1240000 perm   875 sec   (1417 perm/sec)   p_kst 8.661290e-04   p_cons 6.289734e-01   p_joint 8.661290e-04

Joint ci ratio: 1.192855e-01	ci left: 8.117011e-04	ci right 9.154341e-04	k: 1078	n:1250000
Cons ci ratio: 2.692921e-03	ci left: 6.281188e-01	ci right 6.298134e-01	k: 786208	n:1250000
KS ci ratio: 1.192855e-01	ci left: 8.117011e-04	ci right 9.154341e-04	k: 1078	n:1250000
C9orf41   1250000 perm   888 sec   (1408 perm/sec)   p_kst 8.624000e-04   p_cons 6.289664e-01   p_joint 8.624000e-04

Joint ci ratio: 1.186275e-01	ci left: 8.144995e-04	ci right 9.179758e-04	k: 1090	n:1260000
Cons ci ratio: 2.682103e-03	ci left: 6.281415e-01	ci right 6.298293e-01	k: 792522	n:1260000
KS ci ratio: 1.186275e-01	ci left: 8.144995e-04	ci right 9.179758e-04	k: 1090	n:1260000
C9orf41   1260000 perm   900 sec   (1400 perm/sec)   p_kst 8.650794e-04   p_cons 6.289857e-01   p_joint 8.650794e-04

Joint ci ratio: 1.183568e-01	ci left: 8.119064e-04	ci right 9.148013e-04	k: 1095	n:1270000
Cons ci ratio: 2.671499e-03	ci left: 6.281489e-01	ci right 6.298300e-01	k: 798817	n:1270000
KS ci ratio: 1.183568e-01	ci left: 8.119064e-04	ci right 9.148013e-04	k: 1095	n:1270000
C9orf41   1270000 perm   912 sec   (1392 perm/sec)   p_kst 8.622047e-04   p_cons 6.289898e-01   p_joint 8.622047e-04

Joint ci ratio: 1.179807e-01	ci left: 8.108704e-04	ci right 9.132848e-04	k: 1102	n:1280000
Cons ci ratio: 2.660798e-03	ci left: 6.281953e-01	ci right 6.298698e-01	k: 805162	n:1280000
KS ci ratio: 1.179807e-01	ci left: 8.108704e-04	ci right 9.132848e-04	k: 1102	n:1280000
C9orf41   1280000 perm   925 sec   (1384 perm/sec)   p_kst 8.609375e-04   p_cons 6.290328e-01   p_joint 8.609375e-04

Joint ci ratio: 1.177144e-01	ci left: 8.083463e-04	ci right 9.101953e-04	k: 1107	n:1290000
Cons ci ratio: 2.650413e-03	ci left: 6.282076e-01	ci right 6.298756e-01	k: 811464	n:1290000
KS ci ratio: 1.177144e-01	ci left: 8.083463e-04	ci right 9.101953e-04	k: 1107	n:1290000
C9orf41   1290000 perm   938 sec   (1376 perm/sec)   p_kst 8.581395e-04   p_cons 6.290419e-01   p_joint 8.581395e-04

Joint ci ratio: 1.173443e-01	ci left: 8.073545e-04	ci right 9.087367e-04	k: 1114	n:1300000
Cons ci ratio: 2.640149e-03	ci left: 6.282197e-01	ci right 6.298812e-01	k: 817766	n:1300000
KS ci ratio: 1.173443e-01	ci left: 8.073545e-04	ci right 9.087367e-04	k: 1114	n:1300000
C9orf41   1300000 perm   951 sec   (1368 perm/sec)   p_kst 8.569231e-04   p_cons 6.290508e-01   p_joint 8.569231e-04

Joint ci ratio: 1.167697e-01	ci left: 8.093426e-04	ci right 9.104424e-04	k: 1125	n:1310000
Cons ci ratio: 2.630382e-03	ci left: 6.281645e-01	ci right 6.298197e-01	k: 823980	n:1310000
KS ci ratio: 1.167697e-01	ci left: 8.093426e-04	ci right 9.104424e-04	k: 1125	n:1310000
C9orf41   1310000 perm   964 sec   (1359 perm/sec)   p_kst 8.587786e-04   p_cons 6.289924e-01   p_joint 8.587786e-04

Joint ci ratio: 1.163057e-01	ci left: 8.098307e-04	ci right 9.105619e-04	k: 1134	n:1320000
Cons ci ratio: 2.620480e-03	ci left: 6.281533e-01	ci right 6.298022e-01	k: 830251	n:1320000
KS ci ratio: 1.163057e-01	ci left: 8.098307e-04	ci right 9.105619e-04	k: 1134	n:1320000
C9orf41   1320000 perm   977 sec   (1351 perm/sec)   p_kst 8.590909e-04   p_cons 6.289780e-01   p_joint 8.590909e-04

Joint ci ratio: 1.156452e-01	ci left: 8.132327e-04	ci right 9.137734e-04	k: 1147	n:1330000
Cons ci ratio: 2.610521e-03	ci left: 6.281723e-01	ci right 6.298151e-01	k: 836562	n:1330000
KS ci ratio: 1.156452e-01	ci left: 8.132327e-04	ci right 9.137734e-04	k: 1147	n:1330000
C9orf41   1330000 perm   990 sec   (1344 perm/sec)   p_kst 8.624060e-04   p_cons 6.289940e-01   p_joint 8.624060e-04

Joint ci ratio: 1.153442e-01	ci left: 8.115120e-04	ci right 9.115611e-04	k: 1153	n:1340000
Cons ci ratio: 2.600683e-03	ci left: 6.281896e-01	ci right 6.298262e-01	k: 842871	n:1340000
KS ci ratio: 1.153442e-01	ci left: 8.115120e-04	ci right 9.115611e-04	k: 1153	n:1340000
C9orf41   1340000 perm   1003 sec   (1336 perm/sec)   p_kst 8.604478e-04   p_cons 6.290082e-01   p_joint 8.604478e-04

Joint ci ratio: 1.148476e-01	ci left: 8.126950e-04	ci right 9.124293e-04	k: 1163	n:1350000
Cons ci ratio: 2.591066e-03	ci left: 6.281867e-01	ci right 6.298172e-01	k: 849153	n:1350000
KS ci ratio: 1.148476e-01	ci left: 8.126950e-04	ci right 9.124293e-04	k: 1163	n:1350000
C9orf41   1350000 perm   1016 sec   (1328 perm/sec)   p_kst 8.614815e-04   p_cons 6.290022e-01   p_joint 8.614815e-04

Joint ci ratio: 1.144062e-01	ci left: 8.131472e-04	ci right 9.125276e-04	k: 1172	n:1360000
Cons ci ratio: 2.581396e-03	ci left: 6.282125e-01	ci right 6.298370e-01	k: 855474	n:1360000
KS ci ratio: 1.144062e-01	ci left: 8.131472e-04	ci right 9.125276e-04	k: 1172	n:1360000
C9orf41   1360000 perm   1029 sec   (1321 perm/sec)   p_kst 8.617647e-04   p_cons 6.290250e-01   p_joint 8.617647e-04

Joint ci ratio: 1.138734e-01	ci left: 8.150119e-04	ci right 9.141251e-04	k: 1183	n:1370000
Cons ci ratio: 2.571903e-03	ci left: 6.282255e-01	ci right 6.298440e-01	k: 861778	n:1370000
KS ci ratio: 1.138734e-01	ci left: 8.150119e-04	ci right 9.141251e-04	k: 1183	n:1370000
C9orf41   1370000 perm   1043 sec   (1313 perm/sec)   p_kst 8.635036e-04   p_cons 6.290350e-01   p_joint 8.635036e-04

Joint ci ratio: 1.136339e-01	ci left: 8.126260e-04	ci right 9.112273e-04	k: 1188	n:1380000
Cons ci ratio: 2.562533e-03	ci left: 6.282347e-01	ci right 6.298474e-01	k: 868077	n:1380000
KS ci ratio: 1.136339e-01	ci left: 8.126260e-04	ci right 9.112273e-04	k: 1188	n:1380000
C9orf41   1380000 perm   1057 sec   (1306 perm/sec)   p_kst 8.608696e-04   p_cons 6.290413e-01   p_joint 8.608696e-04

Joint ci ratio: 1.132535e-01	ci left: 8.123719e-04	ci right 9.105903e-04	k: 1196	n:1390000
Cons ci ratio: 2.553040e-03	ci left: 6.282848e-01	ci right 6.298916e-01	k: 874433	n:1390000
KS ci ratio: 1.132535e-01	ci left: 8.123719e-04	ci right 9.105903e-04	k: 1196	n:1390000
C9orf41   1390000 perm   1070 sec   (1299 perm/sec)   p_kst 8.604317e-04   p_cons 6.290885e-01   p_joint 8.604317e-04

Joint ci ratio: 1.129709e-01	ci left: 8.107337e-04	ci right 9.084931e-04	k: 1202	n:1400000
Cons ci ratio: 2.543987e-03	ci left: 6.282728e-01	ci right 6.298738e-01	k: 880703	n:1400000
KS ci ratio: 1.129709e-01	ci left: 8.107337e-04	ci right 9.084931e-04	k: 1202	n:1400000
C9orf41   1400000 perm   1084 sec   (1291 perm/sec)   p_kst 8.585714e-04   p_cons 6.290736e-01   p_joint 8.585714e-04

Joint ci ratio: 1.125971e-01	ci left: 8.104975e-04	ci right 9.078836e-04	k: 1210	n:1410000
Cons ci ratio: 2.534895e-03	ci left: 6.282858e-01	ci right 6.298811e-01	k: 887008	n:1410000
KS ci ratio: 1.125971e-01	ci left: 8.104975e-04	ci right 9.078836e-04	k: 1210	n:1410000
C9orf41   1410000 perm   1098 sec   (1284 perm/sec)   p_kst 8.581560e-04   p_cons 6.290837e-01   p_joint 8.581560e-04

Joint ci ratio: 1.121350e-01	ci left: 8.116341e-04	ci right 9.087302e-04	k: 1220	n:1420000
Cons ci ratio: 2.525755e-03	ci left: 6.283253e-01	ci right 6.299150e-01	k: 893351	n:1420000
KS ci ratio: 1.121350e-01	ci left: 8.116341e-04	ci right 9.087302e-04	k: 1220	n:1420000
C9orf41   1420000 perm   1112 sec   (1277 perm/sec)   p_kst 8.591549e-04   p_cons 6.291204e-01   p_joint 8.591549e-04

Joint ci ratio: 1.116786e-01	ci left: 8.127556e-04	ci right 9.095640e-04	k: 1230	n:1430000
Cons ci ratio: 2.517097e-03	ci left: 6.282930e-01	ci right 6.298771e-01	k: 899592	n:1430000
KS ci ratio: 1.116786e-01	ci left: 8.127556e-04	ci right 9.095640e-04	k: 1230	n:1430000
C9orf41   1430000 perm   1126 sec   (1270 perm/sec)   p_kst 8.601399e-04   p_cons 6.290853e-01   p_joint 8.601399e-04

Joint ci ratio: 1.110487e-01	ci left: 8.165630e-04	ci right 9.132404e-04	k: 1244	n:1440000
Cons ci ratio: 2.508304e-03	ci left: 6.283028e-01	ci right 6.298814e-01	k: 905893	n:1440000
KS ci ratio: 1.110487e-01	ci left: 8.165630e-04	ci right 9.132404e-04	k: 1244	n:1440000
C9orf41   1440000 perm   1140 sec   (1264 perm/sec)   p_kst 8.638889e-04   p_cons 6.290924e-01   p_joint 8.638889e-04

Joint ci ratio: 1.106936e-01	ci left: 8.162958e-04	ci right 9.126124e-04	k: 1252	n:1450000
Cons ci ratio: 2.499850e-03	ci left: 6.282662e-01	ci right 6.298394e-01	k: 912127	n:1450000
KS ci ratio: 1.106936e-01	ci left: 8.162958e-04	ci right 9.126124e-04	k: 1252	n:1450000
C9orf41   1450000 perm   1154 sec   (1257 perm/sec)   p_kst 8.634483e-04   p_cons 6.290531e-01   p_joint 8.634483e-04

Joint ci ratio: 1.102982e-01	ci left: 8.166987e-04	ci right 9.126963e-04	k: 1261	n:1460000
Cons ci ratio: 2.491258e-03	ci left: 6.282720e-01	ci right 6.298398e-01	k: 918422	n:1460000
KS ci ratio: 1.102982e-01	ci left: 8.166987e-04	ci right 9.126963e-04	k: 1261	n:1460000
C9orf41   1460000 perm   1168 sec   (1250 perm/sec)   p_kst 8.636986e-04   p_cons 6.290562e-01   p_joint 8.636986e-04

Joint ci ratio: 1.101240e-01	ci left: 8.137890e-04	ci right 9.092836e-04	k: 1265	n:1470000
Cons ci ratio: 2.482768e-03	ci left: 6.282750e-01	ci right 6.298374e-01	k: 924713	n:1470000
KS ci ratio: 1.101240e-01	ci left: 8.137890e-04	ci right 9.092836e-04	k: 1265	n:1470000
C9orf41   1470000 perm   1182 sec   (1243 perm/sec)   p_kst 8.605442e-04   p_cons 6.290565e-01   p_joint 8.605442e-04

Joint ci ratio: 1.098641e-01	ci left: 8.122329e-04	ci right 9.073054e-04	k: 1271	n:1480000
Cons ci ratio: 2.474300e-03	ci left: 6.282901e-01	ci right 6.298472e-01	k: 931022	n:1480000
KS ci ratio: 1.098641e-01	ci left: 8.122329e-04	ci right 9.073054e-04	k: 1271	n:1480000
C9orf41   1480000 perm   1197 sec   (1236 perm/sec)   p_kst 8.587838e-04   p_cons 6.290689e-01   p_joint 8.587838e-04

Joint ci ratio: 1.093920e-01	ci left: 8.139618e-04	ci right 9.088010e-04	k: 1282	n:1490000
Cons ci ratio: 2.466248e-03	ci left: 6.282426e-01	ci right 6.297945e-01	k: 937238	n:1490000
KS ci ratio: 1.093920e-01	ci left: 8.139618e-04	ci right 9.088010e-04	k: 1282	n:1490000
C9orf41   1490000 perm   1211 sec   (1230 perm/sec)   p_kst 8.604027e-04   p_cons 6.290188e-01   p_joint 8.604027e-04

Joint ci ratio: 1.090103e-01	ci left: 8.143715e-04	ci right 9.089061e-04	k: 1291	n:1500000
Cons ci ratio: 2.458243e-03	ci left: 6.282017e-01	ci right 6.297485e-01	k: 943463	n:1500000
KS ci ratio: 1.090103e-01	ci left: 8.143715e-04	ci right 9.089061e-04	k: 1291	n:1500000
C9orf41   1500000 perm   1226 sec   (1223 perm/sec)   p_kst 8.606667e-04   p_cons 6.289753e-01   p_joint 8.606667e-04

Joint ci ratio: 1.086744e-01	ci left: 8.141321e-04	ci right 9.083290e-04	k: 1299	n:1510000
Cons ci ratio: 2.450175e-03	ci left: 6.281878e-01	ci right 6.297295e-01	k: 949728	n:1510000
KS ci ratio: 1.086744e-01	ci left: 8.141321e-04	ci right 9.083290e-04	k: 1299	n:1510000
C9orf41   1510000 perm   1241 sec   (1217 perm/sec)   p_kst 8.602649e-04   p_cons 6.289589e-01   p_joint 8.602649e-04

Joint ci ratio: 1.083416e-01	ci left: 8.138963e-04	ci right 9.077591e-04	k: 1307	n:1520000
Cons ci ratio: 2.442273e-03	ci left: 6.281578e-01	ci right 6.296944e-01	k: 955968	n:1520000
KS ci ratio: 1.083416e-01	ci left: 8.138963e-04	ci right 9.077591e-04	k: 1307	n:1520000
C9orf41   1520000 perm   1256 sec   (1210 perm/sec)   p_kst 8.598684e-04   p_cons 6.289263e-01   p_joint 8.598684e-04

Joint ci ratio: 1.081352e-01	ci left: 8.117562e-04	ci right 9.051825e-04	k: 1312	n:1530000
Cons ci ratio: 2.434365e-03	ci left: 6.281437e-01	ci right 6.296754e-01	k: 962232	n:1530000
KS ci ratio: 1.081352e-01	ci left: 8.117562e-04	ci right 9.051825e-04	k: 1312	n:1530000
C9orf41   1530000 perm   1271 sec   (1204 perm/sec)   p_kst 8.575163e-04   p_cons 6.289098e-01   p_joint 8.575163e-04

Joint ci ratio: 1.078073e-01	ci left: 8.115396e-04	ci right 9.046398e-04	k: 1320	n:1540000
Cons ci ratio: 2.426215e-03	ci left: 6.281910e-01	ci right 6.297176e-01	k: 968590	n:1540000
KS ci ratio: 1.078073e-01	ci left: 8.115396e-04	ci right 9.046398e-04	k: 1320	n:1540000
C9orf41   1540000 perm   1285 sec   (1198 perm/sec)   p_kst 8.571429e-04   p_cons 6.289545e-01   p_joint 8.571429e-04

Joint ci ratio: 1.074419e-01	ci left: 8.119540e-04	ci right 9.047661e-04	k: 1329	n:1550000
Cons ci ratio: 2.418388e-03	ci left: 6.281912e-01	ci right 6.297129e-01	k: 974876	n:1550000
KS ci ratio: 1.074419e-01	ci left: 8.119540e-04	ci right 9.047661e-04	k: 1329	n:1550000
C9orf41   1550000 perm   1300 sec   (1192 perm/sec)   p_kst 8.574194e-04   p_cons 6.289523e-01   p_joint 8.574194e-04

Joint ci ratio: 1.070402e-01	ci left: 8.129875e-04	ci right 9.055484e-04	k: 1339	n:1560000
Cons ci ratio: 2.410411e-03	ci left: 6.282350e-01	ci right 6.297517e-01	k: 981230	n:1560000
KS ci ratio: 1.070402e-01	ci left: 8.129875e-04	ci right 9.055484e-04	k: 1339	n:1560000
C9orf41   1560000 perm   1316 sec   (1186 perm/sec)   p_kst 8.583333e-04   p_cons 6.289936e-01   p_joint 8.583333e-04

Joint ci ratio: 1.066430e-01	ci left: 8.140085e-04	ci right 9.063201e-04	k: 1349	n:1570000
Cons ci ratio: 2.402643e-03	ci left: 6.282527e-01	ci right 6.297646e-01	k: 987544	n:1570000
KS ci ratio: 1.066430e-01	ci left: 8.140085e-04	ci right 9.063201e-04	k: 1349	n:1570000
C9orf41   1570000 perm   1331 sec   (1180 perm/sec)   p_kst 8.592357e-04   p_cons 6.290089e-01   p_joint 8.592357e-04

Joint ci ratio: 1.063676e-01	ci left: 8.131689e-04	ci right 9.051323e-04	k: 1356	n:1580000
Cons ci ratio: 2.395256e-03	ci left: 6.282108e-01	ci right 6.297179e-01	k: 993764	n:1580000
KS ci ratio: 1.063676e-01	ci left: 8.131689e-04	ci right 9.051323e-04	k: 1356	n:1580000
C9orf41   1580000 perm   1346 sec   (1173 perm/sec)   p_kst 8.582278e-04   p_cons 6.289646e-01   p_joint 8.582278e-04

Joint ci ratio: 1.060944e-01	ci left: 8.123401e-04	ci right 9.039591e-04	k: 1363	n:1590000
Cons ci ratio: 2.387501e-03	ci left: 6.282542e-01	ci right 6.297566e-01	k: 1000119	n:1590000
KS ci ratio: 1.060944e-01	ci left: 8.123401e-04	ci right 9.039591e-04	k: 1363	n:1590000
C9orf41   1590000 perm   1362 sec   (1168 perm/sec)   p_kst 8.572327e-04   p_cons 6.290057e-01   p_joint 8.572327e-04

Joint ci ratio: 1.057846e-01	ci left: 8.121305e-04	ci right 9.034418e-04	k: 1371	n:1600000
Cons ci ratio: 2.380029e-03	ci left: 6.282566e-01	ci right 6.297542e-01	k: 1006409	n:1600000
KS ci ratio: 1.057846e-01	ci left: 8.121305e-04	ci right 9.034418e-04	k: 1371	n:1600000
C9orf41   1600000 perm   1377 sec   (1162 perm/sec)   p_kst 8.568750e-04   p_cons 6.290056e-01   p_joint 8.568750e-04

Joint ci ratio: 1.054394e-01	ci left: 8.125286e-04	ci right 9.035680e-04	k: 1380	n:1610000
Cons ci ratio: 2.372547e-03	ci left: 6.282744e-01	ci right 6.297674e-01	k: 1012724	n:1610000
KS ci ratio: 1.054394e-01	ci left: 8.125286e-04	ci right 9.035680e-04	k: 1380	n:1610000
C9orf41   1610000 perm   1393 sec   (1156 perm/sec)   p_kst 8.571429e-04   p_cons 6.290211e-01   p_joint 8.571429e-04

Joint ci ratio: 1.053252e-01	ci left: 8.093160e-04	ci right 8.998912e-04	k: 1383	n:1620000
Cons ci ratio: 2.365117e-03	ci left: 6.282957e-01	ci right 6.297841e-01	k: 1019045	n:1620000
KS ci ratio: 1.053252e-01	ci left: 8.093160e-04	ci right 8.998912e-04	k: 1383	n:1620000
C9orf41   1620000 perm   1408 sec   (1151 perm/sec)   p_kst 8.537037e-04   p_cons 6.290401e-01   p_joint 8.537037e-04

Joint ci ratio: 1.050599e-01	ci left: 8.085323e-04	ci right 8.987778e-04	k: 1390	n:1630000
Cons ci ratio: 2.357812e-03	ci left: 6.283057e-01	ci right 6.297895e-01	k: 1025348	n:1630000
KS ci ratio: 1.050599e-01	ci left: 8.085323e-04	ci right 8.987778e-04	k: 1390	n:1630000
C9orf41   1630000 perm   1424 sec   (1145 perm/sec)   p_kst 8.527607e-04   p_cons 6.290479e-01   p_joint 8.527607e-04

Joint ci ratio: 1.045722e-01	ci left: 8.113214e-04	ci right 9.014319e-04	k: 1403	n:1640000
Cons ci ratio: 2.350789e-03	ci left: 6.282729e-01	ci right 6.297522e-01	k: 1031581	n:1640000
KS ci ratio: 1.045722e-01	ci left: 8.113214e-04	ci right 9.014319e-04	k: 1403	n:1640000
C9orf41   1640000 perm   1439 sec   (1139 perm/sec)   p_kst 8.554878e-04   p_cons 6.290128e-01   p_joint 8.554878e-04

Joint ci ratio: 1.042018e-01	ci left: 8.123067e-04	ci right 9.021875e-04	k: 1413	n:1650000
Cons ci ratio: 2.343907e-03	ci left: 6.282248e-01	ci right 6.296996e-01	k: 1037788	n:1650000
KS ci ratio: 1.042018e-01	ci left: 8.123067e-04	ci right 9.021875e-04	k: 1413	n:1650000
C9orf41   1650000 perm   1455 sec   (1134 perm/sec)   p_kst 8.563636e-04   p_cons 6.289624e-01   p_joint 8.563636e-04

Joint ci ratio: 1.039083e-01	ci left: 8.121071e-04	ci right 9.016973e-04	k: 1421	n:1660000
Cons ci ratio: 2.336875e-03	ci left: 6.282194e-01	ci right 6.296898e-01	k: 1044065	n:1660000
KS ci ratio: 1.039083e-01	ci left: 8.121071e-04	ci right 9.016973e-04	k: 1421	n:1660000
C9orf41   1660000 perm   1471 sec   (1128 perm/sec)   p_kst 8.560241e-04   p_cons 6.289548e-01   p_joint 8.560241e-04

Joint ci ratio: 1.034364e-01	ci left: 8.148268e-04	ci right 9.042840e-04	k: 1434	n:1670000
Cons ci ratio: 2.329890e-03	ci left: 6.282171e-01	ci right 6.296831e-01	k: 1050347	n:1670000
KS ci ratio: 1.034364e-01	ci left: 8.148268e-04	ci right 9.042840e-04	k: 1434	n:1670000
C9orf41   1670000 perm   1488 sec   (1123 perm/sec)   p_kst 8.586826e-04   p_cons 6.289503e-01   p_joint 8.586826e-04

Joint ci ratio: 1.032209e-01	ci left: 8.134558e-04	ci right 9.025651e-04	k: 1440	n:1680000
Cons ci ratio: 2.323086e-03	ci left: 6.281910e-01	ci right 6.296526e-01	k: 1056589	n:1680000
KS ci ratio: 1.032209e-01	ci left: 8.134558e-04	ci right 9.025651e-04	k: 1440	n:1680000
C9orf41   1680000 perm   1504 sec   (1117 perm/sec)   p_kst 8.571429e-04   p_cons 6.289220e-01   p_joint 8.571429e-04

Joint ci ratio: 1.030067e-01	ci left: 8.121011e-04	ci right 9.008663e-04	k: 1446	n:1690000
Cons ci ratio: 2.316174e-03	ci left: 6.281990e-01	ci right 6.296562e-01	k: 1062888	n:1690000
KS ci ratio: 1.030067e-01	ci left: 8.121011e-04	ci right 9.008663e-04	k: 1446	n:1690000
C9orf41   1690000 perm   1520 sec   (1112 perm/sec)   p_kst 8.556213e-04   p_cons 6.289278e-01   p_joint 8.556213e-04

Joint ci ratio: 1.027939e-01	ci left: 8.107626e-04	ci right 8.991874e-04	k: 1452	n:1700000
Cons ci ratio: 2.309443e-03	ci left: 6.281827e-01	ci right 6.296357e-01	k: 1069146	n:1700000
KS ci ratio: 1.027939e-01	ci left: 8.107626e-04	ci right 8.991874e-04	k: 1452	n:1700000
C9orf41   1700000 perm   1536 sec   (1107 perm/sec)   p_kst 8.541176e-04   p_cons 6.289094e-01   p_joint 8.541176e-04

Joint ci ratio: 1.024420e-01	ci left: 8.117192e-04	ci right 8.999269e-04	k: 1462	n:1710000
Cons ci ratio: 2.302672e-03	ci left: 6.281865e-01	ci right 6.296353e-01	k: 1075438	n:1710000
KS ci ratio: 1.024420e-01	ci left: 8.117192e-04	ci right 8.999269e-04	k: 1462	n:1710000
C9orf41   1710000 perm   1553 sec   (1101 perm/sec)   p_kst 8.549708e-04   p_cons 6.289111e-01   p_joint 8.549708e-04

Joint ci ratio: 1.022326e-01	ci left: 8.103990e-04	ci right 8.982724e-04	k: 1468	n:1720000
Cons ci ratio: 2.295923e-03	ci left: 6.281979e-01	ci right 6.296424e-01	k: 1081743	n:1720000
KS ci ratio: 1.022326e-01	ci left: 8.103990e-04	ci right 8.982724e-04	k: 1468	n:1720000
C9orf41   1720000 perm   1569 sec   (1096 perm/sec)   p_kst 8.534884e-04   p_cons 6.289203e-01   p_joint 8.534884e-04

Joint ci ratio: 1.018519e-01	ci left: 8.119107e-04	ci right 8.996007e-04	k: 1479	n:1730000
Cons ci ratio: 2.289437e-03	ci left: 6.281675e-01	ci right 6.296078e-01	k: 1087976	n:1730000
KS ci ratio: 1.018519e-01	ci left: 8.119107e-04	ci right 8.996007e-04	k: 1479	n:1730000
C9orf41   1730000 perm   1586 sec   (1091 perm/sec)   p_kst 8.549133e-04   p_cons 6.288879e-01   p_joint 8.549133e-04

Joint ci ratio: 1.016804e-01	ci left: 8.100450e-04	ci right 8.973773e-04	k: 1484	n:1740000
Cons ci ratio: 2.282795e-03	ci left: 6.281805e-01	ci right 6.296167e-01	k: 1094284	n:1740000
KS ci ratio: 1.016804e-01	ci left: 8.100450e-04	ci right 8.973773e-04	k: 1484	n:1740000
C9orf41   1740000 perm   1602 sec   (1086 perm/sec)   p_kst 8.528736e-04   p_cons 6.288989e-01   p_joint 8.528736e-04

Joint ci ratio: 1.012381e-01	ci left: 8.126563e-04	ci right 8.998663e-04	k: 1497	n:1750000
Cons ci ratio: 2.276406e-03	ci left: 6.281534e-01	ci right 6.295856e-01	k: 1100522	n:1750000
KS ci ratio: 1.012381e-01	ci left: 8.126563e-04	ci right 8.998663e-04	k: 1497	n:1750000
C9orf41   1750000 perm   1619 sec   (1081 perm/sec)   p_kst 8.554286e-04   p_cons 6.288697e-01   p_joint 8.554286e-04

Joint ci ratio: 1.010025e-01	ci left: 8.119156e-04	ci right 8.988313e-04	k: 1504	n:1760000
Cons ci ratio: 2.270221e-03	ci left: 6.280954e-01	ci right 6.295235e-01	k: 1106705	n:1760000
KS ci ratio: 1.010025e-01	ci left: 8.119156e-04	ci right 8.988313e-04	k: 1504	n:1760000
C9orf41   1760000 perm   1636 sec   (1076 perm/sec)   p_kst 8.545455e-04   p_cons 6.288097e-01   p_joint 8.545455e-04

Joint ci ratio: 1.007684e-01	ci left: 8.111835e-04	ci right 8.978077e-04	k: 1511	n:1770000
Cons ci ratio: 2.263638e-03	ci left: 6.281307e-01	ci right 6.295547e-01	k: 1113052	n:1770000
KS ci ratio: 1.007684e-01	ci left: 8.111835e-04	ci right 8.978077e-04	k: 1511	n:1770000
C9orf41   1770000 perm   1653 sec   (1071 perm/sec)   p_kst 8.536723e-04   p_cons 6.288429e-01   p_joint 8.536723e-04

Joint ci ratio: 1.005360e-01	ci left: 8.104598e-04	ci right 8.967954e-04	k: 1518	n:1780000
Cons ci ratio: 2.257367e-03	ci left: 6.281128e-01	ci right 6.295328e-01	k: 1119305	n:1780000
KS ci ratio: 1.005360e-01	ci left: 8.104598e-04	ci right 8.967954e-04	k: 1518	n:1780000
C9orf41   1780000 perm   1670 sec   (1066 perm/sec)   p_kst 8.528090e-04   p_cons 6.288230e-01   p_joint 8.528090e-04

Joint ci ratio: 1.003052e-01	ci left: 8.097445e-04	ci right 8.957942e-04	k: 1525	n:1790000
Cons ci ratio: 2.250999e-03	ci left: 6.281259e-01	ci right 6.295419e-01	k: 1125613	n:1790000
KS ci ratio: 1.003052e-01	ci left: 8.097445e-04	ci right 8.957942e-04	k: 1525	n:1790000
C9orf41   1790000 perm   1687 sec   (1061 perm/sec)   p_kst 8.519553e-04   p_cons 6.288341e-01   p_joint 8.519553e-04

Joint ci ratio: 1.000760e-01	ci left: 8.090374e-04	ci right 8.948039e-04	k: 1532	n:1800000
Cons ci ratio: 2.244533e-03	ci left: 6.281704e-01	ci right 6.295825e-01	k: 1131978	n:1800000
KS ci ratio: 1.000760e-01	ci left: 8.090374e-04	ci right 8.948039e-04	k: 1532	n:1800000
C9orf41   1800000 perm   1704 sec   (1056 perm/sec)   p_kst 8.511111e-04   p_cons 6.288767e-01   p_joint 8.511111e-04

Joint ci ratio: 9.968648e-02	ci left: 8.110318e-04	ci right 8.966556e-04	k: 1544	n:1810000
Cons ci ratio: 2.238456e-03	ci left: 6.281449e-01	ci right 6.295531e-01	k: 1138217	n:1810000
KS ci ratio: 9.968648e-02	ci left: 8.110318e-04	ci right 8.966556e-04	k: 1544	n:1810000
C9orf41   1810000 perm   1722 sec   (1051 perm/sec)   p_kst 8.530387e-04   p_cons 6.288492e-01   p_joint 8.530387e-04

Outputting figure to mutsig2_images.part000000000028/C9orf41.2_1262_1810000_0.00085304_0.62885_0.00085304.png
                gene_name: C9orf41
               theta_stop: 0.100 
                    nperm: 1810000 
                     p_ks: 0.00085 
        ci_ks_bounds_left: 0.00081 
       ci_ks_bounds_right: 0.00090 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.00085 
     ci_joint_bounds_left: 0.00081 
    ci_joint_bounds_right: 0.00090 

Current progress: 40 percent done.
CABC1
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: 6.987054e-02	ci left: 2.309646e-01	ci right 2.477875e-01	k: 2393	n:10000
KS ci ratio: 3.785336e-02	ci left: 5.075522e-01	ci right 5.272376e-01	k: 5174	n:10000
CABC1   10000 perm   2 sec   (6221 perm/sec)   p_kst 5.174000e-01   p_cons 2.393000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000028/CABC1.2_2000_10000_0.5174_0.2393_1.png
                gene_name: CABC1
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.25 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
CACNA1B
Processing conservation and coverage...
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: 4.410837e-02	ci left: 4.314365e-01	ci right 4.509978e-01	k: 4412	n:10000
KS ci ratio: 1.753367e-01	ci left: 4.341336e-02	ci right 5.185268e-02	k: 475	n:10000
CACNA1B   10000 perm   2 sec   (4482 perm/sec)   p_kst 4.750000e-02   p_cons 4.412000e-01   p_joint 2.861000e-01

Joint ci ratio: 5.499005e-02	ci left: 1.969986e-01	ci right 2.081880e-01	k: 4051	n:20000
Cons ci ratio: 3.129345e-02	ci left: 4.327054e-01	ci right 4.465121e-01	k: 8792	n:20000
KS ci ratio: 1.231716e-01	ci left: 4.522388e-02	ci right 5.120834e-02	k: 963	n:20000
CACNA1B   20000 perm   5 sec   (4063 perm/sec)   p_kst 4.815000e-02   p_cons 4.396000e-01   p_joint 2.025500e-01

Joint ci ratio: 1.718535e-02	ci left: 6.287871e-01	ci right 6.397202e-01	k: 19028	n:30000
Cons ci ratio: 2.554828e-02	ci left: 4.340395e-01	ci right 4.453055e-01	k: 13190	n:30000
KS ci ratio: 1.009741e-01	ci left: 4.541306e-02	ci right 5.027498e-02	k: 1434	n:30000
CACNA1B   30000 perm   8 sec   (3902 perm/sec)   p_kst 4.780000e-02   p_cons 4.396667e-01   p_joint 6.342667e-01

Joint ci ratio: 1.485474e-02	ci left: 6.304103e-01	ci right 6.398701e-01	k: 25406	n:40000
Cons ci ratio: 2.214225e-02	ci left: 4.344284e-01	ci right 4.441804e-01	k: 17572	n:40000
KS ci ratio: 8.681299e-02	ci left: 4.639066e-02	ci right 5.062520e-02	k: 1939	n:40000
CACNA1B   40000 perm   11 sec   (3802 perm/sec)   p_kst 4.847500e-02   p_cons 4.393000e-01   p_joint 6.351500e-01

Outputting figure to mutsig2_images.part000000000028/CACNA1B.2_7204_40000_0.048475_0.4393_0.63515.png
                gene_name: CACNA1B
               theta_stop: 0.087 
                    nperm: 40000 
                     p_ks: 0.048 
        ci_ks_bounds_left: 0.046 
       ci_ks_bounds_right: 0.051 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.64 

Current progress: 80 percent done.
CACNA1F
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: 6.565505e-03	ci left: 9.694208e-01	ci right 9.758999e-01	k: 9728	n:10000
KS ci ratio: 1.554831e-02	ci left: 8.572275e-01	ci right 8.707597e-01	k: 8641	n:10000
CACNA1F   10000 perm   2 sec   (4804 perm/sec)   p_kst 8.641000e-01   p_cons 9.728000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000028/CACNA1F.2_6126_10000_0.8641_0.9728_1.png
                gene_name: CACNA1F
               theta_stop: 0.016 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.87 
                   p_cons: 0.97 
      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.165.3896/
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/181708/iteration1/scatter.0000000028
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 28 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1653>
Subject: Job 1119639: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1653>, 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/181708/iteration1/scatter.0000000029> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:45:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000029.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000029.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 29  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    181.13 sec.
    Max Memory :      1415 MB
    Max Swap   :      3864 MB

    Max Processes  :         7
    Max Threads    :        61

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/
-whichjob
29
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 29: processing genes 2534 - 2624
Calculating significance of each gene.
Using projection method.
2534	CACNG6	5.297856e-02
2535	CACNG7	1
2536	CACNG8	1.531261e-02
2537	CACYBP	1
2538	CAD	5.903208e-01
2539	CADM1	1
2540	CADM2	1
2541	CADM3	1
2542	CADM4	1
2543	CADPS	6.427021e-02
2544	CADPS2	1
2545	CAGE1	2.539513e-01
2546	CALB1	1
2547	CALB2	1
2548	CALCA	1
2549	CALCB	1
2550	CALCOCO1	1
2551	CALCOCO2	1.899170e-01
2552	CALCR	1
2553	CALCRL	1
2554	CALD1	1
2555	CALHM1	1
2556	CALHM2	1
2557	CALM1	1.462626e-02
2558	CALM2	1
2559	CALM3	1
2560	CALML3	1
2561	CALML4	1
2562	CALML5	1
2563	CALML6	1
2564	CALN1	1
2565	CALR	1
2566	CALR3	1
2567	CALU	1
2568	CALY	1
2569	CAMK1	1
2570	CAMK1D	1
2571	CAMK1G	1
2572	CAMK2A	1
2573	CAMK2B	1
2574	CAMK2D	1
2575	CAMK2G	1
2576	CAMK2N1	1
2577	CAMK2N2	1
2578	CAMK4	1
2579	CAMKK1	1
2580	CAMKK2	4.103267e-03
2581	CAMKV	2.434598e-01
2582	CAMLG	1
2583	CAMP	1
2584	CAMSAP1	2.207639e-01
2585	CAMSAP1L1	1
2586	CAMTA1	2.358096e-02
2587	CAMTA2	1.868753e-01
2588	CAND1	1
2589	CAND2	1.025044e-01
2590	CANT1	1
2591	CANX	1.135087e-01
2592	CAP1	1
2593	CAP2	1
2594	CAPG	1
2595	CAPN1	1
2596	CAPN10	1.707888e-01
2597	CAPN11	1
2598	CAPN12	1
2599	CAPN13	7.619721e-02
2600	CAPN2	1
2601	CAPN3	1
2602	CAPN5	1
2603	CAPN6	1
2604	CAPN7	1
2605	CAPN9	1
2606	CAPNS1	1
2607	CAPNS2	1
2608	CAPRIN1	1
2609	CAPRIN2	1.044730e-01
2610	CAPS	1
2611	CAPS2	1
2612	CAPSL	5.587599e-02
2613	CAPZA1	1
2614	CAPZA2	1
2615	CAPZA3	1
2616	CAPZB	1
2617	CARD10	1
2618	CARD11	1
2619	CARD14	1
2620	CARD16	8.359611e-02
2621	CARD17	1
2622	CARD18	1
2623	CARD6	1
2624	CARD8	1
Done

Running MutSig 2:
Scatter job 29: processing genes 2534 - 2624
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CAMTA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.350161e-02	ci left: 8.878013e-01	ci right 8.999681e-01	k: 8940	n:10000
Cons ci ratio: 1.600840e-02	ci left: 8.500867e-01	ci right 8.639046e-01	k: 8571	n:10000
KS ci ratio: 1.747133e-02	ci left: 8.268655e-01	ci right 8.415392e-01	k: 8343	n:10000
CAMTA1   10000 perm   2 sec   (4452 perm/sec)   p_kst 8.343000e-01   p_cons 8.571000e-01   p_joint 8.940000e-01

Outputting figure to mutsig2_images.part000000000029/CAMTA1.3_5114_10000_0.8343_0.8571_0.894.png
                gene_name: CAMTA1
               theta_stop: 0.017 
                    nperm: 10000 
                     p_ks: 0.83 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.84 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.89 
     ci_joint_bounds_left: 0.89 
    ci_joint_bounds_right: 0.90 

Current progress: 20 percent done.
CADPS
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.204255e-01	ci left: 9.000254e-02	ci right 1.016341e-01	k: 957	n:10000
Cons ci ratio: 5.509389e-02	ci left: 3.267412e-01	ci right 3.453544e-01	k: 3360	n:10000
KS ci ratio: 2.786829e-01	ci left: 1.669424e-02	ci right 2.219075e-02	k: 193	n:10000
CADPS   10000 perm   3 sec   (3177 perm/sec)   p_kst 1.930000e-02   p_cons 3.360000e-01   p_joint 9.570000e-02

Joint ci ratio: 4.572799e-02	ci left: 2.625159e-01	ci right 2.748515e-01	k: 5373	n:20000
Cons ci ratio: 3.889623e-02	ci left: 3.301994e-01	ci right 3.433481e-01	k: 6735	n:20000
KS ci ratio: 1.955271e-01	ci left: 1.777152e-02	ci right 2.166988e-02	k: 393	n:20000
CADPS   20000 perm   6 sec   (3503 perm/sec)   p_kst 1.965000e-02   p_cons 3.367500e-01   p_joint 2.686500e-01

Joint ci ratio: 9.366089e-02	ci left: 5.257711e-02	ci right 5.777613e-02	k: 1654	n:30000
Cons ci ratio: 3.155826e-02	ci left: 3.342402e-01	ci right 3.449909e-01	k: 10188	n:30000
KS ci ratio: 1.595109e-01	ci left: 1.815744e-02	ci right 2.133653e-02	k: 591	n:30000
CADPS   30000 perm   10 sec   (3047 perm/sec)   p_kst 1.970000e-02   p_cons 3.396000e-01   p_joint 5.513333e-02

Joint ci ratio: 2.859628e-02	ci left: 3.150309e-01	ci right 3.241953e-01	k: 12784	n:40000
Cons ci ratio: 2.737041e-02	ci left: 3.343106e-01	ci right 3.436128e-01	k: 13558	n:40000
KS ci ratio: 1.393465e-01	ci left: 1.804668e-02	ci right 2.077372e-02	k: 775	n:40000
CADPS   40000 perm   13 sec   (3040 perm/sec)   p_kst 1.937500e-02   p_cons 3.389500e-01   p_joint 3.196000e-01

Joint ci ratio: 2.449040e-02	ci left: 3.346309e-01	ci right 3.429478e-01	k: 16939	n:50000
Cons ci ratio: 2.449915e-02	ci left: 3.344714e-01	ci right 3.427873e-01	k: 16931	n:50000
KS ci ratio: 1.250305e-01	ci left: 1.807330e-02	ci right 2.050296e-02	k: 963	n:50000
CADPS   50000 perm   17 sec   (2971 perm/sec)   p_kst 1.926000e-02   p_cons 3.386200e-01   p_joint 3.387800e-01

Joint ci ratio: 2.234992e-02	ci left: 3.351287e-01	ci right 3.427202e-01	k: 20335	n:60000
Cons ci ratio: 2.231008e-02	ci left: 3.359265e-01	ci right 3.435223e-01	k: 20383	n:60000
KS ci ratio: 1.143791e-01	ci left: 1.810074e-02	ci right 2.031278e-02	k: 1151	n:60000
CADPS   60000 perm   21 sec   (2866 perm/sec)   p_kst 1.918333e-02   p_cons 3.397167e-01   p_joint 3.389167e-01

Joint ci ratio: 8.700441e-03	ci left: 7.403338e-01	ci right 7.468174e-01	k: 52051	n:70000
Cons ci ratio: 2.057993e-02	ci left: 3.378440e-01	ci right 3.448834e-01	k: 23895	n:70000
KS ci ratio: 1.059348e-01	ci left: 1.816842e-02	ci right 2.021457e-02	k: 1342	n:70000
CADPS   70000 perm   25 sec   (2848 perm/sec)   p_kst 1.917143e-02   p_cons 3.413571e-01   p_joint 7.435857e-01

Joint ci ratio: 1.935758e-02	ci left: 3.355947e-01	ci right 3.421670e-01	k: 27110	n:80000
Cons ci ratio: 1.920787e-02	ci left: 3.390740e-01	ci right 3.456625e-01	k: 27389	n:80000
KS ci ratio: 1.002259e-01	ci left: 1.782131e-02	ci right 1.971382e-02	k: 1500	n:80000
CADPS   80000 perm   28 sec   (2861 perm/sec)   p_kst 1.875000e-02   p_cons 3.423625e-01   p_joint 3.388750e-01

Joint ci ratio: 4.355459e-05	ci left: 9.999590e-01	ci right 1	k: 90000	n:90000
Cons ci ratio: 1.808782e-02	ci left: 3.397984e-01	ci right 3.460118e-01	k: 30861	n:90000
KS ci ratio: 9.468346e-02	ci left: 1.780327e-02	ci right 1.958350e-02	k: 1681	n:90000
CADPS   90000 perm   31 sec   (2920 perm/sec)   p_kst 1.867778e-02   p_cons 3.429000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000029/CADPS.2_4255_90000_0.018678_0.3429_1.png
                gene_name: CADPS
               theta_stop: 0.095 
                    nperm: 90000 
                     p_ks: 0.019 
        ci_ks_bounds_left: 0.018 
       ci_ks_bounds_right: 0.020 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.35 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 40 percent done.
CAMK2G
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.326530e-03	ci left: 9.419078e-01	ci right 9.508299e-01	k: 9465	n:10000
Cons ci ratio: 1.049122e-01	ci left: 1.160369e-01	ci right 1.289839e-01	k: 1224	n:10000
KS ci ratio: 2.336799e-02	ci left: 7.290610e-01	ci right 7.464003e-01	k: 7378	n:10000
CAMK2G   10000 perm   2 sec   (5379 perm/sec)   p_kst 7.378000e-01   p_cons 1.224000e-01   p_joint 9.465000e-01

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 7.301841e-02	ci left: 1.213321e-01	ci right 1.305770e-01	k: 2518	n:20000
KS ci ratio: 1.666697e-02	ci left: 7.282707e-01	ci right 7.405611e-01	k: 14689	n:20000
CAMK2G   20000 perm   4 sec   (5288 perm/sec)   p_kst 7.344500e-01   p_cons 1.259000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000029/CAMK2G.2_1855_20000_0.73445_0.1259_1.png
                gene_name: CAMK2G
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.13 
      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: 60 percent done.
CAMKK2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.996592e-02	ci left: 3.713681e-01	ci right 3.905013e-01	k: 3809	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: 7.160178e-02	ci left: 2.222750e-01	ci right 2.388823e-01	k: 2305	n:10000
CAMKK2   10000 perm   2 sec   (6421 perm/sec)   p_kst 2.305000e-01   p_cons 3.203000e-01   p_joint 3.809000e-01

Outputting figure to mutsig2_images.part000000000029/CAMKK2.2_1841_10000_0.2305_0.3203_0.3809.png
                gene_name: CAMKK2
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 80 percent done.
CAMTA2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.851453e-02	ci left: 3.853009e-01	ci right 4.045604e-01	k: 3949	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: 2.128566e-01	ci left: 2.930086e-02	ci right 3.637471e-02	k: 327	n:10000
CAMTA2   10000 perm   3 sec   (3162 perm/sec)   p_kst 3.270000e-02   p_cons 7.698000e-01   p_joint 3.949000e-01

Joint ci ratio: 4.488225e-02	ci left: 2.698623e-01	ci right 2.823028e-01	k: 5521	n:20000
Cons ci ratio: 1.455580e-02	ci left: 7.780793e-01	ci right 7.895381e-01	k: 15677	n:20000
KS ci ratio: 1.480826e-01	ci left: 3.133844e-02	ci right 3.639826e-02	k: 676	n:20000
CAMTA2   20000 perm   7 sec   (2785 perm/sec)   p_kst 3.380000e-02   p_cons 7.838500e-01   p_joint 2.760500e-01

Joint ci ratio: 7.266175e-02	ci left: 8.521100e-02	ci right 9.166896e-02	k: 2652	n:30000
Cons ci ratio: 1.191920e-02	ci left: 7.781573e-01	ci right 7.875212e-01	k: 23486	n:30000
KS ci ratio: 1.204502e-01	ci left: 3.204252e-02	ci right 3.618168e-02	k: 1022	n:30000
CAMTA2   30000 perm   11 sec   (2686 perm/sec)   p_kst 3.406667e-02   p_cons 7.828667e-01   p_joint 8.840000e-02

Joint ci ratio: 6.335375e-02	ci left: 8.457593e-02	ci right 9.013414e-02	k: 3493	n:40000
Cons ci ratio: 1.031827e-02	ci left: 7.789275e-01	ci right 7.870314e-01	k: 31320	n:40000
KS ci ratio: 1.041553e-01	ci left: 3.241597e-02	ci right 3.600207e-02	k: 1367	n:40000
CAMTA2   40000 perm   15 sec   (2640 perm/sec)   p_kst 3.417500e-02   p_cons 7.830000e-01   p_joint 8.732500e-02

Joint ci ratio: 6.094403e-02	ci left: 7.408627e-02	ci right 7.876305e-02	k: 3820	n:50000
Cons ci ratio: 9.237079e-03	ci left: 7.790588e-01	ci right 7.863084e-01	k: 39135	n:50000
KS ci ratio: 9.466012e-02	ci left: 3.158816e-02	ci right 3.474635e-02	k: 1657	n:50000
CAMTA2   50000 perm   18 sec   (2818 perm/sec)   p_kst 3.314000e-02   p_cons 7.827000e-01   p_joint 7.640000e-02

Outputting figure to mutsig2_images.part000000000029/CAMTA2.2_3861_50000_0.03314_0.7827_0.0764.png
                gene_name: CAMTA2
               theta_stop: 0.095 
                    nperm: 50000 
                     p_ks: 0.033 
        ci_ks_bounds_left: 0.032 
       ci_ks_bounds_right: 0.035 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.076 
     ci_joint_bounds_left: 0.074 
    ci_joint_bounds_right: 0.079 

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.165.3896/
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/181708/iteration1/scatter.0000000029
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 29 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1542>
Subject: Job 1119646: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1542>, 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/181708/iteration1/scatter.0000000030> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:45:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000030.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000030.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 30  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    175.39 sec.
    Max Memory :      1374 MB
    Max Swap   :      3912 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.165.3896/
-whichjob
30
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 30: processing genes 2625 - 2714
Calculating significance of each gene.
Using projection method.
2625	CARD9	1
2626	CARHSP1	1
2627	CARKD	1
2628	CARM1	2.936700e-02
2629	CARNS1	1
2630	CARS	1
2631	CARS2	1
2632	CARTPT	1
2633	CASC1	1
2634	CASC3	8.170263e-02
2635	CASC4	2.434857e-02
2636	CASC5	7.082959e-01
2637	CASD1	1
2638	CASK	1
2639	CASKIN1	1
2640	CASKIN2	3.891638e-02
2641	CASP1	1
2642	CASP10	1
2643	CASP14	1
2644	CASP2	1
2645	CASP3	1
2646	CASP4	7.096579e-02
2647	CASP5	7.825007e-02
2648	CASP6	1
2649	CASP7	1
2650	CASP8	1.078867e-02
2651	CASP8AP2	2.664081e-01
2652	CASP9	1
2653	CASQ1	1
2654	CASQ2	1
2655	CASR	1
2656	CASS4	1
2657	CAST	1
2658	CASZ1	5.608364e-01
2659	CAT	1.901276e-03
2660	CATSPER1	1
2661	CATSPER2	6.570753e-02
2662	CATSPER3	1
2663	CATSPER4	1
2664	CATSPERB	5.010341e-02
2665	CATSPERG	1
2666	CAV1	1
2667	CAV2	1
2668	CAV3	1
2669	CBARA1	1
2670	CBFA2T2	1
2671	CBFA2T3	1
2672	CBFB	1
2673	CBL	1.254916e-01
2674	CBLB	2.106421e-01
2675	CBLC	1
2676	CBLL1	1
2677	CBLN1	1
2678	CBLN2	1
2679	CBLN3	1
2680	CBLN4	1
2681	CBR1	1
2682	CBR3	1
2683	CBR4	1
2684	CBS	1
2685	CBWD1	1
2686	CBWD2	1
2687	CBWD6	1
2688	CBX1	1
2689	CBX2	1
2690	CBX3	1
2691	CBX4	7.657371e-02
2692	CBX5	1
2693	CBX6	1
2694	CBX7	1
2695	CBX8	1
2696	CBY1	1
2697	CC2D1A	1
2698	CC2D1B	1
2699	CC2D2A	5.122302e-01
2700	CC2D2B	1
2701	CCAR1	1
2702	CCBE1	1
2703	CCBL1	1
2704	CCBL2	2.166093e-01
2705	CCBP2	1.106398e-01
2706	CCDC101	1
2707	CCDC102A	1
2708	CCDC102B	1
2709	CCDC103	1
2710	CCDC104	1
2711	CCDC105	1
2712	CCDC106	1
2713	CCDC107	1
2714	CCDC108	1
Done

Running MutSig 2:
Scatter job 30: processing genes 2625 - 2714
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CAT
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: 1.230957e-02	ci left: 9.045292e-01	ci right 9.158305e-01	k: 9103	n:10000
KS ci ratio: 2.983253e-02	ci left: 6.236666e-01	ci right 6.426558e-01	k: 6332	n:10000
CAT   10000 perm   2 sec   (4813 perm/sec)   p_kst 6.332000e-01   p_cons 9.103000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000030/CAT.3_1636_10000_0.6332_0.9103_1.png
                gene_name: CAT
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.91 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.92 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 17 percent done.
CASC4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.686127e-02	ci left: 8.366363e-01	ci right 8.509628e-01	k: 8439	n:10000
Cons ci ratio: 4.020242e-02	ci left: 4.774582e-01	ci right 4.971492e-01	k: 4873	n:10000
KS ci ratio: 2.497253e-02	ci left: 7.023076e-01	ci right 7.201692e-01	k: 7113	n:10000
CASC4   10000 perm   1 sec   (6699 perm/sec)   p_kst 7.113000e-01   p_cons 4.873000e-01   p_joint 8.439000e-01

Outputting figure to mutsig2_images.part000000000030/CASC4.2_1351_10000_0.7113_0.4873_0.8439.png
                gene_name: CASC4
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.84 
     ci_joint_bounds_left: 0.84 
    ci_joint_bounds_right: 0.85 

Current progress: 33 percent done.
CASKIN2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.245627e-02	ci left: 2.736903e-01	ci right 2.914365e-01	k: 2825	n:10000
Cons ci ratio: 2.818337e-02	ci left: 6.498149e-01	ci right 6.684923e-01	k: 6592	n:10000
KS ci ratio: 1.846975e-01	ci left: 3.910770e-02	ci right 4.716118e-02	k: 430	n:10000
CASKIN2   10000 perm   2 sec   (4643 perm/sec)   p_kst 4.300000e-02   p_cons 6.592000e-01   p_joint 2.825000e-01

Joint ci ratio: 5.373702e-02	ci left: 2.044716e-01	ci right 2.158128e-01	k: 4202	n:20000
Cons ci ratio: 2.015165e-02	ci left: 6.475612e-01	ci right 6.607939e-01	k: 13084	n:20000
KS ci ratio: 1.343100e-01	ci left: 3.810025e-02	ci right 4.363424e-02	k: 816	n:20000
CASKIN2   20000 perm   5 sec   (4112 perm/sec)   p_kst 4.080000e-02   p_cons 6.542000e-01   p_joint 2.101000e-01

Joint ci ratio: 3.024183e-02	ci left: 3.535357e-01	ci right 3.644250e-01	k: 10769	n:30000
Cons ci ratio: 1.652434e-02	ci left: 6.468463e-01	ci right 6.576576e-01	k: 19568	n:30000
KS ci ratio: 1.093162e-01	ci left: 3.884897e-02	ci right 4.337378e-02	k: 1232	n:30000
CASKIN2   30000 perm   8 sec   (3978 perm/sec)   p_kst 4.106667e-02   p_cons 6.522667e-01   p_joint 3.589667e-01

Joint ci ratio: 3.394579e-02	ci left: 2.457623e-01	ci right 2.542740e-01	k: 10000	n:40000
Cons ci ratio: 1.439876e-02	ci left: 6.447760e-01	ci right 6.541523e-01	k: 25979	n:40000
KS ci ratio: 9.452118e-02	ci left: 3.927313e-02	ci right 4.319383e-02	k: 1648	n:40000
CASKIN2   40000 perm   10 sec   (3824 perm/sec)   p_kst 4.120000e-02   p_cons 6.494750e-01   p_joint 2.500000e-01

Outputting figure to mutsig2_images.part000000000030/CASKIN2.2_3685_40000_0.0412_0.64948_0.25.png
                gene_name: CASKIN2
               theta_stop: 0.095 
                    nperm: 40000 
                     p_ks: 0.041 
        ci_ks_bounds_left: 0.039 
       ci_ks_bounds_right: 0.043 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.25 
     ci_joint_bounds_left: 0.25 
    ci_joint_bounds_right: 0.25 

Current progress: 50 percent done.
CASP8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.794543e-02	ci left: 6.536391e-01	ci right 6.722659e-01	k: 6630	n:10000
Cons ci ratio: 1.328380e-01	ci left: 7.475563e-02	ci right 8.549047e-02	k: 800	n:10000
KS ci ratio: 2.614451e-02	ci left: 6.829473e-01	ci right 7.011407e-01	k: 6921	n:10000
CASP8   10000 perm   2 sec   (6147 perm/sec)   p_kst 6.921000e-01   p_cons 8.000000e-02   p_joint 6.630000e-01

Joint ci ratio: 4.740908e-02	ci left: 2.486727e-01	ci right 2.607987e-01	k: 5094	n:20000
Cons ci ratio: 9.506608e-02	ci left: 7.461336e-02	ci right 8.210977e-02	k: 1566	n:20000
KS ci ratio: 1.835534e-02	ci left: 6.887170e-01	ci right 7.015262e-01	k: 13903	n:20000
CASP8   20000 perm   4 sec   (5386 perm/sec)   p_kst 6.951500e-01   p_cons 7.830000e-02   p_joint 2.547000e-01

Outputting figure to mutsig2_images.part000000000030/CASP8.2_1753_20000_0.69515_0.0783_0.2547.png
                gene_name: CASP8
               theta_stop: 0.095 
                    nperm: 20000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.70 
                   p_cons: 0.078 
      ci_cons_bounds_left: 0.075 
     ci_cons_bounds_right: 0.082 
                  p_joint: 0.25 
     ci_joint_bounds_left: 0.25 
    ci_joint_bounds_right: 0.26 

Current progress: 67 percent done.
CASP8AP2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.458093e-01	ci left: 6.246605e-02	ci right 7.238775e-02	k: 673	n:10000
Cons ci ratio: 1.238134e-01	ci left: 8.543267e-02	ci right 9.680682e-02	k: 910	n:10000
KS ci ratio: 1.216226e-01	ci left: 8.834910e-02	ci right 9.988860e-02	k: 940	n:10000
CASP8AP2   10000 perm   2 sec   (4324 perm/sec)   p_kst 9.400000e-02   p_cons 9.100000e-02   p_joint 6.730000e-02

Joint ci ratio: 9.117641e-02	ci left: 8.072986e-02	ci right 8.849141e-02	k: 1691	n:20000
Cons ci ratio: 8.889963e-02	ci left: 8.464776e-02	ci right 9.257232e-02	k: 1771	n:20000
KS ci ratio: 8.612820e-02	ci left: 8.979365e-02	ci right 9.792487e-02	k: 1876	n:20000
CASP8AP2   20000 perm   5 sec   (3917 perm/sec)   p_kst 9.380000e-02   p_cons 8.855000e-02   p_joint 8.455000e-02

Outputting figure to mutsig2_images.part000000000030/CASP8AP2.2_5937_20000_0.0938_0.08855_0.08455.png
                gene_name: CASP8AP2
               theta_stop: 0.091 
                    nperm: 20000 
                     p_ks: 0.094 
        ci_ks_bounds_left: 0.090 
       ci_ks_bounds_right: 0.098 
                   p_cons: 0.089 
      ci_cons_bounds_left: 0.085 
     ci_cons_bounds_right: 0.093 
                  p_joint: 0.085 
     ci_joint_bounds_left: 0.081 
    ci_joint_bounds_right: 0.088 

Current progress: 83 percent done.
CATSPERB
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.398435e-02	ci left: 7.187589e-01	ci right 7.363084e-01	k: 7276	n:10000
Cons ci ratio: 8.895760e-03	ci left: 9.466899e-01	ci right 9.552449e-01	k: 9511	n:10000
KS ci ratio: 4.039597e-02	ci left: 4.750602e-01	ci right 4.947485e-01	k: 4849	n:10000
CATSPERB   10000 perm   2 sec   (5259 perm/sec)   p_kst 4.849000e-01   p_cons 9.511000e-01   p_joint 7.276000e-01

Outputting figure to mutsig2_images.part000000000030/CATSPERB.2_3455_10000_0.4849_0.9511_0.7276.png
                gene_name: CATSPERB
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.73 
     ci_joint_bounds_left: 0.72 
    ci_joint_bounds_right: 0.74 

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.165.3896/
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/181708/iteration1/scatter.0000000030
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 30 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119652: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000031> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:43:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000031.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000031.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 31  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     77.22 sec.
    Max Memory :      1187 MB
    Max Swap   :      3909 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.165.3896/
-whichjob
31
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 31: processing genes 2715 - 2805
Calculating significance of each gene.
Using projection method.
2715	CCDC109A	1
2716	CCDC109B	1
2717	CCDC11	1
2718	CCDC110	1
2719	CCDC111	1
2720	CCDC112	1
2721	CCDC113	1.257445e-01
2722	CCDC114	1
2723	CCDC115	1
2724	CCDC116	1
2725	CCDC117	1
2726	CCDC12	5.394284e-03
2727	CCDC120	1
2728	CCDC121	1
2729	CCDC122	1
2730	CCDC123	1
2731	CCDC124	1
2732	CCDC125	1.148914e-01
2733	CCDC126	1
2734	CCDC127	1
2735	CCDC129	1
2736	CCDC13	1
2737	CCDC130	1.849334e-01
2738	CCDC132	1
2739	CCDC134	1
2740	CCDC135	2.470850e-02
2741	CCDC136	9.870566e-02
2742	CCDC137	1
2743	CCDC138	1
2744	CCDC14	1
2745	CCDC140	1
2746	CCDC141	1
2747	CCDC142	1.900864e-01
2748	CCDC144A	3.296147e-01
2749	CCDC144B	1.252076e-01
2750	CCDC144NL	1
2751	CCDC146	1
2752	CCDC147	1.007484e-01
2753	CCDC148	1
2754	CCDC149	1
2755	CCDC15	1
2756	CCDC150	1
2757	CCDC151	1
2758	CCDC153	1
2759	CCDC155	1
2760	CCDC157	1
2761	CCDC158	1
2762	CCDC159	1
2763	CCDC17	1
2764	CCDC18	8.351745e-02
2765	CCDC19	1.585003e-01
2766	CCDC21	1
2767	CCDC22	1
2768	CCDC23	1
2769	CCDC24	1
2770	CCDC25	1
2771	CCDC27	2.684913e-01
2772	CCDC28A	1
2773	CCDC28B	1
2774	CCDC3	1
2775	CCDC30	7.107229e-02
2776	CCDC33	5.699368e-02
2777	CCDC34	1.464446e-01
2778	CCDC36	1.628324e-02
2779	CCDC37	1
2780	CCDC38	1.671242e-01
2781	CCDC39	1
2782	CCDC40	2.650238e-01
2783	CCDC41	1
2784	CCDC42	1
2785	CCDC43	1
2786	CCDC45	1
2787	CCDC46	1
2788	CCDC47	1.182217e-01
2789	CCDC48	1
2790	CCDC50	1
2791	CCDC51	1.373511e-01
2792	CCDC52	3.474103e-01
2793	CCDC53	1
2794	CCDC54	1
2795	CCDC55	1
2796	CCDC56	1
2797	CCDC57	1.646462e-01
2798	CCDC58	1
2799	CCDC59	1
2800	CCDC6	1
2801	CCDC60	1
2802	CCDC61	1
2803	CCDC62	1
2804	CCDC63	5.367625e-02
2805	CCDC64	1
Done

Running MutSig 2:
Scatter job 31: processing genes 2715 - 2805
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CCDC36
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.036682e-02	ci left: 2.875589e-01	ci right 3.055598e-01	k: 2965	n:10000
Cons ci ratio: 7.987348e-02	ci left: 1.862897e-01	ci right 2.018889e-01	k: 1940	n:10000
KS ci ratio: 4.601925e-02	ci left: 4.106995e-01	ci right 4.301469e-01	k: 4204	n:10000
CCDC36   10000 perm   2 sec   (5857 perm/sec)   p_kst 4.204000e-01   p_cons 1.940000e-01   p_joint 2.965000e-01

Outputting figure to mutsig2_images.part000000000031/CCDC36.3_1813_10000_0.4204_0.194_0.2965.png
                gene_name: CCDC36
               theta_stop: 0.080 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.30 
     ci_joint_bounds_left: 0.29 
    ci_joint_bounds_right: 0.31 

Current progress: 20 percent done.
CCDC135
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.066371e-02	ci left: 4.717634e-01	ci right 4.914473e-01	k: 4816	n:10000
Cons ci ratio: 3.882749e-02	ci left: 4.948504e-01	ci right 5.145468e-01	k: 5047	n:10000
KS ci ratio: 7.979698e-02	ci left: 1.865851e-01	ci right 2.021934e-01	k: 1943	n:10000
CCDC135   10000 perm   2 sec   (6001 perm/sec)   p_kst 1.943000e-01   p_cons 5.047000e-01   p_joint 4.816000e-01

Outputting figure to mutsig2_images.part000000000031/CCDC135.2_2693_10000_0.1943_0.5047_0.4816.png
                gene_name: CCDC135
               theta_stop: 0.080 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 40 percent done.
CCDC18
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: 8.415012e-02	ci left: 1.707441e-01	ci right 1.858438e-01	k: 1782	n:10000
KS ci ratio: 3.112378e-02	ci left: 6.036732e-01	ci right 6.228608e-01	k: 6133	n:10000
CCDC18   10000 perm   2 sec   (5315 perm/sec)   p_kst 6.133000e-01   p_cons 1.782000e-01   p_joint 2.718000e-01

Outputting figure to mutsig2_images.part000000000031/CCDC18.2_4366_10000_0.6133_0.1782_0.2718.png
                gene_name: CCDC18
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.27 
     ci_joint_bounds_left: 0.26 
    ci_joint_bounds_right: 0.28 

Current progress: 60 percent done.
CCDC30
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.274675e-02	ci left: 3.463103e-01	ci right 3.651738e-01	k: 3557	n:10000
Cons ci ratio: 7.037302e-02	ci left: 2.283967e-01	ci right 2.451569e-01	k: 2367	n:10000
KS ci ratio: 4.517048e-02	ci left: 4.197698e-01	ci right 4.392713e-01	k: 4295	n:10000
CCDC30   10000 perm   2 sec   (6372 perm/sec)   p_kst 4.295000e-01   p_cons 2.367000e-01   p_joint 3.557000e-01

Outputting figure to mutsig2_images.part000000000031/CCDC30.2_2412_10000_0.4295_0.2367_0.3557.png
                gene_name: CCDC30
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 80 percent done.
CCDC33
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: 2.530722e-02	ci left: 6.967598e-01	ci right 7.147202e-01	k: 7058	n:10000
KS ci ratio: 6.540060e-02	ci left: 2.555781e-01	ci right 2.729595e-01	k: 2642	n:10000
CCDC33   10000 perm   2 sec   (6021 perm/sec)   p_kst 2.642000e-01   p_cons 7.058000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000031/CCDC33.2_2607_10000_0.2642_0.7058_1.png
                gene_name: CCDC33
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.71 
      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: 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.165.3896/
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/181708/iteration1/scatter.0000000031
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 31 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1539>
Subject: Job 1119658: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1539>, 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/181708/iteration1/scatter.0000000032> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:44:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000032.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000032.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 32  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    120.34 sec.
    Max Memory :       827 MB
    Max Swap   :      3661 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.165.3896/
-whichjob
32
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 32: processing genes 2806 - 2895
Calculating significance of each gene.
Using projection method.
2806	CCDC64B	1
2807	CCDC65	1
2808	CCDC66	1
2809	CCDC67	1
2810	CCDC68	1
2811	CCDC69	1
2812	CCDC7	1
2813	CCDC70	1.233625e-01
2814	CCDC71	1
2815	CCDC72	1
2816	CCDC73	1.474422e-01
2817	CCDC74A	1
2818	CCDC74B	1
2819	CCDC75	1
2820	CCDC76	1
2821	CCDC77	1.519668e-01
2822	CCDC78	1
2823	CCDC8	1
2824	CCDC80	1
2825	CCDC81	1
2826	CCDC82	1
2827	CCDC83	1
2828	CCDC84	1
2829	CCDC85A	1
2830	CCDC86	5.955977e-03
2831	CCDC87	1.841914e-01
2832	CCDC88A	4.201941e-01
2833	CCDC88B	1.277626e-01
2834	CCDC88C	1
2835	CCDC89	1
2836	CCDC9	2.023132e-01
2837	CCDC90A	1
2838	CCDC90B	1
2839	CCDC91	1
2840	CCDC92	1
2841	CCDC93	1
2842	CCDC94	1
2843	CCDC96	1.691937e-01
2844	CCDC97	1
2845	CCDC99	1
2846	CCHCR1	1
2847	CCIN	1
2848	CCK	1
2849	CCKAR	1
2850	CCKBR	8.427159e-02
2851	CCL1	1
2852	CCL11	1
2853	CCL13	1
2854	CCL14	1
2855	CCL15	5.769291e-02
2856	CCL16	1
2857	CCL17	1
2858	CCL18	1
2859	CCL19	1
2860	CCL2	1
2861	CCL20	1
2862	CCL21	1
2863	CCL22	1
2864	CCL23	1
2865	CCL24	1
2866	CCL25	6.022190e-03
2867	CCL26	1
2868	CCL27	1
2869	CCL28	1
2870	CCL3	5.223371e-02
2871	CCL4	1
2872	CCL5	1
2873	CCL7	1
2874	CCL8	1
2875	CCM2	1
2876	CCNA1	1
2877	CCNA2	1
2878	CCNB1	1
2879	CCNB1IP1	1
2880	CCNB2	1
2881	CCNB3	3.844860e-01
2882	CCNC	1
2883	CCND1	1.305567e-01
2884	CCND2	1
2885	CCND3	1
2886	CCNDBP1	1
2887	CCNE1	1
2888	CCNE2	1
2889	CCNF	1
2890	CCNG1	1
2891	CCNG2	1
2892	CCNH	1
2893	CCNI	1
2894	CCNI2	1
2895	CCNJ	1
Done

Running MutSig 2:
Scatter job 32: processing genes 2806 - 2895
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CCDC86
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.721092e-02	ci left: 6.655187e-01	ci right 6.839794e-01	k: 6748	n:10000
Cons ci ratio: 5.673863e-02	ci left: 3.138374e-01	ci right 3.322658e-01	k: 3230	n:10000
KS ci ratio: 6.736596e-03	ci left: 9.679427e-01	ci right 9.745790e-01	k: 9714	n:10000
CCDC86   10000 perm   2 sec   (6011 perm/sec)   p_kst 9.714000e-01   p_cons 3.230000e-01   p_joint 6.748000e-01

Outputting figure to mutsig2_images.part000000000032/CCDC86.2_1099_10000_0.9714_0.323_0.6748.png
                gene_name: CCDC86
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.67 
     ci_joint_bounds_left: 0.67 
    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.165.3896/
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/181708/iteration1/scatter.0000000032
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 32 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119662: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000033> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:44:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000033.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000033.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 33  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    138.11 sec.
    Max Memory :      1226 MB
    Max Swap   :      3763 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.165.3896/
-whichjob
33
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 33: processing genes 2896 - 2986
Calculating significance of each gene.
Using projection method.
2896	CCNJL	1
2897	CCNK	1
2898	CCNL1	1
2899	CCNL2	1
2900	CCNO	1
2901	CCNT1	1
2902	CCNT2	1
2903	CCNY	1
2904	CCNYL1	1
2905	CCPG1	1.356305e-01
2906	CCR1	1
2907	CCR10	1
2908	CCR2	1
2909	CCR3	5.227917e-03
2910	CCR4	1
2911	CCR5	1
2912	CCR6	1
2913	CCR7	1
2914	CCR8	1
2915	CCR9	1
2916	CCRL1	1
2917	CCRL2	1.435010e-01
2918	CCRN4L	1
2919	CCS	1
2920	CCT2	1
2921	CCT3	1
2922	CCT4	1
2923	CCT5	1
2924	CCT6A	1
2925	CCT6B	1
2926	CCT7	1
2927	CCT8	1
2928	CCT8L2	1
2929	CD101	2.745860e-01
2930	CD109	5.353240e-01
2931	CD14	1
2932	CD151	1
2933	CD160	1
2934	CD163	2.485777e-02
2935	CD163L1	5.276565e-01
2936	CD164	1
2937	CD164L2	3.518601e-02
2938	CD177	1
2939	CD180	1
2940	CD19	1.966774e-01
2941	CD1A	8.991125e-02
2942	CD1B	1
2943	CD1C	1
2944	CD1D	8.038107e-03
2945	CD1E	1.969563e-01
2946	CD2	1
2947	CD200	3.674559e-03
2948	CD200R1	1
2949	CD200R1L	1.212599e-01
2950	CD207	1
2951	CD209	1
2952	CD22	2.452584e-01
2953	CD226	8.901976e-02
2954	CD244	1.139455e-01
2955	CD247	1
2956	CD248	1
2957	CD27	3.346637e-02
2958	CD274	1
2959	CD276	1.085978e-01
2960	CD28	1
2961	CD2AP	2.597229e-01
2962	CD2BP2	1
2963	CD300A	9.114418e-02
2964	CD300C	1
2965	CD300E	1
2966	CD300LB	1
2967	CD300LD	1
2968	CD300LF	1
2969	CD300LG	1
2970	CD302	1
2971	CD320	1
2972	CD33	1
2973	CD34	1
2974	CD36	1
2975	CD37	1
2976	CD38	1
2977	CD3D	1
2978	CD3E	1
2979	CD3EAP	1.311191e-01
2980	CD3G	1
2981	CD4	1
2982	CD40	1
2983	CD40LG	1
2984	CD44	1
2985	CD46	1
2986	CD47	7.851722e-02
Done

Running MutSig 2:
Scatter job 33: processing genes 2896 - 2986
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CD163
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.038716e-02	ci left: 6.150242e-01	ci right 6.341032e-01	k: 6246	n:10000
Cons ci ratio: 4.864673e-02	ci left: 3.840068e-01	ci right 4.032552e-01	k: 3936	n:10000
KS ci ratio: 2.682125e-02	ci left: 6.718638e-01	ci right 6.902306e-01	k: 6811	n:10000
CD163   10000 perm   2 sec   (5055 perm/sec)   p_kst 6.811000e-01   p_cons 3.936000e-01   p_joint 6.246000e-01

Outputting figure to mutsig2_images.part000000000033/CD163.3_3535_10000_0.6811_0.3936_0.6246.png
                gene_name: CD163
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.62 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.63 

Current progress: 25 percent done.
CCR3
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: 2.029646e-02	ci left: 7.804640e-01	ci right 7.965676e-01	k: 7886	n:10000
KS ci ratio: 1.749659e-02	ci left: 8.264586e-01	ci right 8.411464e-01	k: 8339	n:10000
CCR3   10000 perm   2 sec   (6516 perm/sec)   p_kst 8.339000e-01   p_cons 7.886000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000033/CCR3.2_1139_10000_0.8339_0.7886_1.png
                gene_name: CCR3
               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: 0.80 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
CD1D
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.195997e-02	ci left: 9.092595e-01	ci right 9.202975e-01	k: 9149	n:10000
Cons ci ratio: 2.398435e-02	ci left: 7.187589e-01	ci right 7.363084e-01	k: 7276	n:10000
KS ci ratio: 2.834659e-02	ci left: 6.471987e-01	ci right 6.659100e-01	k: 6566	n:10000
CD1D   10000 perm   2 sec   (6606 perm/sec)   p_kst 6.566000e-01   p_cons 7.276000e-01   p_joint 9.149000e-01

Outputting figure to mutsig2_images.part000000000033/CD1D.2_1032_10000_0.6566_0.7276_0.9149.png
                gene_name: CD1D
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.74 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 75 percent done.
CD200
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.327604e-02	ci left: 2.142811e-01	ci right 2.306809e-01	k: 2224	n:10000
Cons ci ratio: 2.797670e-02	ci left: 6.531359e-01	ci right 6.717694e-01	k: 6625	n:10000
KS ci ratio: 1.111580e-01	ci left: 1.044194e-01	ci right 1.168085e-01	k: 1105	n:10000
CD200   10000 perm   2 sec   (6186 perm/sec)   p_kst 1.105000e-01   p_cons 6.625000e-01   p_joint 2.224000e-01

Joint ci ratio: 5.053094e-02	ci left: 2.254210e-01	ci right 2.371572e-01	k: 4625	n:20000
Cons ci ratio: 1.885489e-02	ci left: 6.771535e-01	ci right 6.900931e-01	k: 13673	n:20000
KS ci ratio: 7.868207e-02	ci left: 1.060395e-01	ci right 1.147742e-01	k: 2207	n:20000
CD200   20000 perm   4 sec   (5456 perm/sec)   p_kst 1.103500e-01   p_cons 6.836500e-01   p_joint 2.312500e-01

Outputting figure to mutsig2_images.part000000000033/CD200.2_913_20000_0.11035_0.68365_0.23125.png
                gene_name: CD200
               theta_stop: 0.079 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.23 
     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.165.3896/
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/181708/iteration1/scatter.0000000033
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 33 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119666: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000034> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:44:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000034.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000034.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 34  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    131.09 sec.
    Max Memory :       900 MB
    Max Swap   :      3698 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.165.3896/
-whichjob
34
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 34: processing genes 2987 - 3076
Calculating significance of each gene.
Using projection method.
2987	CD48	1
2988	CD5	1
2989	CD52	1
2990	CD53	1
2991	CD55	1.613224e-01
2992	CD58	4.031879e-02
2993	CD59	1
2994	CD5L	1.189867e-01
2995	CD6	1
2996	CD63	1
2997	CD68	1
2998	CD69	1
2999	CD7	1
3000/18094 3000	CD70	1
3001	CD72	1
3002	CD74	1
3003	CD79A	1
3004	CD79B	1
3005	CD80	1
3006	CD81	1
3007	CD82	1
3008	CD83	1
3009	CD84	1
3010	CD86	4.992202e-02
3011	CD8A	7.180156e-02
3012	CD8B	1
3013	CD9	1
3014	CD93	1.357811e-01
3015	CD96	1
3016	CD97	1
3017	CD99	1
3018	CD99L2	7.827575e-02
3019	CDA	1
3020	CDADC1	5.913153e-02
3021	CDAN1	1.078054e-01
3022	CDC123	1
3023	CDC14A	1
3024	CDC14B	1
3025	CDC16	1
3026	CDC20	1
3027	CDC20B	1
3028	CDC23	1
3029	CDC25A	1
3030	CDC25B	1
3031	CDC25C	1
3032	CDC26	1
3033	CDC27	1
3034	CDC34	1
3035	CDC37	1
3036	CDC37L1	1
3037	CDC40	1
3038	CDC42	1
3039	CDC42BPA	3.920796e-01
3040	CDC42BPB	1
3041	CDC42BPG	1
3042	CDC42EP1	1
3043	CDC42EP2	1
3044	CDC42EP3	1
3045	CDC42EP4	1
3046	CDC42SE1	1
3047	CDC42SE2	1
3048	CDC45	1
3049	CDC5L	1
3050	CDC6	2.337816e-01
3051	CDC7	1
3052	CDC73	1
3053	CDCA2	1
3054	CDCA3	1
3055	CDCA4	1
3056	CDCA5	2.200601e-02
3057	CDCA7	1
3058	CDCA7L	4.220580e-02
3059	CDCA8	1
3060	CDCP1	2.702494e-01
3061	CDCP2	1
3062	CDH1	1.019374e-01
3063	CDH10	1
3064	CDH11	1.706371e-02
3065	CDH12	2.069747e-01
3066	CDH13	1
3067	CDH15	2.769230e-01
3068	CDH16	1.403250e-01
3069	CDH17	1
3070	CDH18	1
3071	CDH19	1
3072	CDH2	1
3073	CDH20	1
3074	CDH22	1.109076e-03
3075	CDH23	1
3076	CDH24	2.902168e-01
Done

Running MutSig 2:
Scatter job 34: processing genes 2987 - 3076
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CDH22
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.883062e-02	ci left: 3.822151e-01	ci right 4.014480e-01	k: 3918	n:10000
Cons ci ratio: 5.246035e-02	ci left: 3.487950e-01	ci right 3.676877e-01	k: 3582	n:10000
KS ci ratio: 7.798399e-02	ci left: 1.937745e-01	ci right 2.095997e-01	k: 2016	n:10000
CDH22   10000 perm   3 sec   (3069 perm/sec)   p_kst 2.016000e-01   p_cons 3.582000e-01   p_joint 3.918000e-01

Outputting figure to mutsig2_images.part000000000034/CDH22.3_2531_10000_0.2016_0.3582_0.3918.png
                gene_name: CDH22
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 33 percent done.
CDAN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.290849e-03	ci left: 9.794135e-01	ci right 9.847004e-01	k: 9822	n:10000
Cons ci ratio: 2.578324e-02	ci left: 6.888946e-01	ci right 7.069900e-01	k: 6980	n:10000
KS ci ratio: 5.848272e-02	ci left: 3.008425e-01	ci right 3.190683e-01	k: 3099	n:10000
CDAN1   10000 perm   2 sec   (5491 perm/sec)   p_kst 3.099000e-01   p_cons 6.980000e-01   p_joint 9.822000e-01

Outputting figure to mutsig2_images.part000000000034/CDAN1.2_3796_10000_0.3099_0.698_0.9822.png
                gene_name: CDAN1
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 67 percent done.
CDH11
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: 4.411732e-02	ci left: 4.313368e-01	ci right 4.508976e-01	k: 4411	n:10000
KS ci ratio: 4.269655e-02	ci left: 4.474996e-01	ci right 4.671253e-01	k: 4573	n:10000
CDH11   10000 perm   2 sec   (5828 perm/sec)   p_kst 4.573000e-01   p_cons 4.411000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000034/CDH11.2_2435_10000_0.4573_0.4411_1.png
                gene_name: CDH11
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000034
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 34 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1701>
Subject: Job 1119669: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1701>, 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/181708/iteration1/scatter.0000000035> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:44:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000035.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000035.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 35  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    129.18 sec.
    Max Memory :      1145 MB
    Max Swap   :      3853 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.165.3896/
-whichjob
35
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 35: processing genes 3077 - 3166
Calculating significance of each gene.
Using projection method.
3077	CDH26	3.360301e-01
3078	CDH3	1.488417e-01
3079	CDH4	3.034832e-01
3080	CDH5	1
3081	CDH6	2.734432e-01
3082	CDH7	1
3083	CDH8	4.685431e-03
3084	CDH9	1.435602e-01
3085	CDHR1	1
3086	CDHR2	4.005189e-01
3087	CDHR3	1
3088	CDHR5	1.004752e-01
3089	CDIPT	1
3090	CDK1	1
3091	CDK10	1
3092	CDK11A	1
3093	CDK11B	1
3094	CDK12	1.457904e-01
3095	CDK13	8.064853e-02
3096	CDK14	1
3097	CDK15	1
3098	CDK16	1
3099	CDK17	1
3100	CDK18	1
3101	CDK19	1
3102	CDK2	1
3103	CDK20	6.062780e-02
3104	CDK2AP1	1
3105	CDK2AP2	1
3106	CDK3	1
3107	CDK4	1
3108	CDK5	9.446598e-02
3109	CDK5R1	1
3110	CDK5R2	1
3111	CDK5RAP1	1
3112	CDK5RAP2	4.953439e-01
3113	CDK5RAP3	1
3114	CDK6	1.141242e-01
3115	CDK7	1
3116	CDK8	1.256049e-01
3117	CDK9	1
3118	CDKAL1	1
3119	CDKL1	1
3120	CDKL2	1
3121	CDKL3	1
3122	CDKL4	1.608078e-02
3123	CDKL5	1
3124	CDKN1A	2.694099e-03
3125	CDKN1B	1
3126	CDKN2A	1
3127	CDKN2AIP	1
3128	CDKN2AIPNL	1
3129	CDKN2B	1
3130	CDKN2C	1
3131	CDKN2D	1
3132	CDKN3	1
3133	CDNF	1
3134	CDO1	1
3135	CDON	1
3136	CDR1	1
3137	CDR2	1.132011e-01
3138	CDRT1	1
3139	CDRT15	1
3140	CDRT4	1
3141	CDS1	1
3142	CDS2	1
3143	CDSN	1
3144	CDT1	1
3145	CDV3	1
3146	CDX1	1
3147	CDX2	1
3148	CDX4	1
3149	CDYL	2.592893e-01
3150	CDYL2	3.438981e-02
3151	CEACAM1	1
3152	CEACAM16	1
3153	CEACAM18	1
3154	CEACAM19	1
3155	CEACAM20	1
3156	CEACAM21	6.269381e-02
3157	CEACAM3	1
3158	CEACAM4	7.157491e-02
3159	CEACAM5	8.592990e-02
3160	CEACAM6	1
3161	CEACAM7	1
3162	CEACAM8	1
3163	CEBPB	1
3164	CEBPD	1
3165	CEBPE	1
3166	CEBPG	1
Done

Running MutSig 2:
Scatter job 35: processing genes 3077 - 3166
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CDH8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.301616e-02	ci left: 4.438072e-01	ci right 4.634199e-01	k: 4536	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: 1.404114e-01	ci left: 6.720239e-02	ci right 7.744844e-02	k: 722	n:10000
CDH8   10000 perm   3 sec   (3404 perm/sec)   p_kst 7.220000e-02   p_cons 2.154000e-01   p_joint 4.536000e-01

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 5.198736e-02	ci left: 2.155626e-01	ci right 2.271185e-01	k: 4426	n:20000
KS ci ratio: 9.988490e-02	ci left: 6.791774e-02	ci right 7.510743e-02	k: 1429	n:20000
CDH8   20000 perm   10 sec   (1962 perm/sec)   p_kst 7.145000e-02   p_cons 2.213000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000035/CDH8.2_2444_20000_0.07145_0.2213_1.png
                gene_name: CDH8
               theta_stop: 0.100 
                    nperm: 20000 
                     p_ks: 0.071 
        ci_ks_bounds_left: 0.068 
       ci_ks_bounds_right: 0.075 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.23 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 25 percent done.
CDK12
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.895237e-02	ci left: 6.375415e-01	ci right 6.563728e-01	k: 6470	n:10000
Cons ci ratio: 4.029907e-02	ci left: 4.762592e-01	ci right 4.959489e-01	k: 4861	n:10000
KS ci ratio: 2.855426e-02	ci left: 6.438786e-01	ci right 6.626321e-01	k: 6533	n:10000
CDK12   10000 perm   3 sec   (3826 perm/sec)   p_kst 6.533000e-01   p_cons 4.861000e-01   p_joint 6.470000e-01

Outputting figure to mutsig2_images.part000000000035/CDK12.2_4529_10000_0.6533_0.4861_0.647.png
                gene_name: CDK12
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.65 
     ci_joint_bounds_left: 0.64 
    ci_joint_bounds_right: 0.66 

Current progress: 50 percent done.
CDK13
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: 2.093398e-02	ci left: 7.698255e-01	ci right 7.862122e-01	k: 7781	n:10000
KS ci ratio: 2.316878e-02	ci left: 7.323953e-01	ci right 7.496640e-01	k: 7411	n:10000
CDK13   10000 perm   3 sec   (3388 perm/sec)   p_kst 7.411000e-01   p_cons 7.781000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000035/CDK13.2_4595_10000_0.7411_0.7781_1.png
                gene_name: CDK13
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.75 
                   p_cons: 0.78 
      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: 75 percent done.
CDKN1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.850438e-02	ci left: 3.854004e-01	ci right 4.046607e-01	k: 3950	n:10000
Cons ci ratio: 5.283892e-02	ci left: 3.455153e-01	ci right 3.643693e-01	k: 3549	n:10000
KS ci ratio: 2.558774e-02	ci left: 6.921210e-01	ci right 7.101617e-01	k: 7012	n:10000
CDKN1A   10000 perm   2 sec   (6225 perm/sec)   p_kst 7.012000e-01   p_cons 3.549000e-01   p_joint 3.950000e-01

Outputting figure to mutsig2_images.part000000000035/CDKN1A.2_503_10000_0.7012_0.3549_0.395.png
                gene_name: CDKN1A
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.71 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.36 
                  p_joint: 0.40 
     ci_joint_bounds_left: 0.39 
    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.165.3896/
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/181708/iteration1/scatter.0000000035
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 35 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1642>
Subject: Job 1119675: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, 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/181708/iteration1/scatter.0000000036> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:45:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000036.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000036.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 36  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    199.37 sec.
    Max Memory :      1420 MB
    Max Swap   :      4068 MB

    Max Processes  :         7
    Max Threads    :        94

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/
-whichjob
36
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 36: processing genes 3167 - 3257
Calculating significance of each gene.
Using projection method.
3167	CEBPZ	1
3168	CECR1	1
3169	CECR2	4.643197e-01
3170	CECR5	1
3171	CECR6	1
3172	CEL	1
3173	CELA1	1
3174	CELA2A	1
3175	CELA2B	1
3176	CELA3A	1.160556e-01
3177	CELA3B	8.356275e-02
3178	CELF1	1
3179	CELF2	1
3180	CELF3	1
3181	CELF4	1.069979e-01
3182	CELF5	1
3183	CELF6	1
3184	CELSR1	1
3185	CELSR2	5.505601e-01
3186	CELSR3	2.323892e-01
3187	CEMP1	1
3188	CEND1	1
3189	CENPA	1
3190	CENPB	1
3191	CENPBD1	1
3192	CENPC1	1
3193	CENPE	1
3194	CENPF	7.455972e-01
3195	CENPH	1
3196	CENPI	1
3197	CENPJ	4.714386e-01
3198	CENPK	1
3199	CENPL	1
3200	CENPM	1
3201	CENPN	1
3202	CENPO	1
3203	CENPP	1
3204	CENPQ	1
3205	CENPT	7.733510e-02
3206	CENPV	1
3207	CENPW	1
3208	CEP110	1
3209	CEP120	1
3210	CEP135	2.821112e-01
3211	CEP152	1
3212	CEP164	1
3213	CEP170	3.698079e-01
3214	CEP192	1
3215	CEP250	5.164245e-01
3216	CEP290	1
3217	CEP350	3.266363e-01
3218	CEP55	1
3219	CEP57	1
3220	CEP63	1
3221	CEP68	1
3222	CEP70	1
3223	CEP72	7.377345e-02
3224	CEP76	1.462420e-01
3225	CEP78	2.148890e-01
3226	CEP97	2.864093e-01
3227	CEPT1	1
3228	CER1	1
3229	CERCAM	1
3230	CERK	1
3231	CERKL	1
3232	CES1	1
3233	CES2	2.700014e-01
3234	CES3	1
3235	CES7	1
3236	CES8	1
3237	CETN1	1
3238	CETN2	1
3239	CETN3	1
3240	CETP	1
3241	CFB	6.527736e-02
3242	CFD	1
3243	CFDP1	1
3244	CFH	6.204926e-02
3245	CFHR1	1
3246	CFHR2	1
3247	CFHR3	6.808661e-02
3248	CFHR4	1
3249	CFHR5	1
3250	CFI	1
3251	CFL1	1
3252	CFL2	1
3253	CFLAR	1
3254	CFP	1
3255	CFTR	1
3256	CGA	1
3257	CGB	1
Done

Running MutSig 2:
Scatter job 36: processing genes 3167 - 3257
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CEP350
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.938381e-02	ci left: 1.540423e-01	ci right 1.685555e-01	k: 1612	n:10000
Cons ci ratio: 5.798077e-02	ci left: 3.045120e-01	ci right 3.227967e-01	k: 3136	n:10000
KS ci ratio: 1.418978e-01	ci left: 6.584842e-02	ci right 7.600325e-02	k: 708	n:10000
CEP350   10000 perm   3 sec   (3660 perm/sec)   p_kst 7.080000e-02   p_cons 3.136000e-01   p_joint 1.612000e-01

Joint ci ratio: 6.210645e-02	ci left: 1.609165e-01	ci right 1.712808e-01	k: 3321	n:20000
Cons ci ratio: 4.103203e-02	ci left: 3.068742e-01	ci right 3.197801e-01	k: 6266	n:20000
KS ci ratio: 1.026566e-01	ci left: 6.445142e-02	ci right 7.147482e-02	k: 1358	n:20000
CEP350   20000 perm   8 sec   (2531 perm/sec)   p_kst 6.790000e-02   p_cons 3.133000e-01   p_joint 1.660500e-01

Joint ci ratio: 6.500776e-02	ci left: 1.045749e-01	ci right 1.116345e-01	k: 3242	n:30000
Cons ci ratio: 3.345718e-02	ci left: 3.086501e-01	ci right 3.191859e-01	k: 9417	n:30000
KS ci ratio: 8.461250e-02	ci left: 6.393474e-02	ci right 6.961617e-02	k: 2002	n:30000
CEP350   30000 perm   11 sec   (2671 perm/sec)   p_kst 6.673333e-02   p_cons 3.139000e-01   p_joint 1.080667e-01

Outputting figure to mutsig2_images.part000000000036/CEP350.3_9502_30000_0.066733_0.3139_0.10807.png
                gene_name: CEP350
               theta_stop: 0.085 
                    nperm: 30000 
                     p_ks: 0.067 
        ci_ks_bounds_left: 0.064 
       ci_ks_bounds_right: 0.070 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.10 
    ci_joint_bounds_right: 0.11 

Current progress: 20 percent done.
CELSR2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.283885e-02	ci left: 1.442309e-01	ci right 1.583729e-01	k: 1512	n:10000
Cons ci ratio: 1.058573e-02	ci left: 9.269922e-01	ci right 9.369544e-01	k: 9321	n:10000
KS ci ratio: 2.371212e-01	ci left: 2.344048e-02	ci right 2.983930e-02	k: 265	n:10000
CELSR2   10000 perm   3 sec   (3989 perm/sec)   p_kst 2.650000e-02   p_cons 9.321000e-01   p_joint 1.512000e-01

Joint ci ratio: 3.444866e-02	ci left: 3.861721e-01	ci right 3.997590e-01	k: 7859	n:20000
Cons ci ratio: 6.983439e-03	ci left: 9.369781e-01	ci right 9.435931e-01	k: 18807	n:20000
KS ci ratio: 1.636116e-01	ci left: 2.561344e-02	ci right 3.022518e-02	k: 557	n:20000
CELSR2   20000 perm   5 sec   (3669 perm/sec)   p_kst 2.785000e-02   p_cons 9.403500e-01   p_joint 3.929500e-01

Joint ci ratio: 5.529150e-02	ci left: 1.395179e-01	ci right 1.474846e-01	k: 4304	n:30000
Cons ci ratio: 5.771292e-03	ci left: 9.361983e-01	ci right 9.416496e-01	k: 28169	n:30000
KS ci ratio: 1.309572e-01	ci left: 2.709791e-02	ci right 3.092736e-02	k: 869	n:30000
CELSR2   30000 perm   8 sec   (3546 perm/sec)   p_kst 2.896667e-02   p_cons 9.389667e-01   p_joint 1.434667e-01

Joint ci ratio: 2.926541e-02	ci left: 3.050956e-01	ci right 3.141820e-01	k: 12385	n:40000
Cons ci ratio: 4.981099e-03	ci left: 9.369663e-01	ci right 9.416696e-01	k: 37574	n:40000
KS ci ratio: 1.131118e-01	ci left: 2.749885e-02	ci right 3.081998e-02	k: 1165	n:40000
CELSR2   40000 perm   12 sec   (3461 perm/sec)   p_kst 2.912500e-02   p_cons 9.393500e-01   p_joint 3.096250e-01

Joint ci ratio: 2.516238e-02	ci left: 3.226490e-01	ci right 3.308911e-01	k: 16338	n:50000
Cons ci ratio: 4.502199e-03	ci left: 9.359929e-01	ci right 9.402361e-01	k: 46907	n:50000
KS ci ratio: 1.015840e-01	ci left: 2.744900e-02	ci right 3.040603e-02	k: 1445	n:50000
CELSR2   50000 perm   15 sec   (3397 perm/sec)   p_kst 2.890000e-02   p_cons 9.381400e-01   p_joint 3.267600e-01

Joint ci ratio: 3.794912e-02	ci left: 1.481106e-01	ci right 1.538565e-01	k: 9058	n:60000
Cons ci ratio: 4.120101e-03	ci left: 9.358886e-01	ci right 9.397689e-01	k: 56271	n:60000
KS ci ratio: 9.279383e-02	ci left: 2.754145e-02	ci right 3.023771e-02	k: 1732	n:60000
CELSR2   60000 perm   18 sec   (3340 perm/sec)   p_kst 2.886667e-02   p_cons 9.378500e-01   p_joint 1.509667e-01

Outputting figure to mutsig2_images.part000000000036/CELSR2.2_8908_60000_0.028867_0.93785_0.15097.png
                gene_name: CELSR2
               theta_stop: 0.093 
                    nperm: 60000 
                     p_ks: 0.029 
        ci_ks_bounds_left: 0.028 
       ci_ks_bounds_right: 0.030 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.15 
    ci_joint_bounds_right: 0.15 

Current progress: 40 percent done.
CELSR3
Processing conservation and coverage...
99% 
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: 3.472158e-02	ci left: 5.505053e-01	ci right 5.700595e-01	k: 5603	n:10000
KS ci ratio: 1.682287e-02	ci left: 8.372473e-01	ci right 8.515515e-01	k: 8445	n:10000
CELSR3   10000 perm   3 sec   (3828 perm/sec)   p_kst 8.445000e-01   p_cons 5.603000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000036/CELSR3.2_10079_10000_0.8445_0.5603_1.png
                gene_name: CELSR3
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.84 
       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: 60 percent done.
CEP72
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.640648e-01	ci left: 4.955445e-02	ci right 5.850759e-02	k: 539	n:10000
Cons ci ratio: 7.398202e-02	ci left: 2.110256e-01	ci right 2.273383e-01	k: 2191	n:10000
KS ci ratio: 3.350785e-01	ci left: 1.123901e-02	ci right 1.585081e-02	k: 134	n:10000
CEP72   10000 perm   2 sec   (6170 perm/sec)   p_kst 1.340000e-02   p_cons 2.191000e-01   p_joint 5.390000e-02

Joint ci ratio: 1.816657e-01	ci left: 2.068037e-02	ci right 2.485997e-02	k: 454	n:20000
Cons ci ratio: 5.192711e-02	ci left: 2.159589e-01	ci right 2.275221e-01	k: 4434	n:20000
KS ci ratio: 2.405811e-01	ci left: 1.152325e-02	ci right 1.472062e-02	k: 261	n:20000
CEP72   20000 perm   4 sec   (5466 perm/sec)   p_kst 1.305000e-02   p_cons 2.217000e-01   p_joint 2.270000e-02

Joint ci ratio: 1.604815e-01	ci left: 1.793329e-02	ci right 2.109407e-02	k: 584	n:30000
Cons ci ratio: 4.255260e-02	ci left: 2.157861e-01	ci right 2.252014e-01	k: 6614	n:30000
KS ci ratio: 2.042102e-01	ci left: 1.089357e-02	ci right 1.340224e-02	k: 363	n:30000
CEP72   30000 perm   6 sec   (5203 perm/sec)   p_kst 1.210000e-02   p_cons 2.204667e-01   p_joint 1.946667e-02

Joint ci ratio: 8.704904e-02	ci left: 4.614583e-02	ci right 5.037006e-02	k: 1929	n:40000
Cons ci ratio: 3.664390e-02	ci left: 2.183573e-01	ci right 2.265331e-01	k: 8897	n:40000
KS ci ratio: 1.765454e-01	ci left: 1.109941e-02	ci right 1.327227e-02	k: 486	n:40000
CEP72   40000 perm   8 sec   (5019 perm/sec)   p_kst 1.215000e-02   p_cons 2.224250e-01   p_joint 4.822500e-02

Joint ci ratio: 1.622458e-01	ci left: 1.060309e-02	ci right 1.249425e-02	k: 576	n:50000
Cons ci ratio: 3.278197e-02	ci left: 2.187213e-01	ci right 2.260309e-01	k: 11118	n:50000
KS ci ratio: 1.607031e-01	ci left: 1.081430e-02	ci right 1.272302e-02	k: 587	n:50000
CEP72   50000 perm   10 sec   (4863 perm/sec)   p_kst 1.174000e-02   p_cons 2.223600e-01   p_joint 1.152000e-02

Joint ci ratio: 1.469757e-01	ci left: 1.085493e-02	ci right 1.259278e-02	k: 702	n:60000
Cons ci ratio: 2.979767e-02	ci left: 2.205199e-01	ci right 2.272069e-01	k: 13431	n:60000
KS ci ratio: 1.449042e-01	ci left: 1.117622e-02	ci right 1.293811e-02	k: 722	n:60000
CEP72   60000 perm   13 sec   (4740 perm/sec)   p_kst 1.203333e-02   p_cons 2.238500e-01   p_joint 1.170000e-02

Joint ci ratio: 1.340348e-01	ci left: 1.126176e-02	ci right 1.289334e-02	k: 844	n:70000
Cons ci ratio: 2.754842e-02	ci left: 2.212570e-01	ci right 2.274516e-01	k: 15704	n:70000
KS ci ratio: 1.337148e-01	ci left: 1.131701e-02	ci right 1.295237e-02	k: 848	n:70000
CEP72   70000 perm   15 sec   (4633 perm/sec)   p_kst 1.211429e-02   p_cons 2.243429e-01   p_joint 1.205714e-02

Joint ci ratio: 1.594311e-01	ci left: 6.901801e-03	ci right 8.109328e-03	k: 599	n:80000
Cons ci ratio: 2.576325e-02	ci left: 2.215378e-01	ci right 2.273322e-01	k: 17954	n:80000
KS ci ratio: 1.254909e-01	ci left: 1.129330e-02	ci right 1.281739e-02	k: 963	n:80000
CEP72   80000 perm   18 sec   (4534 perm/sec)   p_kst 1.203750e-02   p_cons 2.244250e-01   p_joint 7.487500e-03

Joint ci ratio: 1.306726e-01	ci left: 9.252707e-03	ci right 1.055695e-02	k: 890	n:90000
Cons ci ratio: 2.428857e-02	ci left: 2.217220e-01	ci right 2.271846e-01	k: 20200	n:90000
KS ci ratio: 1.179568e-01	ci left: 1.140670e-02	ci right 1.284723e-02	k: 1090	n:90000
CEP72   90000 perm   20 sec   (4440 perm/sec)   p_kst 1.211111e-02   p_cons 2.244444e-01   p_joint 9.888889e-03

Joint ci ratio: 1.333290e-01	ci left: 7.998313e-03	ci right 9.150463e-03	k: 856	n:100000
Cons ci ratio: 2.303923e-02	ci left: 2.219069e-01	ci right 2.270890e-01	k: 22449	n:100000
KS ci ratio: 1.131490e-01	ci left: 1.118850e-02	ci right 1.254003e-02	k: 1185	n:100000
CEP72   100000 perm   23 sec   (4351 perm/sec)   p_kst 1.185000e-02   p_cons 2.244900e-01   p_joint 8.560000e-03

Joint ci ratio: 1.269681e-01	ci left: 8.045168e-03	ci right 9.144613e-03	k: 944	n:110000
Cons ci ratio: 2.195272e-02	ci left: 2.222543e-01	ci right 2.271966e-01	k: 24719	n:110000
KS ci ratio: 1.082028e-01	ci left: 1.115252e-02	ci right 1.243705e-02	k: 1296	n:110000
CEP72   110000 perm   26 sec   (4266 perm/sec)   p_kst 1.178182e-02   p_cons 2.247182e-01   p_joint 8.581818e-03

Joint ci ratio: 1.209084e-01	ci left: 8.158047e-03	ci right 9.215902e-03	k: 1041	n:120000
Cons ci ratio: 2.099968e-02	ci left: 2.226648e-01	ci right 2.273985e-01	k: 27003	n:120000
KS ci ratio: 1.028962e-01	ci left: 1.133473e-02	ci right 1.257236e-02	k: 1433	n:120000
CEP72   120000 perm   29 sec   (4185 perm/sec)   p_kst 1.194167e-02   p_cons 2.250250e-01   p_joint 8.675000e-03

Joint ci ratio: 1.156922e-01	ci left: 8.247141e-03	ci right 9.267260e-03	k: 1137	n:130000
Cons ci ratio: 2.013249e-02	ci left: 2.235065e-01	ci right 2.280596e-01	k: 29351	n:130000
KS ci ratio: 9.906944e-02	ci left: 1.131010e-02	ci right 1.249644e-02	k: 1546	n:130000
CEP72   130000 perm   32 sec   (4114 perm/sec)   p_kst 1.189231e-02   p_cons 2.257769e-01   p_joint 8.746154e-03

Joint ci ratio: 1.070979e-01	ci left: 8.970666e-03	ci right 9.992662e-03	k: 1326	n:140000
Cons ci ratio: 1.938702e-02	ci left: 2.238255e-01	ci right 2.282144e-01	k: 31642	n:140000
KS ci ratio: 9.581557e-02	ci left: 1.124788e-02	ci right 1.238676e-02	k: 1653	n:140000
CEP72   140000 perm   35 sec   (4040 perm/sec)   p_kst 1.180714e-02   p_cons 2.260143e-01   p_joint 9.471429e-03

Joint ci ratio: 1.033486e-01	ci left: 9.008771e-03	ci right 9.996994e-03	k: 1424	n:150000
Cons ci ratio: 1.872615e-02	ci left: 2.239652e-01	ci right 2.282054e-01	k: 33912	n:150000
KS ci ratio: 9.222868e-02	ci left: 1.135085e-02	ci right 1.245480e-02	k: 1784	n:150000
CEP72   150000 perm   38 sec   (3977 perm/sec)   p_kst 1.189333e-02   p_cons 2.260800e-01   p_joint 9.493333e-03

Joint ci ratio: 9.332667e-02	ci left: 1.039698e-02	ci right 1.142086e-02	k: 1744	n:160000
Cons ci ratio: 1.813569e-02	ci left: 2.239525e-01	ci right 2.280574e-01	k: 36160	n:160000
KS ci ratio: 8.861953e-02	ci left: 1.154556e-02	ci right 1.262223e-02	k: 1932	n:160000
CEP72   160000 perm   41 sec   (3912 perm/sec)   p_kst 1.207500e-02   p_cons 2.260000e-01   p_joint 1.090000e-02

Outputting figure to mutsig2_images.part000000000036/CEP72.2_1992_160000_0.012075_0.226_0.0109.png
                gene_name: CEP72
               theta_stop: 0.093 
                    nperm: 160000 
                     p_ks: 0.012 
        ci_ks_bounds_left: 0.012 
       ci_ks_bounds_right: 0.013 
                   p_cons: 0.23 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.011 
     ci_joint_bounds_left: 0.010 
    ci_joint_bounds_right: 0.011 

Current progress: 80 percent done.
CFH
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.700555e-02	ci left: 4.004372e-01	ci right 4.198151e-01	k: 4101	n:10000
Cons ci ratio: 5.140488e-02	ci left: 3.581397e-01	ci right 3.771375e-01	k: 3676	n:10000
KS ci ratio: 1.091164e-01	ci left: 1.080293e-01	ci right 1.205964e-01	k: 1142	n:10000
CFH   10000 perm   2 sec   (5588 perm/sec)   p_kst 1.142000e-01   p_cons 3.676000e-01   p_joint 4.101000e-01

Joint ci ratio: 3.162265e-02	ci left: 4.275652e-01	ci right 4.413538e-01	k: 8689	n:20000
Cons ci ratio: 3.635250e-02	ci left: 3.609125e-01	ci right 3.743260e-01	k: 7352	n:20000
KS ci ratio: 7.616503e-02	ci left: 1.124780e-01	ci right 1.214337e-01	k: 2338	n:20000
CFH   20000 perm   4 sec   (4932 perm/sec)   p_kst 1.169000e-01   p_cons 3.676000e-01   p_joint 4.344500e-01

Outputting figure to mutsig2_images.part000000000036/CFH.2_3802_20000_0.1169_0.3676_0.43445.png
                gene_name: CFH
               theta_stop: 0.076 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.37 
                  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.165.3896/
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/181708/iteration1/scatter.0000000036
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 36 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119679: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000037> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 11:39:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000037.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000037.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 37  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :   3471.87 sec.
    Max Memory :      1355 MB
    Max Swap   :      3984 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.165.3896/
-whichjob
37
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 37: processing genes 3258 - 3347
Calculating significance of each gene.
Using projection method.
3258	CGB1	1
3259	CGB2	1
3260	CGB5	1
3261	CGB7	1
3262	CGB8	1
3263	CGGBP1	1
3264	CGN	3.057084e-01
3265	CGNL1	1
3266	CGREF1	1
3267	CGRRF1	1
3268	CH25H	1
3269	CHAC1	1
3270	CHAC2	1
3271	CHAD	1
3272	CHAF1A	1.847040e-01
3273	CHAF1B	1
3274	CHAT	1
3275	CHCHD1	1
3276	CHCHD10	1
3277	CHCHD2	1
3278	CHCHD3	5.818296e-02
3279	CHCHD4	1
3280	CHCHD5	3.356198e-02
3281	CHCHD6	1
3282	CHCHD7	1
3283	CHCHD8	1
3284	CHD1	2.873082e-01
3285	CHD1L	1
3286	CHD2	4.936798e-01
3287	CHD3	4.630492e-01
3288	CHD4	1
3289	CHD5	4.904150e-01
3290	CHD6	6.389735e-01
3291	CHD7	8.165518e-02
3292	CHD8	2.470137e-01
3293	CHD9	4.452181e-01
3294	CHDH	1
3295	CHEK1	1
3296	CHEK2	1
3297	CHERP	3.026369e-01
3298	CHFR	1.487904e-01
3299	CHGA	1
3300	CHGB	1
3301	CHI3L1	1
3302	CHI3L2	1
3303	CHIA	2.302375e-01
3304	CHIC2	1
3305	CHID1	1
3306	CHIT1	1
3307	CHKA	1
3308	CHKB	1.754330e-01
3309	CHL1	1
3310	CHM	1
3311	CHML	1
3312	CHMP1A	1
3313	CHMP1B	7.609819e-02
3314	CHMP2A	1
3315	CHMP2B	1
3316	CHMP4A	1
3317	CHMP4B	1
3318	CHMP4C	1
3319	CHMP5	1
3320	CHMP6	1
3321	CHMP7	1
3322	CHN1	4.251499e-02
3323	CHN2	1.375914e-02
3324	CHODL	3.705735e-02
3325	CHORDC1	1
3326	CHP	1
3327	CHP2	1
3328	CHPF	1
3329	CHPF2	1
3330	CHPT1	5.018928e-02
3331	CHRAC1	1
3332	CHRD	1
3333	CHRDL1	1
3334	CHRDL2	1
3335	CHRFAM7A	1
3336	CHRM1	1
3337	CHRM2	1
3338	CHRM3	1
3339	CHRM4	1
3340	CHRM5	1
3341	CHRNA1	1
3342	CHRNA10	1
3343	CHRNA2	1
3344	CHRNA3	1.360018e-01
3345	CHRNA4	1
3346	CHRNA5	1
3347	CHRNA6	1
Done

Running MutSig 2:
Scatter job 37: processing genes 3258 - 3347
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CHD7
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: 2.325328e-02	ci left: 7.309807e-01	ci right 7.482795e-01	k: 7397	n:10000
KS ci ratio: 1.559459e-02	ci left: 8.565131e-01	ci right 8.700745e-01	k: 8634	n:10000
CHD7   10000 perm   3 sec   (3859 perm/sec)   p_kst 8.634000e-01   p_cons 7.397000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000037/CHD7.3_9142_10000_0.8634_0.7397_1.png
                gene_name: CHD7
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.87 
                   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: 17 percent done.
CHD2
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: 8.971858e-03	ci left: 9.458575e-01	ci right 9.544778e-01	k: 9503	n:10000
KS ci ratio: 1.385306e+00	ci left: 2.814811e-04	ci right 1.441732e-03	k: 7	n:10000
CHD2   10000 perm   2 sec   (4825 perm/sec)   p_kst 7.000000e-04   p_cons 9.503000e-01   p_joint 7.000000e-04

Joint ci ratio: 1.011735e+00	ci left: 3.827477e-04	ci right 1.174202e-03	k: 14	n:20000
Cons ci ratio: 6.737528e-03	ci left: 9.409801e-01	ci right 9.473900e-01	k: 18885	n:20000
KS ci ratio: 1.011735e+00	ci left: 3.827477e-04	ci right 1.174202e-03	k: 14	n:20000
CHD2   20000 perm   5 sec   (4370 perm/sec)   p_kst 7.000000e-04   p_cons 9.442500e-01   p_joint 7.000000e-04

Joint ci ratio: 9.504544e-01	ci left: 3.048758e-04	ci right 8.659558e-04	k: 16	n:30000
Cons ci ratio: 5.508361e-03	ci left: 9.414404e-01	ci right 9.466731e-01	k: 28323	n:30000
KS ci ratio: 9.504544e-01	ci left: 3.048758e-04	ci right 8.659558e-04	k: 16	n:30000
CHD2   30000 perm   7 sec   (4206 perm/sec)   p_kst 5.333333e-04   p_cons 9.441000e-01   p_joint 5.333333e-04

Joint ci ratio: 8.551789e-01	ci left: 3.054389e-04	ci right 7.721043e-04	k: 20	n:40000
Cons ci ratio: 4.816236e-03	ci left: 9.407595e-01	ci right 9.453259e-01	k: 37723	n:40000
KS ci ratio: 8.551789e-01	ci left: 3.054389e-04	ci right 7.721043e-04	k: 20	n:40000
CHD2   40000 perm   10 sec   (4097 perm/sec)   p_kst 5.000000e-04   p_cons 9.430750e-01   p_joint 5.000000e-04

Joint ci ratio: 7.405955e-01	ci left: 3.558926e-04	ci right 7.855751e-04	k: 27	n:50000
Cons ci ratio: 4.312238e-03	ci left: 9.408913e-01	ci right 9.449771e-01	k: 47148	n:50000
KS ci ratio: 7.405955e-01	ci left: 3.558926e-04	ci right 7.855751e-04	k: 27	n:50000
CHD2   50000 perm   12 sec   (4004 perm/sec)   p_kst 5.400000e-04   p_cons 9.429600e-01   p_joint 5.400000e-04

Joint ci ratio: 6.442399e-01	ci left: 4.202669e-04	ci right 8.305571e-04	k: 36	n:60000
Cons ci ratio: 3.942887e-03	ci left: 9.408951e-01	ci right 9.446286e-01	k: 56567	n:60000
KS ci ratio: 6.442399e-01	ci left: 4.202669e-04	ci right 8.305571e-04	k: 36	n:60000
CHD2   60000 perm   15 sec   (3924 perm/sec)   p_kst 6.000000e-04   p_cons 9.427833e-01   p_joint 6.000000e-04

Joint ci ratio: 5.715947e-01	ci left: 4.811501e-04	ci right 8.764403e-04	k: 46	n:70000
Cons ci ratio: 3.496481e-03	ci left: 9.455755e-01	ci right 9.489015e-01	k: 66308	n:70000
KS ci ratio: 5.715947e-01	ci left: 4.811501e-04	ci right 8.764403e-04	k: 46	n:70000
CHD2   70000 perm   18 sec   (3851 perm/sec)   p_kst 6.571429e-04   p_cons 9.472571e-01   p_joint 6.571429e-04

Joint ci ratio: 5.487314e-01	ci left: 4.639215e-04	ci right 8.239026e-04	k: 50	n:80000
Cons ci ratio: 3.276980e-03	ci left: 9.454884e-01	ci right 9.486041e-01	k: 75765	n:80000
KS ci ratio: 5.487314e-01	ci left: 4.639215e-04	ci right 8.239026e-04	k: 50	n:80000
CHD2   80000 perm   21 sec   (3783 perm/sec)   p_kst 6.250000e-04   p_cons 9.470625e-01   p_joint 6.250000e-04

Joint ci ratio: 5.236661e-01	ci left: 4.604047e-04	ci right 7.953718e-04	k: 55	n:90000
Cons ci ratio: 3.079810e-03	ci left: 9.458990e-01	ci right 9.488276e-01	k: 85264	n:90000
KS ci ratio: 5.236661e-01	ci left: 4.604047e-04	ci right 7.953718e-04	k: 55	n:90000
CHD2   90000 perm   24 sec   (3719 perm/sec)   p_kst 6.111111e-04   p_cons 9.473778e-01   p_joint 6.111111e-04

Joint ci ratio: 4.898407e-01	ci left: 4.841422e-04	ci right 8.059727e-04	k: 63	n:100000
Cons ci ratio: 2.918744e-03	ci left: 9.460794e-01	ci right 9.488546e-01	k: 94748	n:100000
KS ci ratio: 4.898407e-01	ci left: 4.841422e-04	ci right 8.059727e-04	k: 63	n:100000
CHD2   100000 perm   27 sec   (3655 perm/sec)   p_kst 6.300000e-04   p_cons 9.474800e-01   p_joint 6.300000e-04

Joint ci ratio: 4.683784e-01	ci left: 4.880874e-04	ci right 7.937877e-04	k: 69	n:110000
Cons ci ratio: 2.785130e-03	ci left: 9.460644e-01	ci right 9.487119e-01	k: 104214	n:110000
KS ci ratio: 4.683784e-01	ci left: 4.880874e-04	ci right 7.937877e-04	k: 69	n:110000
CHD2   110000 perm   31 sec   (3590 perm/sec)   p_kst 6.272727e-04   p_cons 9.474000e-01   p_joint 6.272727e-04

Joint ci ratio: 4.437065e-01	ci left: 5.064254e-04	ci right 8.019090e-04	k: 77	n:120000
Cons ci ratio: 2.665206e-03	ci left: 9.461725e-01	ci right 9.487058e-01	k: 113694	n:120000
KS ci ratio: 4.437065e-01	ci left: 5.064254e-04	ci right 8.019090e-04	k: 77	n:120000
CHD2   120000 perm   34 sec   (3539 perm/sec)   p_kst 6.416667e-04   p_cons 9.474500e-01   p_joint 6.416667e-04

Joint ci ratio: 4.275672e-01	ci left: 5.085621e-04	ci right 7.914086e-04	k: 83	n:130000
Cons ci ratio: 2.567648e-03	ci left: 9.459471e-01	ci right 9.483867e-01	k: 123133	n:130000
KS ci ratio: 4.275672e-01	ci left: 5.085621e-04	ci right 7.914086e-04	k: 83	n:130000
CHD2   130000 perm   37 sec   (3490 perm/sec)   p_kst 6.384615e-04   p_cons 9.471769e-01   p_joint 6.384615e-04

Joint ci ratio: 4.153856e-01	ci left: 5.041622e-04	ci right 7.743611e-04	k: 88	n:140000
Cons ci ratio: 2.477374e-03	ci left: 9.458641e-01	ci right 9.482173e-01	k: 132587	n:140000
KS ci ratio: 4.153856e-01	ci left: 5.041622e-04	ci right 7.743611e-04	k: 88	n:140000
CHD2   140000 perm   41 sec   (3441 perm/sec)   p_kst 6.285714e-04   p_cons 9.470500e-01   p_joint 6.285714e-04

Joint ci ratio: 3.978857e-01	ci left: 5.184319e-04	ci right 7.814942e-04	k: 96	n:150000
Cons ci ratio: 2.392965e-03	ci left: 9.459216e-01	ci right 9.481944e-01	k: 142060	n:150000
KS ci ratio: 3.978857e-01	ci left: 5.184319e-04	ci right 7.814942e-04	k: 96	n:150000
CHD2   150000 perm   44 sec   (3392 perm/sec)   p_kst 6.400000e-04   p_cons 9.470667e-01   p_joint 6.400000e-04

Joint ci ratio: 3.880129e-01	ci left: 5.141920e-04	ci right 7.669739e-04	k: 101	n:160000
Cons ci ratio: 2.314900e-03	ci left: 9.460488e-01	ci right 9.482475e-01	k: 151545	n:160000
KS ci ratio: 3.880129e-01	ci left: 5.141920e-04	ci right 7.669739e-04	k: 101	n:160000
CHD2   160000 perm   48 sec   (3343 perm/sec)   p_kst 6.312500e-04   p_cons 9.471563e-01   p_joint 6.312500e-04

Joint ci ratio: 3.788403e-01	ci left: 5.105221e-04	ci right 7.540916e-04	k: 106	n:170000
Cons ci ratio: 2.247302e-03	ci left: 9.460135e-01	ci right 9.481477e-01	k: 161005	n:170000
KS ci ratio: 3.788403e-01	ci left: 5.105221e-04	ci right 7.540916e-04	k: 106	n:170000
CHD2   170000 perm   52 sec   (3300 perm/sec)   p_kst 6.235294e-04   p_cons 9.470882e-01   p_joint 6.235294e-04

Joint ci ratio: 3.638446e-01	ci left: 5.274962e-04	ci right 7.668403e-04	k: 115	n:180000
Cons ci ratio: 2.186386e-03	ci left: 9.459326e-01	ci right 9.480085e-01	k: 170456	n:180000
KS ci ratio: 3.638446e-01	ci left: 5.274962e-04	ci right 7.668403e-04	k: 115	n:180000
CHD2   180000 perm   55 sec   (3257 perm/sec)   p_kst 6.388889e-04   p_cons 9.469778e-01   p_joint 6.388889e-04

Joint ci ratio: 3.477266e-01	ci left: 5.524574e-04	ci right 7.895240e-04	k: 126	n:190000
Cons ci ratio: 2.125364e-03	ci left: 9.460894e-01	ci right 9.481075e-01	k: 179950	n:190000
KS ci ratio: 3.477266e-01	ci left: 5.524574e-04	ci right 7.895240e-04	k: 126	n:190000
CHD2   190000 perm   59 sec   (3214 perm/sec)   p_kst 6.631579e-04   p_cons 9.471053e-01   p_joint 6.631579e-04

Joint ci ratio: 3.410787e-01	ci left: 5.476721e-04	ci right 7.772023e-04	k: 131	n:200000
Cons ci ratio: 2.071964e-03	ci left: 9.460949e-01	ci right 9.480621e-01	k: 189417	n:200000
KS ci ratio: 3.410787e-01	ci left: 5.476721e-04	ci right 7.772023e-04	k: 131	n:200000
CHD2   200000 perm   63 sec   (3172 perm/sec)   p_kst 6.550000e-04   p_cons 9.470850e-01   p_joint 6.550000e-04

Joint ci ratio: 3.347981e-01	ci left: 5.433816e-04	ci right 7.660155e-04	k: 136	n:210000
Cons ci ratio: 2.018166e-03	ci left: 9.463118e-01	ci right 9.482282e-01	k: 198928	n:210000
KS ci ratio: 3.347981e-01	ci left: 5.433816e-04	ci right 7.660155e-04	k: 136	n:210000
CHD2   210000 perm   67 sec   (3132 perm/sec)   p_kst 6.476190e-04   p_cons 9.472762e-01   p_joint 6.476190e-04

Joint ci ratio: 3.300170e-01	ci left: 5.353466e-04	ci right 7.508910e-04	k: 140	n:220000
Cons ci ratio: 1.974431e-03	ci left: 9.461977e-01	ci right 9.480723e-01	k: 208371	n:220000
KS ci ratio: 3.300170e-01	ci left: 5.353466e-04	ci right 7.508910e-04	k: 140	n:220000
CHD2   220000 perm   71 sec   (3093 perm/sec)   p_kst 6.363636e-04   p_cons 9.471409e-01   p_joint 6.363636e-04

Joint ci ratio: 3.254349e-01	ci left: 5.280309e-04	ci right 7.370613e-04	k: 144	n:230000
Cons ci ratio: 1.929302e-03	ci left: 9.463089e-01	ci right 9.481407e-01	k: 217863	n:230000
KS ci ratio: 3.254349e-01	ci left: 5.280309e-04	ci right 7.370613e-04	k: 144	n:230000
CHD2   230000 perm   75 sec   (3055 perm/sec)   p_kst 6.260870e-04   p_cons 9.472304e-01   p_joint 6.260870e-04

Joint ci ratio: 3.199660e-01	ci left: 5.251755e-04	ci right 7.288658e-04	k: 149	n:240000
Cons ci ratio: 1.889567e-03	ci left: 9.462810e-01	ci right 9.480749e-01	k: 227324	n:240000
KS ci ratio: 3.199660e-01	ci left: 5.251755e-04	ci right 7.288658e-04	k: 149	n:240000
CHD2   240000 perm   79 sec   (3019 perm/sec)   p_kst 6.208333e-04   p_cons 9.471833e-01   p_joint 6.208333e-04

Joint ci ratio: 3.157847e-01	ci left: 5.188918e-04	ci right 7.169839e-04	k: 153	n:250000
Cons ci ratio: 1.851894e-03	ci left: 9.462718e-01	ci right 9.480298e-01	k: 236789	n:250000
KS ci ratio: 3.157847e-01	ci left: 5.188918e-04	ci right 7.169839e-04	k: 153	n:250000
CHD2   250000 perm   84 sec   (2983 perm/sec)   p_kst 6.120000e-04   p_cons 9.471560e-01   p_joint 6.120000e-04

Joint ci ratio: 3.078877e-01	ci left: 5.272967e-04	ci right 7.225761e-04	k: 161	n:260000
Cons ci ratio: 1.815619e-03	ci left: 9.463063e-01	ci right 9.480298e-01	k: 246265	n:260000
KS ci ratio: 3.078877e-01	ci left: 5.272967e-04	ci right 7.225761e-04	k: 161	n:260000
CHD2   260000 perm   88 sec   (2947 perm/sec)   p_kst 6.192308e-04   p_cons 9.471731e-01   p_joint 6.192308e-04

Joint ci ratio: 3.014435e-01	ci left: 5.317118e-04	ci right 7.237154e-04	k: 168	n:270000
Cons ci ratio: 1.782649e-03	ci left: 9.462677e-01	ci right 9.479597e-01	k: 255722	n:270000
KS ci ratio: 3.014435e-01	ci left: 5.317118e-04	ci right 7.237154e-04	k: 168	n:270000
CHD2   270000 perm   93 sec   (2912 perm/sec)   p_kst 6.222222e-04   p_cons 9.471185e-01   p_joint 6.222222e-04

Joint ci ratio: 2.979395e-01	ci left: 5.259336e-04	ci right 7.132254e-04	k: 172	n:280000
Cons ci ratio: 1.749600e-03	ci left: 9.463365e-01	ci right 9.479971e-01	k: 265208	n:280000
KS ci ratio: 2.979395e-01	ci left: 5.259336e-04	ci right 7.132254e-04	k: 172	n:280000
CHD2   280000 perm   97 sec   (2879 perm/sec)   p_kst 6.142857e-04   p_cons 9.471714e-01   p_joint 6.142857e-04

Joint ci ratio: 2.929036e-01	ci left: 5.269546e-04	ci right 7.108498e-04	k: 178	n:290000
Cons ci ratio: 1.717788e-03	ci left: 9.464320e-01	ci right 9.480625e-01	k: 274703	n:290000
KS ci ratio: 2.929036e-01	ci left: 5.269546e-04	ci right 7.108498e-04	k: 178	n:290000
CHD2   290000 perm   102 sec   (2846 perm/sec)   p_kst 6.137931e-04   p_cons 9.472517e-01   p_joint 6.137931e-04

Joint ci ratio: 2.888971e-01	ci left: 5.248401e-04	ci right 7.050344e-04	k: 183	n:300000
Cons ci ratio: 1.688493e-03	ci left: 9.464710e-01	ci right 9.480737e-01	k: 284183	n:300000
KS ci ratio: 2.888971e-01	ci left: 5.248401e-04	ci right 7.050344e-04	k: 183	n:300000
CHD2   300000 perm   107 sec   (2813 perm/sec)   p_kst 6.100000e-04   p_cons 9.472767e-01   p_joint 6.100000e-04

Joint ci ratio: 2.850506e-01	ci left: 5.228779e-04	ci right 6.995782e-04	k: 188	n:310000
Cons ci ratio: 1.659842e-03	ci left: 9.465564e-01	ci right 9.481320e-01	k: 293678	n:310000
KS ci ratio: 2.850506e-01	ci left: 5.228779e-04	ci right 6.995782e-04	k: 188	n:310000
CHD2   310000 perm   111 sec   (2783 perm/sec)   p_kst 6.064516e-04   p_cons 9.473484e-01   p_joint 6.064516e-04

Joint ci ratio: 2.806310e-01	ci left: 5.239582e-04	ci right 6.977928e-04	k: 194	n:320000
Cons ci ratio: 1.633161e-03	ci left: 9.466020e-01	ci right 9.481523e-01	k: 303162	n:320000
KS ci ratio: 2.806310e-01	ci left: 5.239582e-04	ci right 6.977928e-04	k: 194	n:320000
CHD2   320000 perm   116 sec   (2752 perm/sec)   p_kst 6.062500e-04   p_cons 9.473812e-01   p_joint 6.062500e-04

Joint ci ratio: 2.757254e-01	ci left: 5.278135e-04	ci right 6.993352e-04	k: 201	n:330000
Cons ci ratio: 1.609828e-03	ci left: 9.465139e-01	ci right 9.480419e-01	k: 312603	n:330000
KS ci ratio: 2.757254e-01	ci left: 5.278135e-04	ci right 6.993352e-04	k: 201	n:330000
CHD2   330000 perm   121 sec   (2721 perm/sec)   p_kst 6.090909e-04   p_cons 9.472818e-01   p_joint 6.090909e-04

Joint ci ratio: 2.737017e-01	ci left: 5.205051e-04	ci right 6.881968e-04	k: 204	n:340000
Cons ci ratio: 1.588255e-03	ci left: 9.463808e-01	ci right 9.478880e-01	k: 322027	n:340000
KS ci ratio: 2.737017e-01	ci left: 5.205051e-04	ci right 6.881968e-04	k: 204	n:340000
CHD2   340000 perm   126 sec   (2693 perm/sec)   p_kst 6.000000e-04   p_cons 9.471382e-01   p_joint 6.000000e-04

Joint ci ratio: 2.691448e-01	ci left: 5.242728e-04	ci right 6.898915e-04	k: 211	n:350000
Cons ci ratio: 1.563898e-03	ci left: 9.464885e-01	ci right 9.479727e-01	k: 331532	n:350000
KS ci ratio: 2.691448e-01	ci left: 5.242728e-04	ci right 6.898915e-04	k: 211	n:350000
CHD2   350000 perm   131 sec   (2664 perm/sec)   p_kst 6.028571e-04   p_cons 9.472343e-01   p_joint 6.028571e-04

Joint ci ratio: 2.630117e-01	ci left: 5.356353e-04	ci right 7.003534e-04	k: 221	n:360000
Cons ci ratio: 1.542124e-03	ci left: 9.464924e-01	ci right 9.479559e-01	k: 341002	n:360000
KS ci ratio: 2.630117e-01	ci left: 5.356353e-04	ci right 7.003534e-04	k: 221	n:360000
CHD2   360000 perm   137 sec   (2637 perm/sec)   p_kst 6.138889e-04   p_cons 9.472278e-01   p_joint 6.138889e-04

Joint ci ratio: 2.589604e-01	ci left: 5.388402e-04	ci right 7.015785e-04	k: 228	n:370000
Cons ci ratio: 1.520618e-03	ci left: 9.465371e-01	ci right 9.479802e-01	k: 350487	n:370000
KS ci ratio: 2.589604e-01	ci left: 5.388402e-04	ci right 7.015785e-04	k: 228	n:370000
CHD2   370000 perm   142 sec   (2611 perm/sec)   p_kst 6.162162e-04   p_cons 9.472622e-01   p_joint 6.162162e-04

Joint ci ratio: 2.545516e-01	ci left: 5.443584e-04	ci right 7.055201e-04	k: 236	n:380000
Cons ci ratio: 1.499986e-03	ci left: 9.465796e-01	ci right 9.480031e-01	k: 359972	n:380000
KS ci ratio: 2.545516e-01	ci left: 5.443584e-04	ci right 7.055201e-04	k: 236	n:380000
CHD2   380000 perm   147 sec   (2583 perm/sec)   p_kst 6.210526e-04   p_cons 9.472947e-01   p_joint 6.210526e-04

Joint ci ratio: 2.519086e-01	ci left: 5.424073e-04	ci right 7.010624e-04	k: 241	n:390000
Cons ci ratio: 1.481768e-03	ci left: 9.465116e-01	ci right 9.479177e-01	k: 369415	n:390000
KS ci ratio: 2.519086e-01	ci left: 5.424073e-04	ci right 7.010624e-04	k: 241	n:390000
CHD2   390000 perm   153 sec   (2556 perm/sec)   p_kst 6.179487e-04   p_cons 9.472179e-01   p_joint 6.179487e-04

Joint ci ratio: 2.483423e-01	ci left: 5.452503e-04	ci right 7.021304e-04	k: 248	n:400000
Cons ci ratio: 1.463866e-03	ci left: 9.464698e-01	ci right 9.478587e-01	k: 378867	n:400000
KS ci ratio: 2.483423e-01	ci left: 5.452503e-04	ci right 7.021304e-04	k: 248	n:400000
CHD2   400000 perm   158 sec   (2530 perm/sec)   p_kst 6.200000e-04   p_cons 9.471675e-01   p_joint 6.200000e-04

Joint ci ratio: 2.468606e-01	ci left: 5.388144e-04	ci right 6.927758e-04	k: 251	n:410000
Cons ci ratio: 1.444376e-03	ci left: 9.465847e-01	ci right 9.479553e-01	k: 388382	n:410000
KS ci ratio: 2.468606e-01	ci left: 5.388144e-04	ci right 6.927758e-04	k: 251	n:410000
CHD2   410000 perm   164 sec   (2505 perm/sec)   p_kst 6.121951e-04   p_cons 9.472732e-01   p_joint 6.121951e-04

Joint ci ratio: 2.435015e-01	ci left: 5.416283e-04	ci right 6.939696e-04	k: 258	n:420000
Cons ci ratio: 1.426625e-03	ci left: 9.466248e-01	ci right 9.479786e-01	k: 397868	n:420000
KS ci ratio: 2.435015e-01	ci left: 5.416283e-04	ci right 6.939696e-04	k: 258	n:420000
CHD2   420000 perm   169 sec   (2480 perm/sec)   p_kst 6.142857e-04   p_cons 9.473048e-01   p_joint 6.142857e-04

Joint ci ratio: 2.416433e-01	ci left: 5.377691e-04	ci right 6.876976e-04	k: 262	n:430000
Cons ci ratio: 1.411188e-03	ci left: 9.465438e-01	ci right 9.478828e-01	k: 407303	n:430000
KS ci ratio: 2.416433e-01	ci left: 5.377691e-04	ci right 6.876976e-04	k: 262	n:430000
CHD2   430000 perm   175 sec   (2455 perm/sec)   p_kst 6.093023e-04   p_cons 9.472163e-01   p_joint 6.093023e-04

Joint ci ratio: 2.389333e-01	ci left: 5.383625e-04	ci right 6.865239e-04	k: 268	n:440000
Cons ci ratio: 1.394208e-03	ci left: 9.466129e-01	ci right 9.479358e-01	k: 416802	n:440000
KS ci ratio: 2.389333e-01	ci left: 5.383625e-04	ci right 6.865239e-04	k: 268	n:440000
CHD2   440000 perm   181 sec   (2431 perm/sec)   p_kst 6.090909e-04   p_cons 9.472773e-01   p_joint 6.090909e-04

Joint ci ratio: 2.350331e-01	ci left: 5.452118e-04	ci right 6.924528e-04	k: 277	n:450000
Cons ci ratio: 1.379143e-03	ci left: 9.465828e-01	ci right 9.478914e-01	k: 426258	n:450000
KS ci ratio: 2.350331e-01	ci left: 5.452118e-04	ci right 6.924528e-04	k: 277	n:450000
CHD2   450000 perm   187 sec   (2407 perm/sec)   p_kst 6.155556e-04   p_cons 9.472400e-01   p_joint 6.155556e-04

Joint ci ratio: 2.317221e-01	ci left: 5.497340e-04	ci right 6.958055e-04	k: 285	n:460000
Cons ci ratio: 1.364675e-03	ci left: 9.465455e-01	ci right 9.478402e-01	k: 435710	n:460000
KS ci ratio: 2.317221e-01	ci left: 5.497340e-04	ci right 6.958055e-04	k: 285	n:460000
CHD2   460000 perm   193 sec   (2383 perm/sec)   p_kst 6.195652e-04   p_cons 9.471957e-01   p_joint 6.195652e-04

Joint ci ratio: 2.285473e-01	ci left: 5.540777e-04	ci right 6.990018e-04	k: 293	n:470000
Cons ci ratio: 1.350680e-03	ci left: 9.465076e-01	ci right 9.477890e-01	k: 445161	n:470000
KS ci ratio: 2.285473e-01	ci left: 5.540777e-04	ci right 6.990018e-04	k: 293	n:470000
CHD2   470000 perm   199 sec   (2361 perm/sec)   p_kst 6.234043e-04   p_cons 9.471511e-01   p_joint 6.234043e-04

Joint ci ratio: 2.277749e-01	ci left: 5.464627e-04	ci right 6.888441e-04	k: 295	n:480000
Cons ci ratio: 1.337190e-03	ci left: 9.464651e-01	ci right 9.477336e-01	k: 454609	n:480000
KS ci ratio: 2.277749e-01	ci left: 5.464627e-04	ci right 6.888441e-04	k: 295	n:480000
CHD2   480000 perm   205 sec   (2338 perm/sec)   p_kst 6.145833e-04   p_cons 9.471021e-01   p_joint 6.145833e-04

Joint ci ratio: 2.262518e-01	ci left: 5.430094e-04	ci right 6.834129e-04	k: 299	n:490000
Cons ci ratio: 1.322369e-03	ci left: 9.465558e-01	ci right 9.478103e-01	k: 464121	n:490000
KS ci ratio: 2.262518e-01	ci left: 5.430094e-04	ci right 6.834129e-04	k: 299	n:490000
CHD2   490000 perm   211 sec   (2317 perm/sec)   p_kst 6.102041e-04   p_cons 9.471857e-01   p_joint 6.102041e-04

Joint ci ratio: 2.222134e-01	ci left: 5.529139e-04	ci right 6.929778e-04	k: 310	n:500000
Cons ci ratio: 1.308420e-03	ci left: 9.466127e-01	ci right 9.478541e-01	k: 473618	n:500000
KS ci ratio: 2.222134e-01	ci left: 5.529139e-04	ci right 6.929778e-04	k: 310	n:500000
CHD2   500000 perm   218 sec   (2296 perm/sec)   p_kst 6.200000e-04   p_cons 9.472360e-01   p_joint 6.200000e-04

Joint ci ratio: 2.194090e-01	ci left: 5.568914e-04	ci right 6.959422e-04	k: 318	n:510000
Cons ci ratio: 1.295335e-03	ci left: 9.466340e-01	ci right 9.478629e-01	k: 483098	n:510000
KS ci ratio: 2.194090e-01	ci left: 5.568914e-04	ci right 6.959422e-04	k: 318	n:510000
CHD2   510000 perm   224 sec   (2275 perm/sec)   p_kst 6.235294e-04   p_cons 9.472510e-01   p_joint 6.235294e-04

Joint ci ratio: 2.173743e-01	ci left: 5.570893e-04	ci right 6.947273e-04	k: 324	n:520000
Cons ci ratio: 1.282510e-03	ci left: 9.466641e-01	ci right 9.478809e-01	k: 492583	n:520000
KS ci ratio: 2.173743e-01	ci left: 5.570893e-04	ci right 6.947273e-04	k: 324	n:520000
CHD2   520000 perm   231 sec   (2255 perm/sec)   p_kst 6.230769e-04   p_cons 9.472750e-01   p_joint 6.230769e-04

Joint ci ratio: 2.147470e-01	ci left: 5.608559e-04	ci right 6.975290e-04	k: 332	n:530000
Cons ci ratio: 1.269915e-03	ci left: 9.467046e-01	ci right 9.479094e-01	k: 502074	n:530000
KS ci ratio: 2.147470e-01	ci left: 5.608559e-04	ci right 6.975290e-04	k: 332	n:530000
CHD2   530000 perm   237 sec   (2235 perm/sec)   p_kst 6.264151e-04   p_cons 9.473094e-01   p_joint 6.264151e-04

Joint ci ratio: 2.131530e-01	ci left: 5.592327e-04	ci right 6.943665e-04	k: 337	n:540000
Cons ci ratio: 1.318288e-03	ci left: 9.418200e-01	ci right 9.430642e-01	k: 508920	n:540000
KS ci ratio: 2.131530e-01	ci left: 5.592327e-04	ci right 6.943665e-04	k: 337	n:540000
CHD2   540000 perm   244 sec   (2216 perm/sec)   p_kst 6.240741e-04   p_cons 9.424444e-01   p_joint 6.240741e-04

Joint ci ratio: 2.100674e-01	ci left: 5.662834e-04	ci right 7.008853e-04	k: 347	n:550000
Cons ci ratio: 1.306433e-03	ci left: 9.418103e-01	ci right 9.430433e-01	k: 518336	n:550000
KS ci ratio: 2.100674e-01	ci left: 5.662834e-04	ci right 7.008853e-04	k: 347	n:550000
CHD2   550000 perm   250 sec   (2196 perm/sec)   p_kst 6.309091e-04   p_cons 9.424291e-01   p_joint 6.309091e-04

Joint ci ratio: 2.082796e-01	ci left: 5.663243e-04	ci right 6.996442e-04	k: 353	n:560000
Cons ci ratio: 1.294296e-03	ci left: 9.418512e-01	ci right 9.430728e-01	k: 527780	n:560000
KS ci ratio: 2.082796e-01	ci left: 5.663243e-04	ci right 6.996442e-04	k: 353	n:560000
CHD2   560000 perm   257 sec   (2176 perm/sec)   p_kst 6.303571e-04   p_cons 9.424643e-01   p_joint 6.303571e-04

Joint ci ratio: 2.065367e-01	ci left: 5.663684e-04	ci right 6.984420e-04	k: 359	n:570000
Cons ci ratio: 1.283362e-03	ci left: 9.418167e-01	ci right 9.430279e-01	k: 537182	n:570000
KS ci ratio: 2.065367e-01	ci left: 5.663684e-04	ci right 6.984420e-04	k: 359	n:570000
CHD2   570000 perm   264 sec   (2157 perm/sec)   p_kst 6.298246e-04   p_cons 9.424246e-01   p_joint 6.298246e-04

Joint ci ratio: 2.053992e-01	ci left: 5.631442e-04	ci right 6.936518e-04	k: 363	n:580000
Cons ci ratio: 1.271911e-03	ci left: 9.418510e-01	ci right 9.430514e-01	k: 546623	n:580000
KS ci ratio: 2.053992e-01	ci left: 5.631442e-04	ci right 6.936518e-04	k: 363	n:580000
CHD2   580000 perm   271 sec   (2139 perm/sec)   p_kst 6.258621e-04   p_cons 9.424534e-01   p_joint 6.258621e-04

Joint ci ratio: 2.037270e-01	ci left: 5.632479e-04	ci right 6.925847e-04	k: 369	n:590000
Cons ci ratio: 1.261156e-03	ci left: 9.418502e-01	ci right 9.430404e-01	k: 556044	n:590000
KS ci ratio: 2.037270e-01	ci left: 5.632479e-04	ci right 6.925847e-04	k: 369	n:590000
CHD2   590000 perm   278 sec   (2121 perm/sec)   p_kst 6.254237e-04   p_cons 9.424475e-01   p_joint 6.254237e-04

Joint ci ratio: 2.012931e-01	ci left: 5.681000e-04	ci right 6.968010e-04	k: 378	n:600000
Cons ci ratio: 1.250361e-03	ci left: 9.418762e-01	ci right 9.430562e-01	k: 565481	n:600000
KS ci ratio: 2.012931e-01	ci left: 5.681000e-04	ci right 6.968010e-04	k: 378	n:600000
CHD2   600000 perm   285 sec   (2103 perm/sec)   p_kst 6.300000e-04   p_cons 9.424683e-01   p_joint 6.300000e-04

Joint ci ratio: 2.002396e-01	ci left: 5.650146e-04	ci right 6.922647e-04	k: 382	n:610000
Cons ci ratio: 1.239988e-03	ci left: 9.418882e-01	ci right 9.430584e-01	k: 574910	n:610000
KS ci ratio: 2.002396e-01	ci left: 5.650146e-04	ci right 6.922647e-04	k: 382	n:610000
CHD2   610000 perm   293 sec   (2085 perm/sec)   p_kst 6.262295e-04   p_cons 9.424754e-01   p_joint 6.262295e-04

Joint ci ratio: 1.984343e-01	ci left: 5.666283e-04	ci right 6.929522e-04	k: 389	n:620000
Cons ci ratio: 1.230108e-03	ci left: 9.418788e-01	ci right 9.430397e-01	k: 584326	n:620000
KS ci ratio: 1.984343e-01	ci left: 5.666283e-04	ci right 6.929522e-04	k: 389	n:620000
CHD2   620000 perm   300 sec   (2068 perm/sec)   p_kst 6.274194e-04   p_cons 9.424613e-01   p_joint 6.274194e-04

Joint ci ratio: 1.976760e-01	ci left: 5.621599e-04	ci right 6.869509e-04	k: 392	n:630000
Cons ci ratio: 1.221013e-03	ci left: 9.418203e-01	ci right 9.429725e-01	k: 593711	n:630000
KS ci ratio: 1.976760e-01	ci left: 5.621599e-04	ci right 6.869509e-04	k: 392	n:630000
CHD2   630000 perm   307 sec   (2051 perm/sec)   p_kst 6.222222e-04   p_cons 9.423984e-01   p_joint 6.222222e-04

Joint ci ratio: 1.961841e-01	ci left: 5.622889e-04	ci right 6.860540e-04	k: 398	n:640000
Cons ci ratio: 1.211802e-03	ci left: 9.417919e-01	ci right 9.429354e-01	k: 603114	n:640000
KS ci ratio: 1.961841e-01	ci left: 5.622889e-04	ci right 6.860540e-04	k: 398	n:640000
CHD2   640000 perm   315 sec   (2033 perm/sec)   p_kst 6.218750e-04   p_cons 9.423656e-01   p_joint 6.218750e-04

Joint ci ratio: 1.947255e-01	ci left: 5.624173e-04	ci right 6.851812e-04	k: 404	n:650000
Cons ci ratio: 1.203187e-03	ci left: 9.417289e-01	ci right 9.428641e-01	k: 612494	n:650000
KS ci ratio: 1.947255e-01	ci left: 5.624173e-04	ci right 6.851812e-04	k: 404	n:650000
CHD2   650000 perm   322 sec   (2017 perm/sec)   p_kst 6.215385e-04   p_cons 9.422985e-01   p_joint 6.215385e-04

Joint ci ratio: 1.935347e-01	ci left: 5.611034e-04	ci right 6.827432e-04	k: 409	n:660000
Cons ci ratio: 1.194968e-03	ci left: 9.416480e-01	ci right 9.427754e-01	k: 621861	n:660000
KS ci ratio: 1.935347e-01	ci left: 5.611034e-04	ci right 6.827432e-04	k: 409	n:660000
CHD2   660000 perm   330 sec   (2001 perm/sec)   p_kst 6.196970e-04   p_cons 9.422136e-01   p_joint 6.196970e-04

Joint ci ratio: 1.925978e-01	ci left: 5.584102e-04	ci right 6.788115e-04	k: 413	n:670000
Cons ci ratio: 1.186198e-03	ci left: 9.416356e-01	ci right 9.427546e-01	k: 631272	n:670000
KS ci ratio: 1.925978e-01	ci left: 5.584102e-04	ci right 6.788115e-04	k: 413	n:670000
CHD2   670000 perm   338 sec   (1985 perm/sec)   p_kst 6.164179e-04   p_cons 9.421970e-01   p_joint 6.164179e-04

Joint ci ratio: 1.912172e-01	ci left: 5.585979e-04	ci right 6.780759e-04	k: 419	n:680000
Cons ci ratio: 1.177713e-03	ci left: 9.416146e-01	ci right 9.427257e-01	k: 640677	n:680000
KS ci ratio: 1.912172e-01	ci left: 5.585979e-04	ci right 6.780759e-04	k: 419	n:680000
CHD2   680000 perm   345 sec   (1969 perm/sec)   p_kst 6.161765e-04   p_cons 9.421721e-01   p_joint 6.161765e-04

Joint ci ratio: 1.907641e-01	ci left: 5.532621e-04	ci right 6.712859e-04	k: 421	n:690000
Cons ci ratio: 1.169097e-03	ci left: 9.416235e-01	ci right 9.427264e-01	k: 650102	n:690000
KS ci ratio: 1.907641e-01	ci left: 5.532621e-04	ci right 6.712859e-04	k: 421	n:690000
CHD2   690000 perm   353 sec   (1953 perm/sec)   p_kst 6.101449e-04   p_cons 9.421768e-01   p_joint 6.101449e-04

Joint ci ratio: 1.898667e-01	ci left: 5.508003e-04	ci right 6.676824e-04	k: 425	n:700000
Cons ci ratio: 1.160332e-03	ci left: 9.416637e-01	ci right 9.427584e-01	k: 659549	n:700000
KS ci ratio: 1.898667e-01	ci left: 5.508003e-04	ci right 6.676824e-04	k: 425	n:700000
CHD2   700000 perm   361 sec   (1938 perm/sec)   p_kst 6.071429e-04   p_cons 9.422129e-01   p_joint 6.071429e-04

Joint ci ratio: 1.887623e-01	ci left: 5.497510e-04	ci right 6.656541e-04	k: 430	n:710000
Cons ci ratio: 1.151835e-03	ci left: 9.416957e-01	ci right 9.427824e-01	k: 668991	n:710000
KS ci ratio: 1.887623e-01	ci left: 5.497510e-04	ci right 6.656541e-04	k: 430	n:710000
CHD2   710000 perm   369 sec   (1923 perm/sec)   p_kst 6.056338e-04   p_cons 9.422408e-01   p_joint 6.056338e-04

Joint ci ratio: 1.876770e-01	ci left: 5.487328e-04	ci right 6.636803e-04	k: 435	n:720000
Cons ci ratio: 1.143435e-03	ci left: 9.417352e-01	ci right 9.428140e-01	k: 678439	n:720000
KS ci ratio: 1.876770e-01	ci left: 5.487328e-04	ci right 6.636803e-04	k: 435	n:720000
CHD2   720000 perm   378 sec   (1907 perm/sec)   p_kst 6.041667e-04   p_cons 9.422764e-01   p_joint 6.041667e-04

Joint ci ratio: 1.857690e-01	ci left: 5.529685e-04	ci right 6.674930e-04	k: 444	n:730000
Cons ci ratio: 1.135615e-03	ci left: 9.417351e-01	ci right 9.428065e-01	k: 687859	n:730000
KS ci ratio: 1.857690e-01	ci left: 5.529685e-04	ci right 6.674930e-04	k: 444	n:730000
CHD2   730000 perm   386 sec   (1892 perm/sec)   p_kst 6.082192e-04   p_cons 9.422726e-01   p_joint 6.082192e-04

Joint ci ratio: 1.851464e-01	ci left: 5.493617e-04	ci right 6.627150e-04	k: 447	n:740000
Cons ci ratio: 1.128248e-03	ci left: 9.417066e-01	ci right 9.427710e-01	k: 697258	n:740000
KS ci ratio: 1.851464e-01	ci left: 5.493617e-04	ci right 6.627150e-04	k: 447	n:740000
CHD2   740000 perm   394 sec   (1878 perm/sec)   p_kst 6.040541e-04   p_cons 9.422405e-01   p_joint 6.040541e-04

Joint ci ratio: 1.835149e-01	ci left: 5.522115e-04	ci right 6.650370e-04	k: 455	n:750000
Cons ci ratio: 1.120611e-03	ci left: 9.417190e-01	ci right 9.427762e-01	k: 706687	n:750000
KS ci ratio: 1.835149e-01	ci left: 5.522115e-04	ci right 6.650370e-04	k: 455	n:750000
CHD2   750000 perm   402 sec   (1864 perm/sec)   p_kst 6.066667e-04   p_cons 9.422493e-01   p_joint 6.066667e-04

Joint ci ratio: 1.827155e-01	ci left: 5.499674e-04	ci right 6.617908e-04	k: 459	n:760000
Cons ci ratio: 1.112736e-03	ci left: 9.417695e-01	ci right 9.428193e-01	k: 716145	n:760000
KS ci ratio: 1.827155e-01	ci left: 5.499674e-04	ci right 6.617908e-04	k: 459	n:760000
CHD2   760000 perm   411 sec   (1850 perm/sec)   p_kst 6.039474e-04   p_cons 9.422961e-01   p_joint 6.039474e-04

Joint ci ratio: 1.821230e-01	ci left: 5.465431e-04	ci right 6.572700e-04	k: 462	n:770000
Cons ci ratio: 1.105645e-03	ci left: 9.417573e-01	ci right 9.428004e-01	k: 725556	n:770000
KS ci ratio: 1.821230e-01	ci left: 5.465431e-04	ci right 6.572700e-04	k: 462	n:770000
CHD2   770000 perm   419 sec   (1837 perm/sec)   p_kst 6.000000e-04   p_cons 9.422805e-01   p_joint 6.000000e-04

Joint ci ratio: 1.809542e-01	ci left: 5.468789e-04	ci right 6.568850e-04	k: 468	n:780000
Cons ci ratio: 1.098700e-03	ci left: 9.417442e-01	ci right 9.427807e-01	k: 734966	n:780000
KS ci ratio: 1.809542e-01	ci left: 5.468789e-04	ci right 6.568850e-04	k: 468	n:780000
CHD2   780000 perm   428 sec   (1823 perm/sec)   p_kst 6.000000e-04   p_cons 9.422641e-01   p_joint 6.000000e-04

Joint ci ratio: 1.798077e-01	ci left: 5.472084e-04	ci right 6.565075e-04	k: 474	n:790000
Cons ci ratio: 1.091834e-03	ci left: 9.417365e-01	ci right 9.427666e-01	k: 744380	n:790000
KS ci ratio: 1.798077e-01	ci left: 5.472084e-04	ci right 6.565075e-04	k: 474	n:790000
CHD2   790000 perm   437 sec   (1810 perm/sec)   p_kst 6.000000e-04   p_cons 9.422532e-01   p_joint 6.000000e-04

Joint ci ratio: 1.790556e-01	ci left: 5.451436e-04	ci right 6.535255e-04	k: 478	n:800000
Cons ci ratio: 1.085456e-03	ci left: 9.416927e-01	ci right 9.427166e-01	k: 753765	n:800000
KS ci ratio: 1.790556e-01	ci left: 5.451436e-04	ci right 6.535255e-04	k: 478	n:800000
CHD2   800000 perm   445 sec   (1796 perm/sec)   p_kst 5.975000e-04   p_cons 9.422063e-01   p_joint 5.975000e-04

Joint ci ratio: 1.783129e-01	ci left: 5.431308e-04	ci right 6.506163e-04	k: 482	n:810000
Cons ci ratio: 1.078087e-03	ci left: 9.417615e-01	ci right 9.427786e-01	k: 763240	n:810000
KS ci ratio: 1.783129e-01	ci left: 5.431308e-04	ci right 6.506163e-04	k: 482	n:810000
CHD2   810000 perm   454 sec   (1783 perm/sec)   p_kst 5.950617e-04   p_cons 9.422716e-01   p_joint 5.950617e-04

Joint ci ratio: 1.770345e-01	ci left: 5.446643e-04	ci right 6.515977e-04	k: 489	n:820000
Cons ci ratio: 1.071129e-03	ci left: 9.418017e-01	ci right 9.428122e-01	k: 772693	n:820000
KS ci ratio: 1.770345e-01	ci left: 5.446643e-04	ci right 6.515977e-04	k: 489	n:820000
CHD2   820000 perm   463 sec   (1771 perm/sec)   p_kst 5.963415e-04   p_cons 9.423085e-01   p_joint 5.963415e-04

Joint ci ratio: 1.764954e-01	ci left: 5.415565e-04	ci right 6.475215e-04	k: 492	n:830000
Cons ci ratio: 1.064304e-03	ci left: 9.418410e-01	ci right 9.428451e-01	k: 782146	n:830000
KS ci ratio: 1.764954e-01	ci left: 5.415565e-04	ci right 6.475215e-04	k: 492	n:830000
CHD2   830000 perm   472 sec   (1758 perm/sec)   p_kst 5.927711e-04   p_cons 9.423446e-01   p_joint 5.927711e-04

Joint ci ratio: 1.756072e-01	ci left: 5.407995e-04	ci right 6.460273e-04	k: 497	n:840000
Cons ci ratio: 1.057654e-03	ci left: 9.418745e-01	ci right 9.428724e-01	k: 791595	n:840000
KS ci ratio: 1.756072e-01	ci left: 5.407995e-04	ci right 6.460273e-04	k: 497	n:840000
CHD2   840000 perm   481 sec   (1745 perm/sec)   p_kst 5.916667e-04   p_cons 9.423750e-01   p_joint 5.916667e-04

Joint ci ratio: 1.747323e-01	ci left: 5.400616e-04	ci right 6.445670e-04	k: 502	n:850000
Cons ci ratio: 1.051695e-03	ci left: 9.418483e-01	ci right 9.428405e-01	k: 800994	n:850000
KS ci ratio: 1.747323e-01	ci left: 5.400616e-04	ci right 6.445670e-04	k: 502	n:850000
CHD2   850000 perm   491 sec   (1733 perm/sec)   p_kst 5.905882e-04   p_cons 9.423459e-01   p_joint 5.905882e-04

Joint ci ratio: 1.742139e-01	ci left: 5.371177e-04	ci right 6.407127e-04	k: 505	n:860000
Cons ci ratio: 1.045523e-03	ci left: 9.418553e-01	ci right 9.428417e-01	k: 810421	n:860000
KS ci ratio: 1.742139e-01	ci left: 5.371177e-04	ci right 6.407127e-04	k: 505	n:860000
CHD2   860000 perm   500 sec   (1720 perm/sec)   p_kst 5.872093e-04   p_cons 9.423500e-01   p_joint 5.872093e-04

Joint ci ratio: 1.730211e-01	ci left: 5.386404e-04	ci right 6.417434e-04	k: 512	n:870000
Cons ci ratio: 1.039393e-03	ci left: 9.418691e-01	ci right 9.428497e-01	k: 819854	n:870000
KS ci ratio: 1.730211e-01	ci left: 5.386404e-04	ci right 6.417434e-04	k: 512	n:870000
CHD2   870000 perm   509 sec   (1708 perm/sec)   p_kst 5.885057e-04   p_cons 9.423609e-01   p_joint 5.885057e-04

Joint ci ratio: 1.720181e-01	ci left: 5.390432e-04	ci right 6.415632e-04	k: 518	n:880000
Cons ci ratio: 1.033606e-03	ci left: 9.418576e-01	ci right 9.428327e-01	k: 829265	n:880000
KS ci ratio: 1.720181e-01	ci left: 5.390432e-04	ci right 6.415632e-04	k: 518	n:880000
CHD2   880000 perm   519 sec   (1695 perm/sec)   p_kst 5.886364e-04   p_cons 9.423466e-01   p_joint 5.886364e-04

Joint ci ratio: 1.711955e-01	ci left: 5.383632e-04	ci right 6.402137e-04	k: 523	n:890000
Cons ci ratio: 1.027097e-03	ci left: 9.419331e-01	ci right 9.429022e-01	k: 838753	n:890000
KS ci ratio: 1.711955e-01	ci left: 5.383632e-04	ci right 6.402137e-04	k: 523	n:890000
CHD2   890000 perm   529 sec   (1683 perm/sec)   p_kst 5.876404e-04   p_cons 9.424191e-01   p_joint 5.876404e-04

Joint ci ratio: 1.702237e-01	ci left: 5.387633e-04	ci right 6.400514e-04	k: 529	n:900000
Cons ci ratio: 1.021116e-03	ci left: 9.419635e-01	ci right 9.429270e-01	k: 848202	n:900000
KS ci ratio: 1.702237e-01	ci left: 5.387633e-04	ci right 6.400514e-04	k: 529	n:900000
CHD2   900000 perm   539 sec   (1671 perm/sec)   p_kst 5.877778e-04   p_cons 9.424467e-01   p_joint 5.877778e-04

Joint ci ratio: 1.697442e-01	ci left: 5.359992e-04	ci right 6.364548e-04	k: 532	n:910000
Cons ci ratio: 1.015515e-03	ci left: 9.419635e-01	ci right 9.429216e-01	k: 857624	n:910000
KS ci ratio: 1.697442e-01	ci left: 5.359992e-04	ci right 6.364548e-04	k: 532	n:910000
CHD2   910000 perm   548 sec   (1660 perm/sec)   p_kst 5.846154e-04   p_cons 9.424440e-01   p_joint 5.846154e-04

Joint ci ratio: 1.687968e-01	ci left: 5.364186e-04	ci right 6.363345e-04	k: 538	n:920000
Cons ci ratio: 1.010076e-03	ci left: 9.419558e-01	ci right 9.429088e-01	k: 867039	n:920000
KS ci ratio: 1.687968e-01	ci left: 5.364186e-04	ci right 6.363345e-04	k: 538	n:920000
CHD2   920000 perm   558 sec   (1649 perm/sec)   p_kst 5.847826e-04   p_cons 9.424337e-01   p_joint 5.847826e-04

Joint ci ratio: 1.678651e-01	ci left: 5.368305e-04	ci right 6.362154e-04	k: 544	n:930000
Cons ci ratio: 1.004584e-03	ci left: 9.419634e-01	ci right 9.429112e-01	k: 876468	n:930000
KS ci ratio: 1.678651e-01	ci left: 5.368305e-04	ci right 6.362154e-04	k: 544	n:930000
CHD2   930000 perm   568 sec   (1638 perm/sec)   p_kst 5.849462e-04   p_cons 9.424387e-01   p_joint 5.849462e-04

Joint ci ratio: 1.658975e-01	ci left: 5.443719e-04	ci right 6.438538e-04	k: 557	n:940000
Cons ci ratio: 9.989951e-04	ci left: 9.419912e-01	ci right 9.429337e-01	k: 885916	n:940000
KS ci ratio: 1.658975e-01	ci left: 5.443719e-04	ci right 6.438538e-04	k: 557	n:940000
CHD2   940000 perm   578 sec   (1628 perm/sec)   p_kst 5.925532e-04   p_cons 9.424638e-01   p_joint 5.925532e-04

Joint ci ratio: 1.639975e-01	ci left: 5.517612e-04	ci right 6.513247e-04	k: 570	n:950000
Cons ci ratio: 9.935365e-04	ci left: 9.420141e-01	ci right 9.429516e-01	k: 895360	n:950000
KS ci ratio: 1.639975e-01	ci left: 5.517612e-04	ci right 6.513247e-04	k: 570	n:950000
CHD2   950000 perm   588 sec   (1616 perm/sec)   p_kst 6.000000e-04   p_cons 9.424842e-01   p_joint 6.000000e-04

Joint ci ratio: 1.631426e-01	ci left: 5.520078e-04	ci right 6.510457e-04	k: 576	n:960000
Cons ci ratio: 9.882707e-04	ci left: 9.420251e-01	ci right 9.429576e-01	k: 904793	n:960000
KS ci ratio: 1.631426e-01	ci left: 5.520078e-04	ci right 6.510457e-04	k: 576	n:960000
CHD2   960000 perm   598 sec   (1605 perm/sec)   p_kst 6.000000e-04   p_cons 9.424927e-01   p_joint 6.000000e-04

Joint ci ratio: 1.621618e-01	ci left: 5.532398e-04	ci right 6.518438e-04	k: 583	n:970000
Cons ci ratio: 9.832748e-04	ci left: 9.420152e-01	ci right 9.429430e-01	k: 914206	n:970000
KS ci ratio: 1.621618e-01	ci left: 5.532398e-04	ci right 6.518438e-04	k: 583	n:970000
CHD2   970000 perm   608 sec   (1595 perm/sec)   p_kst 6.010309e-04   p_cons 9.424804e-01   p_joint 6.010309e-04

Joint ci ratio: 1.614722e-01	ci left: 5.524899e-04	ci right 6.505009e-04	k: 588	n:980000
Cons ci ratio: 9.780960e-04	ci left: 9.420342e-01	ci right 9.429571e-01	k: 923647	n:980000
KS ci ratio: 1.614722e-01	ci left: 5.524899e-04	ci right 6.505009e-04	k: 588	n:980000
CHD2   980000 perm   619 sec   (1584 perm/sec)   p_kst 6.000000e-04   p_cons 9.424969e-01   p_joint 6.000000e-04

Joint ci ratio: 1.601183e-01	ci left: 5.566039e-04	ci right 6.544371e-04	k: 598	n:990000
Cons ci ratio: 9.731614e-04	ci left: 9.420346e-01	ci right 9.429527e-01	k: 933070	n:990000
KS ci ratio: 1.601183e-01	ci left: 5.566039e-04	ci right 6.544371e-04	k: 598	n:990000
CHD2   990000 perm   629 sec   (1574 perm/sec)   p_kst 6.040404e-04   p_cons 9.424949e-01   p_joint 6.040404e-04

Joint ci ratio: 1.598520e-01	ci left: 5.529577e-04	ci right 6.499729e-04	k: 600	n:1000000
Cons ci ratio: 9.684347e-04	ci left: 9.420199e-01	ci right 9.429336e-01	k: 942478	n:1000000
KS ci ratio: 1.598520e-01	ci left: 5.529577e-04	ci right 6.499729e-04	k: 600	n:1000000
CHD2   1000000 perm   640 sec   (1564 perm/sec)   p_kst 6.000000e-04   p_cons 9.424780e-01   p_joint 6.000000e-04

Joint ci ratio: 1.586681e-01	ci left: 5.560387e-04	ci right 6.528032e-04	k: 609	n:1010000
Cons ci ratio: 9.637321e-04	ci left: 9.420104e-01	ci right 9.429197e-01	k: 951891	n:1010000
KS ci ratio: 1.586681e-01	ci left: 5.560387e-04	ci right 6.528032e-04	k: 609	n:1010000
CHD2   1010000 perm   650 sec   (1554 perm/sec)   p_kst 6.029703e-04   p_cons 9.424663e-01   p_joint 6.029703e-04

Joint ci ratio: 1.582796e-01	ci left: 5.534118e-04	ci right 6.494609e-04	k: 612	n:1020000
Cons ci ratio: 9.589066e-04	ci left: 9.420229e-01	ci right 9.429276e-01	k: 961326	n:1020000
KS ci ratio: 1.582796e-01	ci left: 5.534118e-04	ci right 6.494609e-04	k: 612	n:1020000
CHD2   1020000 perm   661 sec   (1543 perm/sec)   p_kst 6.000000e-04   p_cons 9.424765e-01   p_joint 6.000000e-04

Joint ci ratio: 1.563773e-01	ci left: 5.620289e-04	ci right 6.582912e-04	k: 627	n:1030000
Cons ci ratio: 9.540247e-04	ci left: 9.420497e-01	ci right 9.429498e-01	k: 970776	n:1030000
KS ci ratio: 1.563773e-01	ci left: 5.620289e-04	ci right 6.582912e-04	k: 627	n:1030000
CHD2   1030000 perm   672 sec   (1534 perm/sec)   p_kst 6.087379e-04   p_cons 9.425010e-01   p_joint 6.087379e-04

Joint ci ratio: 1.556356e-01	ci left: 5.621687e-04	ci right 6.579557e-04	k: 633	n:1040000
Cons ci ratio: 9.493175e-04	ci left: 9.420644e-01	ci right 9.429601e-01	k: 980214	n:1040000
KS ci ratio: 1.556356e-01	ci left: 5.621687e-04	ci right 6.579557e-04	k: 633	n:1040000
CHD2   1040000 perm   682 sec   (1524 perm/sec)   p_kst 6.086538e-04   p_cons 9.425135e-01   p_joint 6.086538e-04

Joint ci ratio: 1.545423e-01	ci left: 5.650536e-04	ci right 6.605932e-04	k: 642	n:1050000
Cons ci ratio: 9.447955e-04	ci left: 9.420655e-01	ci right 9.429569e-01	k: 989638	n:1050000
KS ci ratio: 1.545423e-01	ci left: 5.650536e-04	ci right 6.605932e-04	k: 642	n:1050000
CHD2   1050000 perm   694 sec   (1514 perm/sec)   p_kst 6.114286e-04   p_cons 9.425124e-01   p_joint 6.114286e-04

Joint ci ratio: 1.541833e-01	ci left: 5.624437e-04	ci right 6.573007e-04	k: 645	n:1060000
Cons ci ratio: 9.401410e-04	ci left: 9.420892e-01	ci right 9.429763e-01	k: 999086	n:1060000
KS ci ratio: 1.541833e-01	ci left: 5.624437e-04	ci right 6.573007e-04	k: 645	n:1060000
CHD2   1060000 perm   704 sec   (1505 perm/sec)   p_kst 6.084906e-04   p_cons 9.425340e-01   p_joint 6.084906e-04

Joint ci ratio: 1.531201e-01	ci left: 5.652751e-04	ci right 6.598920e-04	k: 654	n:1070000
Cons ci ratio: 9.361115e-04	ci left: 9.420479e-01	ci right 9.429311e-01	k: 1008465	n:1070000
KS ci ratio: 1.531201e-01	ci left: 5.652751e-04	ci right 6.598920e-04	k: 654	n:1070000
CHD2   1070000 perm   715 sec   (1496 perm/sec)   p_kst 6.112150e-04   p_cons 9.424907e-01   p_joint 6.112150e-04

Joint ci ratio: 1.523084e-01	ci left: 5.662749e-04	ci right 6.605108e-04	k: 661	n:1080000
Cons ci ratio: 9.315757e-04	ci left: 9.420723e-01	ci right 9.429512e-01	k: 1017914	n:1080000
KS ci ratio: 1.523084e-01	ci left: 5.662749e-04	ci right 6.605108e-04	k: 661	n:1080000
CHD2   1080000 perm   726 sec   (1487 perm/sec)   p_kst 6.120370e-04   p_cons 9.425130e-01   p_joint 6.120370e-04

Joint ci ratio: 1.513962e-01	ci left: 5.681404e-04	ci right 6.620692e-04	k: 669	n:1090000
Cons ci ratio: 9.274192e-04	ci left: 9.420595e-01	ci right 9.429345e-01	k: 1027323	n:1090000
KS ci ratio: 1.513962e-01	ci left: 5.681404e-04	ci right 6.620692e-04	k: 669	n:1090000
CHD2   1090000 perm   738 sec   (1477 perm/sec)   p_kst 6.137615e-04   p_cons 9.424982e-01   p_joint 6.137615e-04

Joint ci ratio: 1.510586e-01	ci left: 5.655995e-04	ci right 6.588808e-04	k: 672	n:1100000
Cons ci ratio: 9.231938e-04	ci left: 9.420615e-01	ci right 9.429325e-01	k: 1036748	n:1100000
KS ci ratio: 1.510586e-01	ci left: 5.655995e-04	ci right 6.588808e-04	k: 672	n:1100000
CHD2   1100000 perm   749 sec   (1468 perm/sec)   p_kst 6.109091e-04   p_cons 9.424982e-01   p_joint 6.109091e-04

Joint ci ratio: 1.502790e-01	ci left: 5.665726e-04	ci right 6.594888e-04	k: 679	n:1110000
Cons ci ratio: 9.189340e-04	ci left: 9.420744e-01	ci right 9.429413e-01	k: 1046185	n:1110000
KS ci ratio: 1.502790e-01	ci left: 5.665726e-04	ci right 6.594888e-04	k: 679	n:1110000
CHD2   1110000 perm   760 sec   (1460 perm/sec)   p_kst 6.117117e-04   p_cons 9.425090e-01   p_joint 6.117117e-04

Joint ci ratio: 1.496204e-01	ci left: 5.666700e-04	ci right 6.591585e-04	k: 685	n:1120000
Cons ci ratio: 9.146874e-04	ci left: 9.420924e-01	ci right 9.429553e-01	k: 1055628	n:1120000
KS ci ratio: 1.496204e-01	ci left: 5.666700e-04	ci right 6.591585e-04	k: 685	n:1120000
CHD2   1120000 perm   772 sec   (1451 perm/sec)   p_kst 6.116071e-04   p_cons 9.425250e-01   p_joint 6.116071e-04

Joint ci ratio: 1.487554e-01	ci left: 5.684707e-04	ci right 6.606689e-04	k: 693	n:1130000
Cons ci ratio: 9.109825e-04	ci left: 9.420523e-01	ci right 9.429118e-01	k: 1065006	n:1130000
KS ci ratio: 1.487554e-01	ci left: 5.684707e-04	ci right 6.606689e-04	k: 693	n:1130000
CHD2   1130000 perm   783 sec   (1443 perm/sec)   p_kst 6.132743e-04   p_cons 9.424832e-01   p_joint 6.132743e-04

Joint ci ratio: 1.481165e-01	ci left: 5.685518e-04	ci right 6.603321e-04	k: 699	n:1140000
Cons ci ratio: 9.070722e-04	ci left: 9.420429e-01	ci right 9.428987e-01	k: 1074418	n:1140000
KS ci ratio: 1.481165e-01	ci left: 5.685518e-04	ci right 6.603321e-04	k: 699	n:1140000
CHD2   1140000 perm   795 sec   (1435 perm/sec)   p_kst 6.131579e-04   p_cons 9.424719e-01   p_joint 6.131579e-04

Joint ci ratio: 1.481169e-01	ci left: 5.636077e-04	ci right 6.545902e-04	k: 699	n:1150000
Cons ci ratio: 9.030960e-04	ci left: 9.420477e-01	ci right 9.428997e-01	k: 1083846	n:1150000
KS ci ratio: 1.481169e-01	ci left: 5.636077e-04	ci right 6.545902e-04	k: 699	n:1150000
CHD2   1150000 perm   806 sec   (1426 perm/sec)   p_kst 6.078261e-04   p_cons 9.424748e-01   p_joint 6.078261e-04

Joint ci ratio: 1.476957e-01	ci left: 5.620697e-04	ci right 6.525230e-04	k: 703	n:1160000
Cons ci ratio: 8.991287e-04	ci left: 9.420575e-01	ci right 9.429058e-01	k: 1093280	n:1160000
KS ci ratio: 1.476957e-01	ci left: 5.620697e-04	ci right 6.525230e-04	k: 703	n:1160000
CHD2   1160000 perm   818 sec   (1418 perm/sec)   p_kst 6.060345e-04   p_cons 9.424828e-01   p_joint 6.060345e-04

Joint ci ratio: 1.474866e-01	ci left: 5.589119e-04	ci right 6.487185e-04	k: 705	n:1170000
Cons ci ratio: 8.952415e-04	ci left: 9.420638e-01	ci right 9.429084e-01	k: 1102710	n:1170000
KS ci ratio: 1.474866e-01	ci left: 5.589119e-04	ci right 6.487185e-04	k: 705	n:1170000
CHD2   1170000 perm   830 sec   (1410 perm/sec)   p_kst 6.025641e-04   p_cons 9.424872e-01   p_joint 6.025641e-04

Joint ci ratio: 1.466579e-01	ci left: 5.607055e-04	ci right 6.502498e-04	k: 713	n:1180000
Cons ci ratio: 8.912858e-04	ci left: 9.420844e-01	ci right 9.429253e-01	k: 1112157	n:1180000
KS ci ratio: 1.466579e-01	ci left: 5.607055e-04	ci right 6.502498e-04	k: 713	n:1180000
CHD2   1180000 perm   842 sec   (1402 perm/sec)   p_kst 6.042373e-04   p_cons 9.425059e-01   p_joint 6.042373e-04

Joint ci ratio: 1.463509e-01	ci left: 5.584223e-04	ci right 6.473989e-04	k: 716	n:1190000
Cons ci ratio: 8.872168e-04	ci left: 9.421249e-01	ci right 9.429620e-01	k: 1121628	n:1190000
KS ci ratio: 1.463509e-01	ci left: 5.584223e-04	ci right 6.473989e-04	k: 716	n:1190000
CHD2   1190000 perm   854 sec   (1394 perm/sec)   p_kst 6.016807e-04   p_cons 9.425445e-01   p_joint 6.016807e-04

Joint ci ratio: 1.455411e-01	ci left: 5.601920e-04	ci right 6.489138e-04	k: 724	n:1200000
Cons ci ratio: 8.832433e-04	ci left: 9.421598e-01	ci right 9.429931e-01	k: 1131093	n:1200000
KS ci ratio: 1.455411e-01	ci left: 5.601920e-04	ci right 6.489138e-04	k: 724	n:1200000
CHD2   1200000 perm   866 sec   (1386 perm/sec)   p_kst 6.033333e-04   p_cons 9.425775e-01   p_joint 6.033333e-04

Joint ci ratio: 1.451414e-01	ci left: 5.587479e-04	ci right 6.469768e-04	k: 728	n:1210000
Cons ci ratio: 8.797322e-04	ci left: 9.421434e-01	ci right 9.429734e-01	k: 1140497	n:1210000
KS ci ratio: 1.451414e-01	ci left: 5.587479e-04	ci right 6.469768e-04	k: 728	n:1210000
CHD2   1210000 perm   878 sec   (1378 perm/sec)   p_kst 6.016529e-04   p_cons 9.425595e-01   p_joint 6.016529e-04

Joint ci ratio: 1.450422e-01	ci left: 5.549578e-04	ci right 6.425233e-04	k: 729	n:1220000
Cons ci ratio: 8.760237e-04	ci left: 9.421570e-01	ci right 9.429835e-01	k: 1149937	n:1220000
KS ci ratio: 1.450422e-01	ci left: 5.549578e-04	ci right 6.425233e-04	k: 729	n:1220000
CHD2   1220000 perm   889 sec   (1372 perm/sec)   p_kst 5.975410e-04   p_cons 9.425713e-01   p_joint 5.975410e-04

Joint ci ratio: 1.444498e-01	ci left: 5.551474e-04	ci right 6.423541e-04	k: 735	n:1230000
Cons ci ratio: 8.722700e-04	ci left: 9.421818e-01	ci right 9.430048e-01	k: 1159391	n:1230000
KS ci ratio: 1.444498e-01	ci left: 5.551474e-04	ci right 6.423541e-04	k: 735	n:1230000
CHD2   1230000 perm   902 sec   (1364 perm/sec)   p_kst 5.975610e-04   p_cons 9.425943e-01   p_joint 5.975610e-04

Joint ci ratio: 1.439617e-01	ci left: 5.545571e-04	ci right 6.413515e-04	k: 740	n:1240000
Cons ci ratio: 8.687323e-04	ci left: 9.421851e-01	ci right 9.430048e-01	k: 1168819	n:1240000
KS ci ratio: 1.439617e-01	ci left: 5.545571e-04	ci right 6.413515e-04	k: 740	n:1240000
CHD2   1240000 perm   913 sec   (1358 perm/sec)   p_kst 5.967742e-04   p_cons 9.425960e-01   p_joint 5.967742e-04

Joint ci ratio: 1.432864e-01	ci left: 5.555195e-04	ci right 6.420217e-04	k: 747	n:1250000
Cons ci ratio: 8.652949e-04	ci left: 9.421812e-01	ci right 9.429976e-01	k: 1178238	n:1250000
KS ci ratio: 1.432864e-01	ci left: 5.555195e-04	ci right 6.420217e-04	k: 747	n:1250000
CHD2   1250000 perm   926 sec   (1351 perm/sec)   p_kst 5.976000e-04   p_cons 9.425904e-01   p_joint 5.976000e-04

Joint ci ratio: 1.427152e-01	ci left: 5.557021e-04	ci right 6.418585e-04	k: 753	n:1260000
Cons ci ratio: 8.618347e-04	ci left: 9.421853e-01	ci right 9.429984e-01	k: 1187667	n:1260000
KS ci ratio: 1.427152e-01	ci left: 5.557021e-04	ci right 6.418585e-04	k: 753	n:1260000
CHD2   1260000 perm   938 sec   (1343 perm/sec)   p_kst 5.976190e-04   p_cons 9.425929e-01   p_joint 5.976190e-04

Joint ci ratio: 1.424323e-01	ci left: 5.536044e-04	ci right 6.392509e-04	k: 756	n:1270000
Cons ci ratio: 8.584095e-04	ci left: 9.421901e-01	ci right 9.430000e-01	k: 1197097	n:1270000
KS ci ratio: 1.424323e-01	ci left: 5.536044e-04	ci right 6.392509e-04	k: 756	n:1270000
CHD2   1270000 perm   953 sec   (1333 perm/sec)   p_kst 5.952756e-04   p_cons 9.425961e-01   p_joint 5.952756e-04

Joint ci ratio: 1.418712e-01	ci left: 5.538002e-04	ci right 6.391109e-04	k: 762	n:1280000
Cons ci ratio: 8.548952e-04	ci left: 9.422113e-01	ci right 9.430179e-01	k: 1206548	n:1280000
KS ci ratio: 1.418712e-01	ci left: 5.538002e-04	ci right 6.391109e-04	k: 762	n:1280000
CHD2   1280000 perm   966 sec   (1326 perm/sec)   p_kst 5.953125e-04   p_cons 9.426156e-01   p_joint 5.953125e-04

Joint ci ratio: 1.415009e-01	ci left: 5.524980e-04	ci right 6.373672e-04	k: 766	n:1290000
Cons ci ratio: 8.517225e-04	ci left: 9.421941e-01	ci right 9.429977e-01	k: 1215950	n:1290000
KS ci ratio: 1.415009e-01	ci left: 5.524980e-04	ci right 6.373672e-04	k: 766	n:1290000
CHD2   1290000 perm   981 sec   (1315 perm/sec)   p_kst 5.937984e-04   p_cons 9.425969e-01   p_joint 5.937984e-04

Joint ci ratio: 1.411334e-01	ci left: 5.512161e-04	ci right 6.356500e-04	k: 770	n:1300000
Cons ci ratio: 8.484823e-04	ci left: 9.421903e-01	ci right 9.429908e-01	k: 1225369	n:1300000
KS ci ratio: 1.411334e-01	ci left: 5.512161e-04	ci right 6.356500e-04	k: 770	n:1300000
CHD2   1300000 perm   994 sec   (1308 perm/sec)   p_kst 5.923077e-04   p_cons 9.425915e-01   p_joint 5.923077e-04

Joint ci ratio: 1.405875e-01	ci left: 5.514271e-04	ci right 6.355392e-04	k: 776	n:1310000
Cons ci ratio: 8.450881e-04	ci left: 9.422110e-01	ci right 9.430084e-01	k: 1234820	n:1310000
KS ci ratio: 1.405875e-01	ci left: 5.514271e-04	ci right 6.355392e-04	k: 776	n:1310000
CHD2   1310000 perm   1009 sec   (1298 perm/sec)   p_kst 5.923664e-04   p_cons 9.426107e-01   p_joint 5.923664e-04

Joint ci ratio: 1.400478e-01	ci left: 5.516355e-04	ci right 6.354294e-04	k: 782	n:1320000
Cons ci ratio: 8.419758e-04	ci left: 9.422003e-01	ci right 9.429947e-01	k: 1244230	n:1320000
KS ci ratio: 1.400478e-01	ci left: 5.516355e-04	ci right 6.354294e-04	k: 782	n:1320000
CHD2   1320000 perm   1022 sec   (1292 perm/sec)   p_kst 5.924242e-04   p_cons 9.425985e-01   p_joint 5.924242e-04

Joint ci ratio: 1.396915e-01	ci left: 5.503901e-04	ci right 6.337645e-04	k: 786	n:1330000
Cons ci ratio: 8.389501e-04	ci left: 9.421830e-01	ci right 9.429745e-01	k: 1253631	n:1330000
KS ci ratio: 1.396915e-01	ci left: 5.503901e-04	ci right 6.337645e-04	k: 786	n:1330000
CHD2   1330000 perm   1034 sec   (1286 perm/sec)   p_kst 5.909774e-04   p_cons 9.425797e-01   p_joint 5.909774e-04

Joint ci ratio: 1.394262e-01	ci left: 5.484433e-04	ci right 6.313519e-04	k: 789	n:1340000
Cons ci ratio: 8.358472e-04	ci left: 9.421801e-01	ci right 9.429687e-01	k: 1263051	n:1340000
KS ci ratio: 1.394262e-01	ci left: 5.484433e-04	ci right 6.313519e-04	k: 789	n:1340000
CHD2   1340000 perm   1046 sec   (1281 perm/sec)   p_kst 5.888060e-04   p_cons 9.425754e-01   p_joint 5.888060e-04

Joint ci ratio: 1.387254e-01	ci left: 5.501005e-04	ci right 6.328072e-04	k: 797	n:1350000
Cons ci ratio: 8.326189e-04	ci left: 9.421981e-01	ci right 9.429837e-01	k: 1272499	n:1350000
KS ci ratio: 1.387254e-01	ci left: 5.501005e-04	ci right 6.328072e-04	k: 797	n:1350000
CHD2   1350000 perm   1060 sec   (1274 perm/sec)   p_kst 5.903704e-04   p_cons 9.425919e-01   p_joint 5.903704e-04

Joint ci ratio: 1.383791e-01	ci left: 5.488949e-04	ci right 6.311973e-04	k: 801	n:1360000
Cons ci ratio: 8.295122e-04	ci left: 9.422048e-01	ci right 9.429874e-01	k: 1281932	n:1360000
KS ci ratio: 1.383791e-01	ci left: 5.488949e-04	ci right 6.311973e-04	k: 801	n:1360000
CHD2   1360000 perm   1073 sec   (1268 perm/sec)   p_kst 5.889706e-04   p_cons 9.425971e-01   p_joint 5.889706e-04

Joint ci ratio: 1.379498e-01	ci left: 5.484118e-04	ci right 6.303657e-04	k: 806	n:1370000
Cons ci ratio: 8.260163e-04	ci left: 9.422670e-01	ci right 9.430464e-01	k: 1291441	n:1370000
KS ci ratio: 1.379498e-01	ci left: 5.484118e-04	ci right 6.303657e-04	k: 806	n:1370000
CHD2   1370000 perm   1086 sec   (1261 perm/sec)   p_kst 5.883212e-04   p_cons 9.426577e-01   p_joint 5.883212e-04

Joint ci ratio: 1.372710e-01	ci left: 5.500354e-04	ci right 6.317944e-04	k: 814	n:1380000
Cons ci ratio: 8.228005e-04	ci left: 9.422971e-01	ci right 9.430735e-01	k: 1300907	n:1380000
KS ci ratio: 1.372710e-01	ci left: 5.500354e-04	ci right 6.317944e-04	k: 814	n:1380000
CHD2   1380000 perm   1100 sec   (1255 perm/sec)   p_kst 5.898551e-04   p_cons 9.426862e-01   p_joint 5.898551e-04

Joint ci ratio: 1.371871e-01	ci left: 5.467730e-04	ci right 6.279933e-04	k: 815	n:1390000
Cons ci ratio: 8.198183e-04	ci left: 9.423008e-01	ci right 9.430743e-01	k: 1310337	n:1390000
KS ci ratio: 1.371871e-01	ci left: 5.467730e-04	ci right 6.279933e-04	k: 815	n:1390000
CHD2   1390000 perm   1113 sec   (1249 perm/sec)   p_kst 5.863309e-04   p_cons 9.426885e-01   p_joint 5.863309e-04

Joint ci ratio: 1.367688e-01	ci left: 5.463165e-04	ci right 6.272013e-04	k: 820	n:1400000
Cons ci ratio: 8.169006e-04	ci left: 9.423001e-01	ci right 9.430709e-01	k: 1319761	n:1400000
KS ci ratio: 1.367688e-01	ci left: 5.463165e-04	ci right 6.272013e-04	k: 820	n:1400000
CHD2   1400000 perm   1127 sec   (1242 perm/sec)   p_kst 5.857143e-04   p_cons 9.426864e-01   p_joint 5.857143e-04

Joint ci ratio: 1.356983e-01	ci left: 5.513476e-04	ci right 6.322869e-04	k: 833	n:1410000
Cons ci ratio: 8.140674e-04	ci left: 9.422923e-01	ci right 9.430604e-01	k: 1329175	n:1410000
KS ci ratio: 1.356983e-01	ci left: 5.513476e-04	ci right 6.322869e-04	k: 833	n:1410000
CHD2   1410000 perm   1140 sec   (1236 perm/sec)   p_kst 5.907801e-04   p_cons 9.426773e-01   p_joint 5.907801e-04

Joint ci ratio: 1.353741e-01	ci left: 5.501862e-04	ci right 6.307466e-04	k: 837	n:1420000
Cons ci ratio: 8.112422e-04	ci left: 9.422875e-01	ci right 9.430529e-01	k: 1338593	n:1420000
KS ci ratio: 1.353741e-01	ci left: 5.501862e-04	ci right 6.307466e-04	k: 837	n:1420000
CHD2   1420000 perm   1154 sec   (1230 perm/sec)   p_kst 5.894366e-04   p_cons 9.426711e-01   p_joint 5.894366e-04

Joint ci ratio: 1.352131e-01	ci left: 5.476900e-04	ci right 6.277817e-04	k: 839	n:1430000
Cons ci ratio: 8.083992e-04	ci left: 9.422891e-01	ci right 9.430518e-01	k: 1348020	n:1430000
KS ci ratio: 1.352131e-01	ci left: 5.476900e-04	ci right 6.277817e-04	k: 839	n:1430000
CHD2   1430000 perm   1168 sec   (1224 perm/sec)   p_kst 5.867133e-04   p_cons 9.426713e-01   p_joint 5.867133e-04

Joint ci ratio: 1.348125e-01	ci left: 5.472415e-04	ci right 6.270116e-04	k: 844	n:1440000
Cons ci ratio: 8.055703e-04	ci left: 9.422927e-01	ci right 9.430528e-01	k: 1357450	n:1440000
KS ci ratio: 1.348125e-01	ci left: 5.472415e-04	ci right 6.270116e-04	k: 844	n:1440000
CHD2   1440000 perm   1182 sec   (1218 perm/sec)   p_kst 5.861111e-04   p_cons 9.426736e-01   p_joint 5.861111e-04

Joint ci ratio: 1.342575e-01	ci left: 5.481326e-04	ci right 6.276773e-04	k: 851	n:1450000
Cons ci ratio: 8.029502e-04	ci left: 9.422721e-01	ci right 9.430296e-01	k: 1366845	n:1450000
KS ci ratio: 1.342575e-01	ci left: 5.481326e-04	ci right 6.276773e-04	k: 851	n:1450000
CHD2   1450000 perm   1197 sec   (1212 perm/sec)   p_kst 5.868966e-04   p_cons 9.426517e-01   p_joint 5.868966e-04

Joint ci ratio: 1.338653e-01	ci left: 5.476880e-04	ci right 6.269176e-04	k: 856	n:1460000
Cons ci ratio: 8.001729e-04	ci left: 9.422764e-01	ci right 9.430314e-01	k: 1376276	n:1460000
KS ci ratio: 1.338653e-01	ci left: 5.476880e-04	ci right 6.269176e-04	k: 856	n:1460000
CHD2   1460000 perm   1211 sec   (1206 perm/sec)   p_kst 5.863014e-04   p_cons 9.426548e-01   p_joint 5.863014e-04

Joint ci ratio: 1.335541e-01	ci left: 5.465923e-04	ci right 6.254649e-04	k: 860	n:1470000
Cons ci ratio: 7.974092e-04	ci left: 9.422828e-01	ci right 9.430352e-01	k: 1385710	n:1470000
KS ci ratio: 1.335541e-01	ci left: 5.465923e-04	ci right 6.254649e-04	k: 860	n:1470000
CHD2   1470000 perm   1225 sec   (1200 perm/sec)   p_kst 5.850340e-04   p_cons 9.426599e-01   p_joint 5.850340e-04

Joint ci ratio: 1.332450e-01	ci left: 5.455116e-04	ci right 6.240317e-04	k: 864	n:1480000
Cons ci ratio: 7.946739e-04	ci left: 9.422891e-01	ci right 9.430389e-01	k: 1395144	n:1480000
KS ci ratio: 1.332450e-01	ci left: 5.455116e-04	ci right 6.240317e-04	k: 864	n:1480000
CHD2   1480000 perm   1239 sec   (1195 perm/sec)   p_kst 5.837838e-04   p_cons 9.426649e-01   p_joint 5.837838e-04

Joint ci ratio: 1.326330e-01	ci left: 5.470410e-04	ci right 6.253911e-04	k: 872	n:1490000
Cons ci ratio: 7.920944e-04	ci left: 9.422778e-01	ci right 9.430252e-01	k: 1404552	n:1490000
KS ci ratio: 1.326330e-01	ci left: 5.470410e-04	ci right 6.253911e-04	k: 872	n:1490000
CHD2   1490000 perm   1253 sec   (1189 perm/sec)   p_kst 5.852349e-04   p_cons 9.426523e-01   p_joint 5.852349e-04

Joint ci ratio: 1.323302e-01	ci left: 5.459724e-04	ci right 6.239769e-04	k: 876	n:1500000
Cons ci ratio: 7.894668e-04	ci left: 9.422767e-01	ci right 9.430216e-01	k: 1413975	n:1500000
KS ci ratio: 1.323302e-01	ci left: 5.459724e-04	ci right 6.239769e-04	k: 876	n:1500000
CHD2   1500000 perm   1268 sec   (1183 perm/sec)   p_kst 5.840000e-04   p_cons 9.426500e-01   p_joint 5.840000e-04

Joint ci ratio: 1.318052e-01	ci left: 5.468393e-04	ci right 6.246334e-04	k: 883	n:1510000
Cons ci ratio: 7.869278e-04	ci left: 9.422670e-01	ci right 9.430094e-01	k: 1423385	n:1510000
KS ci ratio: 1.318052e-01	ci left: 5.468393e-04	ci right 6.246334e-04	k: 883	n:1510000
CHD2   1510000 perm   1282 sec   (1178 perm/sec)   p_kst 5.847682e-04   p_cons 9.426391e-01   p_joint 5.847682e-04

Joint ci ratio: 1.314341e-01	ci left: 5.464228e-04	ci right 6.239217e-04	k: 888	n:1520000
Cons ci ratio: 7.843463e-04	ci left: 9.422667e-01	ci right 9.430067e-01	k: 1432809	n:1520000
KS ci ratio: 1.314341e-01	ci left: 5.464228e-04	ci right 6.239217e-04	k: 888	n:1520000
CHD2   1520000 perm   1297 sec   (1172 perm/sec)   p_kst 5.842105e-04   p_cons 9.426375e-01   p_joint 5.842105e-04

Joint ci ratio: 1.307737e-01	ci left: 5.485409e-04	ci right 6.259189e-04	k: 897	n:1530000
Cons ci ratio: 7.817901e-04	ci left: 9.422663e-01	ci right 9.430039e-01	k: 1442233	n:1530000
KS ci ratio: 1.307737e-01	ci left: 5.485409e-04	ci right 6.259189e-04	k: 897	n:1530000
CHD2   1530000 perm   1312 sec   (1166 perm/sec)   p_kst 5.862745e-04   p_cons 9.426359e-01   p_joint 5.862745e-04

Joint ci ratio: 1.303389e-01	ci left: 5.487478e-04	ci right 6.258778e-04	k: 903	n:1540000
Cons ci ratio: 7.792259e-04	ci left: 9.422705e-01	ci right 9.430057e-01	k: 1451664	n:1540000
KS ci ratio: 1.303389e-01	ci left: 5.487478e-04	ci right 6.258778e-04	k: 903	n:1540000
CHD2   1540000 perm   1327 sec   (1161 perm/sec)   p_kst 5.863636e-04   p_cons 9.426390e-01   p_joint 5.863636e-04

Joint ci ratio: 1.301233e-01	ci left: 5.470799e-04	ci right 6.238384e-04	k: 906	n:1550000
Cons ci ratio: 7.766637e-04	ci left: 9.422780e-01	ci right 9.430107e-01	k: 1461100	n:1550000
KS ci ratio: 1.301233e-01	ci left: 5.470799e-04	ci right 6.238384e-04	k: 906	n:1550000
CHD2   1550000 perm   1342 sec   (1155 perm/sec)   p_kst 5.845161e-04   p_cons 9.426452e-01   p_joint 5.845161e-04

Joint ci ratio: 1.299088e-01	ci left: 5.454335e-04	ci right 6.218250e-04	k: 909	n:1560000
Cons ci ratio: 7.742000e-04	ci left: 9.422750e-01	ci right 9.430054e-01	k: 1470520	n:1560000
KS ci ratio: 1.299088e-01	ci left: 5.454335e-04	ci right 6.218250e-04	k: 909	n:1560000
CHD2   1560000 perm   1356 sec   (1150 perm/sec)   p_kst 5.826923e-04   p_cons 9.426410e-01   p_joint 5.826923e-04

Joint ci ratio: 1.294120e-01	ci left: 5.462733e-04	ci right 6.224675e-04	k: 916	n:1570000
Cons ci ratio: 7.715322e-04	ci left: 9.423040e-01	ci right 9.430319e-01	k: 1479990	n:1570000
KS ci ratio: 1.294120e-01	ci left: 5.462733e-04	ci right 6.224675e-04	k: 916	n:1570000
CHD2   1570000 perm   1371 sec   (1145 perm/sec)   p_kst 5.834395e-04   p_cons 9.426688e-01   p_joint 5.834395e-04

Joint ci ratio: 1.289906e-01	ci left: 5.464907e-04	ci right 6.224480e-04	k: 922	n:1580000
Cons ci ratio: 7.692520e-04	ci left: 9.422819e-01	ci right 9.430076e-01	k: 1489380	n:1580000
KS ci ratio: 1.289906e-01	ci left: 5.464907e-04	ci right 6.224480e-04	k: 922	n:1580000
CHD2   1580000 perm   1386 sec   (1140 perm/sec)   p_kst 5.835443e-04   p_cons 9.426456e-01   p_joint 5.835443e-04

Joint ci ratio: 1.287121e-01	ci left: 5.454882e-04	ci right 6.211300e-04	k: 926	n:1590000
Cons ci ratio: 7.669382e-04	ci left: 9.422676e-01	ci right 9.429912e-01	k: 1498782	n:1590000
KS ci ratio: 1.287121e-01	ci left: 5.454882e-04	ci right 6.211300e-04	k: 926	n:1590000
CHD2   1590000 perm   1402 sec   (1134 perm/sec)   p_kst 5.823899e-04   p_cons 9.426302e-01   p_joint 5.823899e-04

Joint ci ratio: 1.281602e-01	ci left: 5.469183e-04	ci right 6.224085e-04	k: 934	n:1600000
Cons ci ratio: 7.645037e-04	ci left: 9.422736e-01	ci right 9.429948e-01	k: 1508216	n:1600000
KS ci ratio: 1.281602e-01	ci left: 5.469183e-04	ci right 6.224085e-04	k: 934	n:1600000
CHD2   1600000 perm   1417 sec   (1129 perm/sec)   p_kst 5.837500e-04   p_cons 9.426350e-01   p_joint 5.837500e-04

Joint ci ratio: 1.277510e-01	ci left: 5.471287e-04	ci right 6.223885e-04	k: 940	n:1610000
Cons ci ratio: 7.621054e-04	ci left: 9.422776e-01	ci right 9.429966e-01	k: 1517647	n:1610000
KS ci ratio: 1.277510e-01	ci left: 5.471287e-04	ci right 6.223885e-04	k: 940	n:1610000
CHD2   1610000 perm   1432 sec   (1124 perm/sec)   p_kst 5.838509e-04   p_cons 9.426379e-01   p_joint 5.838509e-04

Joint ci ratio: 1.273456e-01	ci left: 5.473369e-04	ci right 6.223684e-04	k: 946	n:1620000
Cons ci ratio: 7.598596e-04	ci left: 9.422630e-01	ci right 9.429799e-01	k: 1527048	n:1620000
KS ci ratio: 1.273456e-01	ci left: 5.473369e-04	ci right 6.223684e-04	k: 946	n:1620000
CHD2   1620000 perm   1447 sec   (1119 perm/sec)   p_kst 5.839506e-04   p_cons 9.426222e-01   p_joint 5.839506e-04

Joint ci ratio: 1.266784e-01	ci left: 5.499191e-04	ci right 6.248799e-04	k: 956	n:1630000
Cons ci ratio: 7.576765e-04	ci left: 9.422424e-01	ci right 9.429572e-01	k: 1536439	n:1630000
KS ci ratio: 1.266784e-01	ci left: 5.499191e-04	ci right 6.248799e-04	k: 956	n:1630000
CHD2   1630000 perm   1463 sec   (1114 perm/sec)   p_kst 5.865031e-04   p_cons 9.426006e-01   p_joint 5.865031e-04

Joint ci ratio: 1.264145e-01	ci left: 5.489277e-04	ci right 6.235859e-04	k: 960	n:1640000
Cons ci ratio: 7.553417e-04	ci left: 9.422466e-01	ci right 9.429592e-01	k: 1545870	n:1640000
KS ci ratio: 1.264145e-01	ci left: 5.489277e-04	ci right 6.235859e-04	k: 960	n:1640000
CHD2   1640000 perm   1479 sec   (1109 perm/sec)   p_kst 5.853659e-04   p_cons 9.426037e-01   p_joint 5.853659e-04

Joint ci ratio: 1.260217e-01	ci left: 5.491225e-04	ci right 6.235577e-04	k: 966	n:1650000
Cons ci ratio: 7.529609e-04	ci left: 9.422604e-01	ci right 9.429708e-01	k: 1555317	n:1650000
KS ci ratio: 1.260217e-01	ci left: 5.491225e-04	ci right 6.235577e-04	k: 966	n:1650000
CHD2   1650000 perm   1494 sec   (1104 perm/sec)   p_kst 5.854545e-04   p_cons 9.426164e-01   p_joint 5.854545e-04

Joint ci ratio: 1.258268e-01	ci left: 5.475648e-04	ci right 6.216655e-04	k: 969	n:1660000
Cons ci ratio: 7.506065e-04	ci left: 9.422735e-01	ci right 9.429816e-01	k: 1564763	n:1660000
KS ci ratio: 1.258268e-01	ci left: 5.475648e-04	ci right 6.216655e-04	k: 969	n:1660000
CHD2   1660000 perm   1510 sec   (1100 perm/sec)   p_kst 5.837349e-04   p_cons 9.426283e-01   p_joint 5.837349e-04

Joint ci ratio: 1.255682e-01	ci left: 5.466058e-04	ci right 6.204134e-04	k: 973	n:1670000
Cons ci ratio: 7.482576e-04	ci left: 9.422888e-01	ci right 9.429947e-01	k: 1574213	n:1670000
KS ci ratio: 1.255682e-01	ci left: 5.466058e-04	ci right 6.204134e-04	k: 973	n:1670000
CHD2   1670000 perm   1526 sec   (1095 perm/sec)   p_kst 5.826347e-04   p_cons 9.426425e-01   p_joint 5.826347e-04

Joint ci ratio: 1.252472e-01	ci left: 5.462350e-04	ci right 6.197900e-04	k: 978	n:1680000
Cons ci ratio: 7.459715e-04	ci left: 9.422979e-01	ci right 9.430017e-01	k: 1583653	n:1680000
KS ci ratio: 1.252472e-01	ci left: 5.462350e-04	ci right 6.197900e-04	k: 978	n:1680000
CHD2   1680000 perm   1542 sec   (1090 perm/sec)   p_kst 5.821429e-04   p_cons 9.426506e-01   p_joint 5.821429e-04

Joint ci ratio: 1.249286e-01	ci left: 5.458689e-04	ci right 6.191737e-04	k: 983	n:1690000
Cons ci ratio: 7.436615e-04	ci left: 9.423135e-01	ci right 9.430151e-01	k: 1593104	n:1690000
KS ci ratio: 1.249286e-01	ci left: 5.458689e-04	ci right 6.191737e-04	k: 983	n:1690000
CHD2   1690000 perm   1558 sec   (1085 perm/sec)   p_kst 5.816568e-04   p_cons 9.426651e-01   p_joint 5.816568e-04

Joint ci ratio: 1.246124e-01	ci left: 5.455072e-04	ci right 6.185645e-04	k: 988	n:1700000
Cons ci ratio: 7.414535e-04	ci left: 9.423171e-01	ci right 9.430167e-01	k: 1602535	n:1700000
KS ci ratio: 1.246124e-01	ci left: 5.455072e-04	ci right 6.185645e-04	k: 988	n:1700000
CHD2   1700000 perm   1574 sec   (1080 perm/sec)   p_kst 5.811765e-04   p_cons 9.426676e-01   p_joint 5.811765e-04

Joint ci ratio: 1.242362e-01	ci left: 5.457167e-04	ci right 6.185651e-04	k: 994	n:1710000
Cons ci ratio: 7.394170e-04	ci left: 9.422984e-01	ci right 9.429960e-01	k: 1611928	n:1710000
KS ci ratio: 1.242362e-01	ci left: 5.457167e-04	ci right 6.185651e-04	k: 994	n:1710000
CHD2   1710000 perm   1590 sec   (1076 perm/sec)   p_kst 5.812865e-04   p_cons 9.426480e-01   p_joint 5.812865e-04

Joint ci ratio: 1.239252e-01	ci left: 5.453607e-04	ci right 6.179659e-04	k: 999	n:1720000
Cons ci ratio: 7.371870e-04	ci left: 9.423108e-01	ci right 9.430063e-01	k: 1621374	n:1720000
KS ci ratio: 1.239252e-01	ci left: 5.453607e-04	ci right 6.179659e-04	k: 999	n:1720000
CHD2   1720000 perm   1606 sec   (1071 perm/sec)   p_kst 5.808140e-04   p_cons 9.426593e-01   p_joint 5.808140e-04

Joint ci ratio: 1.234937e-01	ci left: 5.461294e-04	ci right 6.185652e-04	k: 1006	n:1730000
Cons ci ratio: 7.351538e-04	ci left: 9.422970e-01	ci right 9.429905e-01	k: 1630775	n:1730000
KS ci ratio: 1.234937e-01	ci left: 5.461294e-04	ci right 6.185652e-04	k: 1006	n:1730000
CHD2   1730000 perm   1623 sec   (1066 perm/sec)   p_kst 5.815029e-04   p_cons 9.426445e-01   p_joint 5.815029e-04

Joint ci ratio: 1.232492e-01	ci left: 5.452186e-04	ci right 6.173801e-04	k: 1010	n:1740000
Cons ci ratio: 7.330712e-04	ci left: 9.422931e-01	ci right 9.429847e-01	k: 1640193	n:1740000
KS ci ratio: 1.232492e-01	ci left: 5.452186e-04	ci right 6.173801e-04	k: 1010	n:1740000
CHD2   1740000 perm   1639 sec   (1062 perm/sec)   p_kst 5.804598e-04   p_cons 9.426397e-01   p_joint 5.804598e-04

Joint ci ratio: 1.225240e-01	ci left: 5.487495e-04	ci right 6.209199e-04	k: 1022	n:1750000
Cons ci ratio: 7.310911e-04	ci left: 9.422767e-01	ci right 9.429664e-01	k: 1649589	n:1750000
KS ci ratio: 1.225240e-01	ci left: 5.487495e-04	ci right 6.209199e-04	k: 1022	n:1750000
CHD2   1750000 perm   1656 sec   (1057 perm/sec)   p_kst 5.840000e-04   p_cons 9.426223e-01   p_joint 5.840000e-04

Joint ci ratio: 1.221663e-01	ci left: 5.489363e-04	ci right 6.209053e-04	k: 1028	n:1760000
Cons ci ratio: 7.290081e-04	ci left: 9.422781e-01	ci right 9.429659e-01	k: 1659016	n:1760000
KS ci ratio: 1.221663e-01	ci left: 5.489363e-04	ci right 6.209053e-04	k: 1028	n:1760000
CHD2   1760000 perm   1673 sec   (1052 perm/sec)   p_kst 5.840909e-04   p_cons 9.426227e-01   p_joint 5.840909e-04

Joint ci ratio: 1.216940e-01	ci left: 5.502169e-04	ci right 6.220549e-04	k: 1036	n:1770000
Cons ci ratio: 7.268670e-04	ci left: 9.422909e-01	ci right 9.429766e-01	k: 1668463	n:1770000
KS ci ratio: 1.216940e-01	ci left: 5.502169e-04	ci right 6.220549e-04	k: 1036	n:1770000
CHD2   1770000 perm   1689 sec   (1048 perm/sec)   p_kst 5.853107e-04   p_cons 9.426345e-01   p_joint 5.853107e-04

Joint ci ratio: 1.215770e-01	ci left: 5.482152e-04	ci right 6.197180e-04	k: 1038	n:1780000
Cons ci ratio: 7.249253e-04	ci left: 9.422764e-01	ci right 9.429603e-01	k: 1677862	n:1780000
KS ci ratio: 1.215770e-01	ci left: 5.482152e-04	ci right 6.197180e-04	k: 1038	n:1780000
CHD2   1780000 perm   1706 sec   (1043 perm/sec)   p_kst 5.831461e-04   p_cons 9.426191e-01   p_joint 5.831461e-04

Joint ci ratio: 1.214019e-01	ci left: 5.467776e-04	ci right 6.179828e-04	k: 1041	n:1790000
Cons ci ratio: 7.228870e-04	ci left: 9.422790e-01	ci right 9.429609e-01	k: 1687291	n:1790000
KS ci ratio: 1.214019e-01	ci left: 5.467776e-04	ci right 6.179828e-04	k: 1041	n:1790000
CHD2   1790000 perm   1723 sec   (1039 perm/sec)   p_kst 5.815642e-04   p_cons 9.426207e-01   p_joint 5.815642e-04

Joint ci ratio: 1.211697e-01	ci left: 5.458947e-04	ci right 6.168392e-04	k: 1045	n:1800000
Cons ci ratio: 7.208140e-04	ci left: 9.422893e-01	ci right 9.429693e-01	k: 1696734	n:1800000
KS ci ratio: 1.211697e-01	ci left: 5.458947e-04	ci right 6.168392e-04	k: 1045	n:1800000
CHD2   1800000 perm   1740 sec   (1034 perm/sec)   p_kst 5.805556e-04   p_cons 9.426300e-01   p_joint 5.805556e-04

Joint ci ratio: 1.208236e-01	ci left: 5.460933e-04	ci right 6.168465e-04	k: 1051	n:1810000
Cons ci ratio: 7.188065e-04	ci left: 9.422923e-01	ci right 9.429704e-01	k: 1706164	n:1810000
KS ci ratio: 1.208236e-01	ci left: 5.460933e-04	ci right 6.168465e-04	k: 1051	n:1810000
CHD2   1810000 perm   1757 sec   (1030 perm/sec)   p_kst 5.806630e-04   p_cons 9.426320e-01   p_joint 5.806630e-04

Joint ci ratio: 1.206518e-01	ci left: 5.446913e-04	ci right 6.151554e-04	k: 1054	n:1820000
Cons ci ratio: 7.169467e-04	ci left: 9.422754e-01	ci right 9.429518e-01	k: 1715558	n:1820000
KS ci ratio: 1.206518e-01	ci left: 5.446913e-04	ci right 6.151554e-04	k: 1054	n:1820000
CHD2   1820000 perm   1775 sec   (1026 perm/sec)   p_kst 5.791209e-04   p_cons 9.426143e-01   p_joint 5.791209e-04

Joint ci ratio: 1.203102e-01	ci left: 5.448948e-04	ci right 6.151713e-04	k: 1060	n:1830000
Cons ci ratio: 7.149892e-04	ci left: 9.422757e-01	ci right 9.429502e-01	k: 1724983	n:1830000
KS ci ratio: 1.203102e-01	ci left: 5.448948e-04	ci right 6.151713e-04	k: 1060	n:1830000
CHD2   1830000 perm   1792 sec   (1021 perm/sec)   p_kst 5.792350e-04   p_cons 9.426137e-01   p_joint 5.792350e-04

Joint ci ratio: 1.199714e-01	ci left: 5.450963e-04	ci right 6.151868e-04	k: 1066	n:1840000
Cons ci ratio: 7.130406e-04	ci left: 9.422771e-01	ci right 9.429498e-01	k: 1734410	n:1840000
KS ci ratio: 1.199714e-01	ci left: 5.450963e-04	ci right 6.151868e-04	k: 1066	n:1840000
CHD2   1840000 perm   1809 sec   (1017 perm/sec)   p_kst 5.793478e-04   p_cons 9.426141e-01   p_joint 5.793478e-04

Joint ci ratio: 1.198032e-01	ci left: 5.437228e-04	ci right 6.135317e-04	k: 1069	n:1850000
Cons ci ratio: 7.111824e-04	ci left: 9.422671e-01	ci right 9.429380e-01	k: 1743816	n:1850000
KS ci ratio: 1.198032e-01	ci left: 5.437228e-04	ci right 6.135317e-04	k: 1069	n:1850000
CHD2   1850000 perm   1827 sec   (1013 perm/sec)   p_kst 5.778378e-04   p_cons 9.426032e-01   p_joint 5.778378e-04

Joint ci ratio: 1.194132e-01	ci left: 5.444504e-04	ci right 6.141091e-04	k: 1076	n:1860000
Cons ci ratio: 7.094795e-04	ci left: 9.422356e-01	ci right 9.429049e-01	k: 1753182	n:1860000
KS ci ratio: 1.194132e-01	ci left: 5.444504e-04	ci right 6.141091e-04	k: 1076	n:1860000
CHD2   1860000 perm   1844 sec   (1009 perm/sec)   p_kst 5.784946e-04   p_cons 9.425710e-01   p_joint 5.784946e-04

Joint ci ratio: 1.191921e-01	ci left: 5.436141e-04	ci right 6.130280e-04	k: 1080	n:1870000
Cons ci ratio: 7.074811e-04	ci left: 9.422517e-01	ci right 9.429191e-01	k: 1762636	n:1870000
KS ci ratio: 1.191921e-01	ci left: 5.436141e-04	ci right 6.130280e-04	k: 1080	n:1870000
CHD2   1870000 perm   1861 sec   (1005 perm/sec)   p_kst 5.775401e-04   p_cons 9.425861e-01   p_joint 5.775401e-04

Joint ci ratio: 1.190272e-01	ci left: 5.422707e-04	ci right 6.114105e-04	k: 1083	n:1880000
Cons ci ratio: 7.056416e-04	ci left: 9.422458e-01	ci right 9.429114e-01	k: 1772049	n:1880000
KS ci ratio: 1.190272e-01	ci left: 5.422707e-04	ci right 6.114105e-04	k: 1083	n:1880000
CHD2   1880000 perm   1879 sec   (1000 perm/sec)   p_kst 5.760638e-04   p_cons 9.425793e-01   p_joint 5.760638e-04

Joint ci ratio: 1.186991e-01	ci left: 5.424817e-04	ci right 6.114444e-04	k: 1089	n:1890000
Cons ci ratio: 7.038473e-04	ci left: 9.422351e-01	ci right 9.428990e-01	k: 1781453	n:1890000
KS ci ratio: 1.186991e-01	ci left: 5.424817e-04	ci right 6.114444e-04	k: 1089	n:1890000
CHD2   1890000 perm   1897 sec   (996 perm/sec)   p_kst 5.761905e-04   p_cons 9.425677e-01   p_joint 5.761905e-04

Joint ci ratio: 1.182658e-01	ci left: 5.437123e-04	ci right 6.125615e-04	k: 1097	n:1900000
Cons ci ratio: 7.020290e-04	ci left: 9.422303e-01	ci right 9.428925e-01	k: 1790868	n:1900000
KS ci ratio: 1.182658e-01	ci left: 5.437123e-04	ci right 6.125615e-04	k: 1097	n:1900000
CHD2   1900000 perm   1915 sec   (992 perm/sec)   p_kst 5.773684e-04   p_cons 9.425621e-01   p_joint 5.773684e-04

Joint ci ratio: 1.177840e-01	ci left: 5.454386e-04	ci right 6.142055e-04	k: 1106	n:1910000
Cons ci ratio: 7.001334e-04	ci left: 9.422398e-01	ci right 9.429002e-01	k: 1800310	n:1910000
KS ci ratio: 1.177840e-01	ci left: 5.454386e-04	ci right 6.142055e-04	k: 1106	n:1910000
CHD2   1910000 perm   1933 sec   (988 perm/sec)   p_kst 5.790576e-04   p_cons 9.425707e-01   p_joint 5.790576e-04

Joint ci ratio: 1.174661e-01	ci left: 5.456309e-04	ci right 6.142234e-04	k: 1112	n:1920000
Cons ci ratio: 6.982731e-04	ci left: 9.422460e-01	ci right 9.429047e-01	k: 1809746	n:1920000
KS ci ratio: 1.174661e-01	ci left: 5.456309e-04	ci right 6.142234e-04	k: 1112	n:1920000
CHD2   1920000 perm   1951 sec   (984 perm/sec)   p_kst 5.791667e-04   p_cons 9.425760e-01   p_joint 5.791667e-04

Joint ci ratio: 1.169939e-01	ci left: 5.473303e-04	ci right 6.158407e-04	k: 1121	n:1930000
Cons ci ratio: 6.963243e-04	ci left: 9.422683e-01	ci right 9.429252e-01	k: 1819213	n:1930000
KS ci ratio: 1.169939e-01	ci left: 5.473303e-04	ci right 6.158407e-04	k: 1121	n:1930000
CHD2   1930000 perm   1969 sec   (980 perm/sec)   p_kst 5.808290e-04   p_cons 9.425974e-01   p_joint 5.808290e-04

Joint ci ratio: 1.166306e-01	ci left: 5.480118e-04	ci right 6.163799e-04	k: 1128	n:1940000
Cons ci ratio: 6.945735e-04	ci left: 9.422619e-01	ci right 9.429171e-01	k: 1828625	n:1940000
KS ci ratio: 1.166306e-01	ci left: 5.480118e-04	ci right 6.163799e-04	k: 1128	n:1940000
CHD2   1940000 perm   1987 sec   (976 perm/sec)   p_kst 5.814433e-04   p_cons 9.425902e-01   p_joint 5.814433e-04

Joint ci ratio: 1.164246e-01	ci left: 5.471930e-04	ci right 6.153301e-04	k: 1132	n:1950000
Cons ci ratio: 6.927965e-04	ci left: 9.422618e-01	ci right 9.429153e-01	k: 1838049	n:1950000
KS ci ratio: 1.164246e-01	ci left: 5.471930e-04	ci right 6.153301e-04	k: 1132	n:1950000
CHD2   1950000 perm   2006 sec   (972 perm/sec)   p_kst 5.805128e-04   p_cons 9.425892e-01   p_joint 5.805128e-04

Joint ci ratio: 1.160666e-01	ci left: 5.478688e-04	ci right 6.158658e-04	k: 1139	n:1960000
Cons ci ratio: 6.910168e-04	ci left: 9.422642e-01	ci right 9.429161e-01	k: 1847478	n:1960000
KS ci ratio: 1.160666e-01	ci left: 5.478688e-04	ci right 6.158658e-04	k: 1139	n:1960000
CHD2   1960000 perm   2024 sec   (968 perm/sec)   p_kst 5.811224e-04   p_cons 9.425908e-01   p_joint 5.811224e-04

Joint ci ratio: 1.157623e-01	ci left: 5.480451e-04	ci right 6.158736e-04	k: 1145	n:1970000
Cons ci ratio: 6.892119e-04	ci left: 9.422728e-01	ci right 9.429229e-01	k: 1856919	n:1970000
KS ci ratio: 1.157623e-01	ci left: 5.480451e-04	ci right 6.158736e-04	k: 1145	n:1970000
CHD2   1970000 perm   2043 sec   (964 perm/sec)   p_kst 5.812183e-04   p_cons 9.425985e-01   p_joint 5.812183e-04

Joint ci ratio: 1.154605e-01	ci left: 5.482199e-04	ci right 6.158810e-04	k: 1151	n:1980000
Cons ci ratio: 6.874275e-04	ci left: 9.422802e-01	ci right 9.429286e-01	k: 1866358	n:1980000
KS ci ratio: 1.154605e-01	ci left: 5.482199e-04	ci right 6.158810e-04	k: 1151	n:1980000
CHD2   1980000 perm   2061 sec   (960 perm/sec)   p_kst 5.813131e-04   p_cons 9.426051e-01   p_joint 5.813131e-04

Joint ci ratio: 1.149625e-01	ci left: 5.503454e-04	ci right 6.179559e-04	k: 1161	n:1990000
Cons ci ratio: 6.856887e-04	ci left: 9.422825e-01	ci right 9.429293e-01	k: 1875787	n:1990000
KS ci ratio: 1.149625e-01	ci left: 5.503454e-04	ci right 6.179559e-04	k: 1161	n:1990000
CHD2   1990000 perm   2080 sec   (957 perm/sec)   p_kst 5.834171e-04   p_cons 9.426065e-01   p_joint 5.834171e-04

Joint ci ratio: 1.146177e-01	ci left: 5.509931e-04	ci right 6.184666e-04	k: 1168	n:2000000
Cons ci ratio: 6.838145e-04	ci left: 9.423083e-01	ci right 9.429534e-01	k: 1885263	n:2000000
KS ci ratio: 1.146177e-01	ci left: 5.509931e-04	ci right 6.184666e-04	k: 1168	n:2000000
CHD2   2000000 perm   2099 sec   (953 perm/sec)   p_kst 5.840000e-04   p_cons 9.426315e-01   p_joint 5.840000e-04

Joint ci ratio: 1.141789e-01	ci left: 5.526014e-04	ci right 6.199953e-04	k: 1177	n:2010000
Cons ci ratio: 6.820841e-04	ci left: 9.423135e-01	ci right 9.429569e-01	k: 1894698	n:2010000
KS ci ratio: 1.141789e-01	ci left: 5.526014e-04	ci right 6.199953e-04	k: 1177	n:2010000
CHD2   2010000 perm   2118 sec   (949 perm/sec)   p_kst 5.855721e-04   p_cons 9.426358e-01   p_joint 5.855721e-04

Joint ci ratio: 1.139374e-01	ci left: 5.522704e-04	ci right 6.194718e-04	k: 1182	n:2020000
Cons ci ratio: 6.803605e-04	ci left: 9.423195e-01	ci right 9.429614e-01	k: 1904135	n:2020000
KS ci ratio: 1.139374e-01	ci left: 5.522704e-04	ci right 6.194718e-04	k: 1182	n:2020000
CHD2   2020000 perm   2137 sec   (945 perm/sec)   p_kst 5.851485e-04   p_cons 9.426411e-01   p_joint 5.851485e-04

Joint ci ratio: 1.136496e-01	ci left: 5.524214e-04	ci right 6.194600e-04	k: 1188	n:2030000
Cons ci ratio: 6.787705e-04	ci left: 9.423063e-01	ci right 9.429466e-01	k: 1913533	n:2030000
KS ci ratio: 1.136496e-01	ci left: 5.524214e-04	ci right 6.194600e-04	k: 1188	n:2030000
CHD2   2030000 perm   2156 sec   (942 perm/sec)   p_kst 5.852217e-04   p_cons 9.426271e-01   p_joint 5.852217e-04

Joint ci ratio: 1.134589e-01	ci left: 5.516185e-04	ci right 6.184399e-04	k: 1192	n:2040000
Cons ci ratio: 6.769429e-04	ci left: 9.423330e-01	ci right 9.429716e-01	k: 1923012	n:2040000
KS ci ratio: 1.134589e-01	ci left: 5.516185e-04	ci right 6.184399e-04	k: 1192	n:2040000
CHD2   2040000 perm   2175 sec   (938 perm/sec)   p_kst 5.843137e-04   p_cons 9.426529e-01   p_joint 5.843137e-04

Joint ci ratio: 1.131747e-01	ci left: 5.517716e-04	ci right 6.184329e-04	k: 1198	n:2050000
Cons ci ratio: 6.750660e-04	ci left: 9.423697e-01	ci right 9.430066e-01	k: 1932512	n:2050000
KS ci ratio: 1.131747e-01	ci left: 5.517716e-04	ci right 6.184329e-04	k: 1198	n:2050000
CHD2   2050000 perm   2194 sec   (934 perm/sec)   p_kst 5.843902e-04   p_cons 9.426888e-01   p_joint 5.843902e-04

Joint ci ratio: 1.127990e-01	ci left: 5.528668e-04	ci right 6.194240e-04	k: 1206	n:2060000
Cons ci ratio: 6.734614e-04	ci left: 9.423647e-01	ci right 9.430001e-01	k: 1941927	n:2060000
KS ci ratio: 1.127990e-01	ci left: 5.528668e-04	ci right 6.194240e-04	k: 1206	n:2060000
CHD2   2060000 perm   2213 sec   (931 perm/sec)   p_kst 5.854369e-04   p_cons 9.426830e-01   p_joint 5.854369e-04

Joint ci ratio: 1.125196e-01	ci left: 5.530128e-04	ci right 6.194118e-04	k: 1212	n:2070000
Cons ci ratio: 6.717541e-04	ci left: 9.423782e-01	ci right 9.430119e-01	k: 1951380	n:2070000
KS ci ratio: 1.125196e-01	ci left: 5.530128e-04	ci right 6.194118e-04	k: 1212	n:2070000
CHD2   2070000 perm   2232 sec   (927 perm/sec)   p_kst 5.855072e-04   p_cons 9.426957e-01   p_joint 5.855072e-04

Joint ci ratio: 1.122424e-01	ci left: 5.531577e-04	ci right 6.193995e-04	k: 1218	n:2080000
Cons ci ratio: 6.702446e-04	ci left: 9.423616e-01	ci right 9.429939e-01	k: 1960771	n:2080000
KS ci ratio: 1.122424e-01	ci left: 5.531577e-04	ci right 6.193995e-04	k: 1218	n:2080000
CHD2   2080000 perm   2251 sec   (924 perm/sec)   p_kst 5.855769e-04   p_cons 9.426784e-01   p_joint 5.855769e-04

Joint ci ratio: 1.119671e-01	ci left: 5.533013e-04	ci right 6.193871e-04	k: 1224	n:2090000
Cons ci ratio: 6.686474e-04	ci left: 9.423610e-01	ci right 9.429918e-01	k: 1970195	n:2090000
KS ci ratio: 1.119671e-01	ci left: 5.533013e-04	ci right 6.193871e-04	k: 1224	n:2090000
CHD2   2090000 perm   2271 sec   (920 perm/sec)   p_kst 5.856459e-04   p_cons 9.426770e-01   p_joint 5.856459e-04

Joint ci ratio: 1.116033e-01	ci left: 5.543696e-04	ci right 6.203536e-04	k: 1232	n:2100000
Cons ci ratio: 6.670323e-04	ci left: 9.423652e-01	ci right 9.429945e-01	k: 1979629	n:2100000
KS ci ratio: 1.116033e-01	ci left: 5.543696e-04	ci right 6.203536e-04	k: 1232	n:2100000
CHD2   2100000 perm   2290 sec   (917 perm/sec)   p_kst 5.866667e-04   p_cons 9.426805e-01   p_joint 5.866667e-04

Joint ci ratio: 1.114678e-01	ci left: 5.531243e-04	ci right 6.188750e-04	k: 1235	n:2110000
Cons ci ratio: 6.654170e-04	ci left: 9.423713e-01	ci right 9.429990e-01	k: 1989067	n:2110000
KS ci ratio: 1.114678e-01	ci left: 5.531243e-04	ci right 6.188750e-04	k: 1235	n:2110000
CHD2   2110000 perm   2309 sec   (914 perm/sec)   p_kst 5.853081e-04   p_cons 9.426858e-01   p_joint 5.853081e-04

Joint ci ratio: 1.112431e-01	ci left: 5.528081e-04	ci right 6.183800e-04	k: 1240	n:2120000
Cons ci ratio: 6.638309e-04	ci left: 9.423745e-01	ci right 9.430007e-01	k: 1998499	n:2120000
KS ci ratio: 1.112431e-01	ci left: 5.528081e-04	ci right 6.183800e-04	k: 1240	n:2120000
CHD2   2120000 perm   2329 sec   (910 perm/sec)   p_kst 5.849057e-04   p_cons 9.426882e-01   p_joint 5.849057e-04

Joint ci ratio: 1.109751e-01	ci left: 5.529513e-04	ci right 6.183719e-04	k: 1246	n:2130000
Cons ci ratio: 6.623280e-04	ci left: 9.423659e-01	ci right 9.429907e-01	k: 2007906	n:2130000
KS ci ratio: 1.109751e-01	ci left: 5.529513e-04	ci right 6.183719e-04	k: 1246	n:2130000
CHD2   2130000 perm   2349 sec   (907 perm/sec)   p_kst 5.849765e-04   p_cons 9.426789e-01   p_joint 5.849765e-04

Joint ci ratio: 1.107533e-01	ci left: 5.526391e-04	ci right 6.178836e-04	k: 1251	n:2140000
Cons ci ratio: 6.608009e-04	ci left: 9.423629e-01	ci right 9.429863e-01	k: 2017325	n:2140000
KS ci ratio: 1.107533e-01	ci left: 5.526391e-04	ci right 6.178836e-04	k: 1251	n:2140000
CHD2   2140000 perm   2368 sec   (904 perm/sec)   p_kst 5.845794e-04   p_cons 9.426752e-01   p_joint 5.845794e-04

Joint ci ratio: 1.106209e-01	ci left: 5.514254e-04	ci right 6.164437e-04	k: 1254	n:2150000
Cons ci ratio: 6.592078e-04	ci left: 9.423727e-01	ci right 9.429945e-01	k: 2026771	n:2150000
KS ci ratio: 1.106209e-01	ci left: 5.514254e-04	ci right 6.164437e-04	k: 1254	n:2150000
CHD2   2150000 perm   2388 sec   (900 perm/sec)   p_kst 5.832558e-04   p_cons 9.426842e-01   p_joint 5.832558e-04

Joint ci ratio: 1.104451e-01	ci left: 5.506731e-04	ci right 6.154928e-04	k: 1258	n:2160000
Cons ci ratio: 6.575415e-04	ci left: 9.423962e-01	ci right 9.430165e-01	k: 2036247	n:2160000
KS ci ratio: 1.104451e-01	ci left: 5.506731e-04	ci right 6.154928e-04	k: 1258	n:2160000
CHD2   2160000 perm   2408 sec   (897 perm/sec)   p_kst 5.824074e-04   p_cons 9.427069e-01   p_joint 5.824074e-04

Joint ci ratio: 1.101393e-01	ci left: 5.512723e-04	ci right 6.159712e-04	k: 1265	n:2170000
Cons ci ratio: 6.559885e-04	ci left: 9.424029e-01	ci right 9.430217e-01	k: 2045687	n:2170000
KS ci ratio: 1.101393e-01	ci left: 5.512723e-04	ci right 6.159712e-04	k: 1265	n:2170000
CHD2   2170000 perm   2428 sec   (894 perm/sec)   p_kst 5.829493e-04   p_cons 9.427129e-01   p_joint 5.829493e-04

Joint ci ratio: 1.098792e-01	ci left: 5.514201e-04	ci right 6.159736e-04	k: 1271	n:2180000
Cons ci ratio: 6.545548e-04	ci left: 9.423916e-01	ci right 9.430091e-01	k: 2055088	n:2180000
KS ci ratio: 1.098792e-01	ci left: 5.514201e-04	ci right 6.159736e-04	k: 1271	n:2180000
CHD2   2180000 perm   2447 sec   (891 perm/sec)   p_kst 5.830275e-04   p_cons 9.427009e-01   p_joint 5.830275e-04

Joint ci ratio: 1.096639e-01	ci left: 5.511226e-04	ci right 6.155067e-04	k: 1276	n:2190000
Cons ci ratio: 6.531360e-04	ci left: 9.423795e-01	ci right 9.429956e-01	k: 2064487	n:2190000
KS ci ratio: 1.096639e-01	ci left: 5.511226e-04	ci right 6.155067e-04	k: 1276	n:2190000
CHD2   2190000 perm   2467 sec   (888 perm/sec)   p_kst 5.826484e-04   p_cons 9.426881e-01   p_joint 5.826484e-04

Joint ci ratio: 1.095783e-01	ci left: 5.495016e-04	ci right 6.136430e-04	k: 1278	n:2200000
Cons ci ratio: 6.516413e-04	ci left: 9.423816e-01	ci right 9.429963e-01	k: 2073917	n:2200000
KS ci ratio: 1.095783e-01	ci left: 5.495016e-04	ci right 6.136430e-04	k: 1278	n:2200000
CHD2   2200000 perm   2488 sec   (884 perm/sec)   p_kst 5.809091e-04   p_cons 9.426895e-01   p_joint 5.809091e-04

Joint ci ratio: 1.093647e-01	ci left: 5.492157e-04	ci right 6.131907e-04	k: 1283	n:2210000
Cons ci ratio: 6.501896e-04	ci left: 9.423783e-01	ci right 9.429916e-01	k: 2083335	n:2210000
KS ci ratio: 1.093647e-01	ci left: 5.492157e-04	ci right 6.131907e-04	k: 1283	n:2210000
CHD2   2210000 perm   2508 sec   (881 perm/sec)   p_kst 5.805430e-04   p_cons 9.426855e-01   p_joint 5.805430e-04

Joint ci ratio: 1.090678e-01	ci left: 5.498088e-04	ci right 6.136678e-04	k: 1290	n:2220000
Cons ci ratio: 6.487475e-04	ci left: 9.423750e-01	ci right 9.429870e-01	k: 2092753	n:2220000
KS ci ratio: 1.090678e-01	ci left: 5.498088e-04	ci right 6.136678e-04	k: 1290	n:2220000
CHD2   2220000 perm   2528 sec   (878 perm/sec)   p_kst 5.810811e-04   p_cons 9.426815e-01   p_joint 5.810811e-04

Joint ci ratio: 1.087314e-01	ci left: 5.508330e-04	ci right 6.146011e-04	k: 1298	n:2230000
Cons ci ratio: 6.473095e-04	ci left: 9.423726e-01	ci right 9.429832e-01	k: 2102173	n:2230000
KS ci ratio: 1.087314e-01	ci left: 5.508330e-04	ci right 6.146011e-04	k: 1298	n:2230000
CHD2   2230000 perm   2549 sec   (875 perm/sec)   p_kst 5.820628e-04   p_cons 9.426785e-01   p_joint 5.820628e-04

Joint ci ratio: 1.083980e-01	ci left: 5.518484e-04	ci right 6.155256e-04	k: 1306	n:2240000
Cons ci ratio: 6.458625e-04	ci left: 9.423734e-01	ci right 9.429826e-01	k: 2111600	n:2240000
KS ci ratio: 1.083980e-01	ci left: 5.518484e-04	ci right 6.155256e-04	k: 1306	n:2240000
CHD2   2240000 perm   2570 sec   (872 perm/sec)   p_kst 5.830357e-04   p_cons 9.426786e-01   p_joint 5.830357e-04

Joint ci ratio: 1.083153e-01	ci left: 5.502605e-04	ci right 6.137030e-04	k: 1308	n:2250000
Cons ci ratio: 6.445363e-04	ci left: 9.423554e-01	ci right 9.429634e-01	k: 2120985	n:2250000
KS ci ratio: 1.083153e-01	ci left: 5.502605e-04	ci right 6.137030e-04	k: 1308	n:2250000
CHD2   2250000 perm   2591 sec   (868 perm/sec)   p_kst 5.813333e-04   p_cons 9.426600e-01   p_joint 5.813333e-04

Joint ci ratio: 1.080679e-01	ci left: 5.504088e-04	ci right 6.137142e-04	k: 1314	n:2260000
Cons ci ratio: 6.430919e-04	ci left: 9.423589e-01	ci right 9.429656e-01	k: 2130418	n:2260000
KS ci ratio: 1.080679e-01	ci left: 5.504088e-04	ci right 6.137142e-04	k: 1314	n:2260000
CHD2   2260000 perm   2612 sec   (865 perm/sec)   p_kst 5.814159e-04   p_cons 9.426628e-01   p_joint 5.814159e-04

Joint ci ratio: 1.077814e-01	ci left: 5.509845e-04	ci right 6.141775e-04	k: 1321	n:2270000
Cons ci ratio: 6.415186e-04	ci left: 9.423858e-01	ci right 9.429910e-01	k: 2139904	n:2270000
KS ci ratio: 1.077814e-01	ci left: 5.509845e-04	ci right 6.141775e-04	k: 1321	n:2270000
CHD2   2270000 perm   2633 sec   (862 perm/sec)   p_kst 5.819383e-04   p_cons 9.426890e-01   p_joint 5.819383e-04

Joint ci ratio: 1.074163e-01	ci left: 5.524091e-04	ci right 6.155372e-04	k: 1330	n:2280000
Cons ci ratio: 6.401723e-04	ci left: 9.423760e-01	ci right 9.429799e-01	k: 2149307	n:2280000
KS ci ratio: 1.074163e-01	ci left: 5.524091e-04	ci right 6.155372e-04	k: 1330	n:2280000
CHD2   2280000 perm   2653 sec   (859 perm/sec)   p_kst 5.833333e-04   p_cons 9.426785e-01   p_joint 5.833333e-04

Joint ci ratio: 1.070549e-01	ci left: 5.538216e-04	ci right 6.168848e-04	k: 1339	n:2290000
Cons ci ratio: 6.387647e-04	ci left: 9.423781e-01	ci right 9.429806e-01	k: 2158737	n:2290000
KS ci ratio: 1.070549e-01	ci left: 5.538216e-04	ci right 6.168848e-04	k: 1339	n:2290000
CHD2   2290000 perm   2674 sec   (856 perm/sec)   p_kst 5.847162e-04   p_cons 9.426799e-01   p_joint 5.847162e-04

Joint ci ratio: 1.067367e-01	ci left: 5.547990e-04	ci right 6.177739e-04	k: 1347	n:2300000
Cons ci ratio: 6.373432e-04	ci left: 9.423840e-01	ci right 9.429853e-01	k: 2168176	n:2300000
KS ci ratio: 1.067367e-01	ci left: 5.547990e-04	ci right 6.177739e-04	k: 1347	n:2300000
CHD2   2300000 perm   2695 sec   (853 perm/sec)   p_kst 5.856522e-04   p_cons 9.426852e-01   p_joint 5.856522e-04

Joint ci ratio: 1.064213e-01	ci left: 5.557681e-04	ci right 6.186550e-04	k: 1355	n:2310000
Cons ci ratio: 6.359058e-04	ci left: 9.423943e-01	ci right 9.429942e-01	k: 2177625	n:2310000
KS ci ratio: 1.064213e-01	ci left: 5.557681e-04	ci right 6.186550e-04	k: 1355	n:2310000
CHD2   2310000 perm   2716 sec   (850 perm/sec)   p_kst 5.865801e-04   p_cons 9.426948e-01   p_joint 5.865801e-04

Joint ci ratio: 1.062257e-01	ci left: 5.554704e-04	ci right 6.182008e-04	k: 1360	n:2320000
Cons ci ratio: 6.344552e-04	ci left: 9.424084e-01	ci right 9.430069e-01	k: 2187083	n:2320000
KS ci ratio: 1.062257e-01	ci left: 5.554704e-04	ci right 6.182008e-04	k: 1360	n:2320000
CHD2   2320000 perm   2737 sec   (848 perm/sec)   p_kst 5.862069e-04   p_cons 9.427082e-01   p_joint 5.862069e-04

Joint ci ratio: 1.061089e-01	ci left: 5.543398e-04	ci right 6.168694e-04	k: 1363	n:2330000
Cons ci ratio: 6.331176e-04	ci left: 9.424047e-01	ci right 9.430019e-01	k: 2196500	n:2330000
KS ci ratio: 1.061089e-01	ci left: 5.543398e-04	ci right 6.168694e-04	k: 1363	n:2330000
CHD2   2330000 perm   2758 sec   (845 perm/sec)   p_kst 5.849785e-04   p_cons 9.427039e-01   p_joint 5.849785e-04

Joint ci ratio: 1.058762e-01	ci left: 5.544669e-04	ci right 6.168652e-04	k: 1369	n:2340000
Cons ci ratio: 6.316160e-04	ci left: 9.424306e-01	ci right 9.430264e-01	k: 2205986	n:2340000
KS ci ratio: 1.058762e-01	ci left: 5.544669e-04	ci right 6.168652e-04	k: 1369	n:2340000
CHD2   2340000 perm   2779 sec   (842 perm/sec)   p_kst 5.850427e-04   p_cons 9.427291e-01   p_joint 5.850427e-04

Joint ci ratio: 1.056836e-01	ci left: 5.541789e-04	ci right 6.164242e-04	k: 1374	n:2350000
Cons ci ratio: 6.304129e-04	ci left: 9.424068e-01	ci right 9.430015e-01	k: 2215356	n:2350000
KS ci ratio: 1.056836e-01	ci left: 5.541789e-04	ci right 6.164242e-04	k: 1374	n:2350000
CHD2   2350000 perm   2801 sec   (839 perm/sec)   p_kst 5.846809e-04   p_cons 9.427047e-01   p_joint 5.846809e-04

Joint ci ratio: 1.053393e-01	ci left: 5.555436e-04	ci right 6.177264e-04	k: 1383	n:2360000
Cons ci ratio: 6.291328e-04	ci left: 9.423976e-01	ci right 9.429911e-01	k: 2224760	n:2360000
KS ci ratio: 1.053393e-01	ci left: 5.555436e-04	ci right 6.177264e-04	k: 1383	n:2360000
CHD2   2360000 perm   2822 sec   (836 perm/sec)   p_kst 5.860169e-04   p_cons 9.426949e-01   p_joint 5.860169e-04

Joint ci ratio: 1.049607e-01	ci left: 5.573080e-04	ci right 6.194502e-04	k: 1393	n:2370000
Cons ci ratio: 6.277647e-04	ci left: 9.424050e-01	ci right 9.429972e-01	k: 2234203	n:2370000
KS ci ratio: 1.049607e-01	ci left: 5.573080e-04	ci right 6.194502e-04	k: 1393	n:2370000
CHD2   2370000 perm   2843 sec   (833 perm/sec)   p_kst 5.877637e-04   p_cons 9.427017e-01   p_joint 5.877637e-04

Joint ci ratio: 1.046608e-01	ci left: 5.582396e-04	ci right 6.202969e-04	k: 1401	n:2380000
Cons ci ratio: 6.264372e-04	ci left: 9.424069e-01	ci right 9.429979e-01	k: 2243633	n:2380000
KS ci ratio: 1.046608e-01	ci left: 5.582396e-04	ci right 6.202969e-04	k: 1401	n:2380000
CHD2   2380000 perm   2865 sec   (831 perm/sec)   p_kst 5.886555e-04   p_cons 9.427029e-01   p_joint 5.886555e-04

Joint ci ratio: 1.042894e-01	ci left: 5.599787e-04	ci right 6.219949e-04	k: 1411	n:2390000
Cons ci ratio: 6.251689e-04	ci left: 9.424000e-01	ci right 9.429897e-01	k: 2253042	n:2390000
KS ci ratio: 1.042894e-01	ci left: 5.599787e-04	ci right 6.219949e-04	k: 1411	n:2390000
CHD2   2390000 perm   2887 sec   (828 perm/sec)   p_kst 5.903766e-04   p_cons 9.426954e-01   p_joint 5.903766e-04

Joint ci ratio: 1.040686e-01	ci left: 5.600803e-04	ci right 6.219684e-04	k: 1417	n:2400000
Cons ci ratio: 6.237616e-04	ci left: 9.424186e-01	ci right 9.430070e-01	k: 2262512	n:2400000
KS ci ratio: 1.040686e-01	ci left: 5.600803e-04	ci right 6.219684e-04	k: 1417	n:2400000
CHD2   2400000 perm   2908 sec   (825 perm/sec)   p_kst 5.904167e-04   p_cons 9.427133e-01   p_joint 5.904167e-04

Joint ci ratio: 1.037398e-01	ci left: 5.613937e-04	ci right 6.232190e-04	k: 1426	n:2410000
Cons ci ratio: 6.225214e-04	ci left: 9.424096e-01	ci right 9.429968e-01	k: 2271916	n:2410000
KS ci ratio: 1.037398e-01	ci left: 5.613937e-04	ci right 6.232190e-04	k: 1426	n:2410000
CHD2   2410000 perm   2930 sec   (823 perm/sec)   p_kst 5.917012e-04   p_cons 9.427037e-01   p_joint 5.917012e-04

Joint ci ratio: 1.035224e-01	ci left: 5.614890e-04	ci right 6.231873e-04	k: 1432	n:2420000
Cons ci ratio: 6.212268e-04	ci left: 9.424114e-01	ci right 9.429974e-01	k: 2281346	n:2420000
KS ci ratio: 1.035224e-01	ci left: 5.614890e-04	ci right 6.231873e-04	k: 1432	n:2420000
CHD2   2420000 perm   2951 sec   (820 perm/sec)   p_kst 5.917355e-04   p_cons 9.427050e-01   p_joint 5.917355e-04

Joint ci ratio: 1.033423e-01	ci left: 5.611827e-04	ci right 6.227336e-04	k: 1437	n:2430000
Cons ci ratio: 6.200537e-04	ci left: 9.423934e-01	ci right 9.429783e-01	k: 2290728	n:2430000
KS ci ratio: 1.033423e-01	ci left: 5.611827e-04	ci right 6.227336e-04	k: 1437	n:2430000
CHD2   2430000 perm   2974 sec   (817 perm/sec)   p_kst 5.913580e-04   p_cons 9.426864e-01   p_joint 5.913580e-04

Joint ci ratio: 1.031989e-01	ci left: 5.604798e-04	ci right 6.218631e-04	k: 1441	n:2440000
Cons ci ratio: 6.187462e-04	ci left: 9.424003e-01	ci right 9.429839e-01	k: 2300170	n:2440000
KS ci ratio: 1.031989e-01	ci left: 5.604798e-04	ci right 6.218631e-04	k: 1441	n:2440000
CHD2   2440000 perm   2995 sec   (815 perm/sec)   p_kst 5.905738e-04   p_cons 9.426926e-01   p_joint 5.905738e-04

Joint ci ratio: 1.030204e-01	ci left: 5.601803e-04	ci right 6.214183e-04	k: 1446	n:2450000
Cons ci ratio: 6.174330e-04	ci left: 9.424095e-01	ci right 9.429919e-01	k: 2309618	n:2450000
KS ci ratio: 1.030204e-01	ci left: 5.601803e-04	ci right 6.214183e-04	k: 1446	n:2450000
CHD2   2450000 perm   3017 sec   (812 perm/sec)   p_kst 5.902041e-04   p_cons 9.427012e-01   p_joint 5.902041e-04

Joint ci ratio: 1.028075e-01	ci left: 5.602794e-04	ci right 6.213940e-04	k: 1452	n:2460000
Cons ci ratio: 6.161768e-04	ci left: 9.424101e-01	ci right 9.429913e-01	k: 2319045	n:2460000
KS ci ratio: 1.028075e-01	ci left: 5.602794e-04	ci right 6.213940e-04	k: 1452	n:2460000
CHD2   2460000 perm   3039 sec   (809 perm/sec)   p_kst 5.902439e-04   p_cons 9.427012e-01   p_joint 5.902439e-04

Joint ci ratio: 1.027369e-01	ci left: 5.588000e-04	ci right 6.197087e-04	k: 1454	n:2470000
Cons ci ratio: 6.149190e-04	ci left: 9.424123e-01	ci right 9.429924e-01	k: 2328476	n:2470000
KS ci ratio: 1.027369e-01	ci left: 5.588000e-04	ci right 6.197087e-04	k: 1454	n:2470000
CHD2   2470000 perm   3062 sec   (807 perm/sec)   p_kst 5.886640e-04   p_cons 9.427028e-01   p_joint 5.886640e-04

Joint ci ratio: 1.023506e-01	ci left: 5.608685e-04	ci right 6.217591e-04	k: 1465	n:2480000
Cons ci ratio: 6.135590e-04	ci left: 9.424339e-01	ci right 9.430127e-01	k: 2337955	n:2480000
KS ci ratio: 1.023506e-01	ci left: 5.608685e-04	ci right 6.217591e-04	k: 1465	n:2480000
CHD2   2480000 perm   3084 sec   (804 perm/sec)   p_kst 5.907258e-04   p_cons 9.427238e-01   p_joint 5.907258e-04

Joint ci ratio: 1.020725e-01	ci left: 5.617467e-04	ci right 6.225570e-04	k: 1473	n:2490000
Cons ci ratio: 6.123490e-04	ci left: 9.424303e-01	ci right 9.430080e-01	k: 2347372	n:2490000
KS ci ratio: 1.020725e-01	ci left: 5.617467e-04	ci right 6.225570e-04	k: 1473	n:2490000
CHD2   2490000 perm   3107 sec   (801 perm/sec)   p_kst 5.915663e-04   p_cons 9.427197e-01   p_joint 5.915663e-04

Joint ci ratio: 1.017966e-01	ci left: 5.626182e-04	ci right 6.233483e-04	k: 1481	n:2500000
Cons ci ratio: 6.110103e-04	ci left: 9.424509e-01	ci right 9.430273e-01	k: 2356849	n:2500000
KS ci ratio: 1.017966e-01	ci left: 5.626182e-04	ci right 6.233483e-04	k: 1481	n:2500000
CHD2   2500000 perm   3130 sec   (799 perm/sec)   p_kst 5.924000e-04   p_cons 9.427396e-01   p_joint 5.924000e-04

Joint ci ratio: 1.016937e-01	ci left: 5.615415e-04	ci right 6.220905e-04	k: 1484	n:2510000
Cons ci ratio: 6.098131e-04	ci left: 9.424477e-01	ci right 9.430230e-01	k: 2366267	n:2510000
KS ci ratio: 1.016937e-01	ci left: 5.615415e-04	ci right 6.220905e-04	k: 1484	n:2510000
CHD2   2510000 perm   3152 sec   (796 perm/sec)   p_kst 5.912351e-04   p_cons 9.427359e-01   p_joint 5.912351e-04

Joint ci ratio: 1.013191e-01	ci left: 5.635674e-04	ci right 6.240977e-04	k: 1495	n:2520000
Cons ci ratio: 6.085826e-04	ci left: 9.424517e-01	ci right 9.430258e-01	k: 2375703	n:2520000
KS ci ratio: 1.013191e-01	ci left: 5.635674e-04	ci right 6.240977e-04	k: 1495	n:2520000
CHD2   2520000 perm   3175 sec   (794 perm/sec)   p_kst 5.932540e-04   p_cons 9.427393e-01   p_joint 5.932540e-04

Joint ci ratio: 1.012515e-01	ci left: 5.621104e-04	ci right 6.224415e-04	k: 1497	n:2530000
Cons ci ratio: 6.074551e-04	ci left: 9.424387e-01	ci right 9.430117e-01	k: 2385096	n:2530000
KS ci ratio: 1.012515e-01	ci left: 5.621104e-04	ci right 6.224415e-04	k: 1497	n:2530000
CHD2   2530000 perm   3198 sec   (791 perm/sec)   p_kst 5.916996e-04   p_cons 9.427257e-01   p_joint 5.916996e-04

Joint ci ratio: 1.009151e-01	ci left: 5.637348e-04	ci right 6.240274e-04	k: 1507	n:2540000
Cons ci ratio: 6.062212e-04	ci left: 9.424458e-01	ci right 9.430177e-01	k: 2394540	n:2540000
KS ci ratio: 1.009151e-01	ci left: 5.637348e-04	ci right 6.240274e-04	k: 1507	n:2540000
CHD2   2540000 perm   3221 sec   (789 perm/sec)   p_kst 5.933071e-04   p_cons 9.427323e-01   p_joint 5.933071e-04

Joint ci ratio: 1.006153e-01	ci left: 5.649646e-04	ci right 6.251985e-04	k: 1516	n:2550000
Cons ci ratio: 6.050452e-04	ci left: 9.424439e-01	ci right 9.430147e-01	k: 2403961	n:2550000
KS ci ratio: 1.006153e-01	ci left: 5.649646e-04	ci right 6.251985e-04	k: 1516	n:2550000
CHD2   2550000 perm   3244 sec   (786 perm/sec)   p_kst 5.945098e-04   p_cons 9.427298e-01   p_joint 5.945098e-04

Joint ci ratio: 1.004499e-01	ci left: 5.646617e-04	ci right 6.247586e-04	k: 1521	n:2560000
Cons ci ratio: 6.038368e-04	ci left: 9.424491e-01	ci right 9.430187e-01	k: 2413400	n:2560000
KS ci ratio: 1.004499e-01	ci left: 5.646617e-04	ci right 6.247586e-04	k: 1521	n:2560000
CHD2   2560000 perm   3267 sec   (783 perm/sec)   p_kst 5.941406e-04   p_cons 9.427344e-01   p_joint 5.941406e-04

Joint ci ratio: 1.003511e-01	ci left: 5.636026e-04	ci right 6.235242e-04	k: 1524	n:2570000
Cons ci ratio: 6.025812e-04	ci left: 9.424639e-01	ci right 9.430324e-01	k: 2422864	n:2570000
KS ci ratio: 1.003511e-01	ci left: 5.636026e-04	ci right 6.235242e-04	k: 1524	n:2570000
CHD2   2570000 perm   3291 sec   (781 perm/sec)   p_kst 5.929961e-04   p_cons 9.427486e-01   p_joint 5.929961e-04

Joint ci ratio: 1.002198e-01	ci left: 5.629295e-04	ci right 6.226967e-04	k: 1528	n:2580000
Cons ci ratio: 6.014522e-04	ci left: 9.424573e-01	ci right 9.430247e-01	k: 2432273	n:2580000
KS ci ratio: 1.002198e-01	ci left: 5.629295e-04	ci right 6.226967e-04	k: 1528	n:2580000
CHD2   2580000 perm   3314 sec   (779 perm/sec)   p_kst 5.922481e-04   p_cons 9.427415e-01   p_joint 5.922481e-04

Joint ci ratio: 9.976395e-02	ci left: 5.660264e-04	ci right 6.258330e-04	k: 1542	n:2590000
Cons ci ratio: 6.002651e-04	ci left: 9.424623e-01	ci right 9.430286e-01	k: 2441712	n:2590000
KS ci ratio: 9.976395e-02	ci left: 5.660264e-04	ci right 6.258330e-04	k: 1542	n:2590000
CHD2   2590000 perm   3337 sec   (776 perm/sec)   p_kst 5.953668e-04   p_cons 9.427459e-01   p_joint 5.953668e-04

Outputting figure to mutsig2_images.part000000000037/CHD2.2_5643_2590000_0.00059537_0.94275_0.00059537.png
                gene_name: CHD2
               theta_stop: 0.100 
                    nperm: 2590000 
                     p_ks: 0.00060 
        ci_ks_bounds_left: 0.00057 
       ci_ks_bounds_right: 0.00063 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.00060 
     ci_joint_bounds_left: 0.00057 
    ci_joint_bounds_right: 0.00063 

Current progress: 33 percent done.
CHD4
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: 1.067577e-01	ci left: 1.124225e-01	ci right 1.252005e-01	k: 1187	n:10000
KS ci ratio: 1.139578e-01	ci left: 9.973948e-02	ci right 1.118912e-01	k: 1057	n:10000
CHD4   10000 perm   2 sec   (5094 perm/sec)   p_kst 1.057000e-01   p_cons 1.187000e-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: 7.511428e-02	ci left: 1.153301e-01	ci right 1.243808e-01	k: 2396	n:20000
KS ci ratio: 8.144539e-02	ci left: 9.955670e-02	ci right 1.080589e-01	k: 2075	n:20000
CHD4   20000 perm   4 sec   (4583 perm/sec)   p_kst 1.037500e-01   p_cons 1.198000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000037/CHD4.2_5895_20000_0.10375_0.1198_1.png
                gene_name: CHD4
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.100 
       ci_ks_bounds_right: 0.11 
                   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: 50 percent done.
CHD8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.896187e-02	ci left: 2.357064e-01	ci right 2.526429e-01	k: 2441	n:10000
Cons ci ratio: 5.649311e-02	ci left: 3.157228e-01	ci right 3.341792e-01	k: 3249	n:10000
KS ci ratio: 9.312912e-02	ci left: 1.434464e-01	ci right 1.575578e-01	k: 1504	n:10000
CHD8   10000 perm   2 sec   (4454 perm/sec)   p_kst 1.504000e-01   p_cons 3.249000e-01   p_joint 2.441000e-01

Outputting figure to mutsig2_images.part000000000037/CHD8.2_7904_10000_0.1504_0.3249_0.2441.png
                gene_name: CHD8
               theta_stop: 0.093 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.25 

Current progress: 67 percent done.
CHERP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.642413e-02	ci left: 8.435630e-01	ci right 8.576321e-01	k: 8507	n:10000
Cons ci ratio: 3.362839e-02	ci left: 5.662431e-01	ci right 5.857126e-01	k: 5760	n:10000
KS ci ratio: 4.204869e-02	ci left: 4.550858e-01	ci right 4.747347e-01	k: 4649	n:10000
CHERP   10000 perm   2 sec   (6236 perm/sec)   p_kst 4.649000e-01   p_cons 5.760000e-01   p_joint 8.507000e-01

Outputting figure to mutsig2_images.part000000000037/CHERP.2_2819_10000_0.4649_0.576_0.8507.png
                gene_name: CHERP
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.85 
     ci_joint_bounds_left: 0.84 
    ci_joint_bounds_right: 0.86 

Current progress: 83 percent done.
CHN2
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: 3.204988e-02	ci left: 5.896176e-01	ci right 6.089245e-01	k: 5993	n:10000
KS ci ratio: 1.571990e-02	ci left: 8.545745e-01	ci right 8.682142e-01	k: 8615	n:10000
CHN2   10000 perm   2 sec   (6491 perm/sec)   p_kst 8.615000e-01   p_cons 5.993000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000037/CHN2.2_1627_10000_0.8615_0.5993_1.png
                gene_name: CHN2
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.87 
                   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.165.3896/
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/181708/iteration1/scatter.0000000037
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 37 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119683: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000038> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:44:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000038.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000038.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 38  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    164.64 sec.
    Max Memory :      1285 MB
    Max Swap   :      3968 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.165.3896/
-whichjob
38
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 38: processing genes 3348 - 3438
Calculating significance of each gene.
Using projection method.
3348	CHRNA7	1
3349	CHRNA9	1
3350	CHRNB1	1
3351	CHRNB2	1.269332e-01
3352	CHRNB3	1.881411e-02
3353	CHRNB4	1
3354	CHRND	1
3355	CHRNE	1
3356	CHRNG	1
3357	CHST1	1
3358	CHST10	1
3359	CHST11	1
3360	CHST12	1
3361	CHST13	1
3362	CHST14	1
3363	CHST15	1
3364	CHST2	1
3365	CHST3	1
3366	CHST4	1
3367	CHST5	1
3368	CHST6	1
3369	CHST8	1
3370	CHST9	1
3371	CHSY1	1
3372	CHSY3	1.011619e-01
3373	CHTF18	1
3374	CHTF8	1
3375	CHUK	1
3376	CHURC1	1
3377	CIAO1	1
3378	CIAPIN1	7.066694e-02
3379	CIB1	1
3380	CIB2	1
3381	CIB3	1
3382	CIB4	1
3383	CIC	2.153963e-01
3384	CIDEA	1
3385	CIDEB	3.550850e-02
3386	CIDEC	1
3387	CIITA	1
3388	CILP	3.444054e-01
3389	CILP2	4.181187e-01
3390	CINP	1
3391	CIR1	1
3392	CIRBP	1
3393	CIRH1A	2.267397e-01
3394	CISD1	1
3395	CISD2	1
3396	CISH	1
3397	CIT	1
3398	CITED1	1
3399	CITED2	1
3400	CIZ1	2.634266e-02
3401	CKAP2	2.609466e-01
3402	CKAP2L	1
3403	CKAP4	1
3404	CKAP5	1
3405	CKB	1
3406	CKLF	1
3407	CKM	1
3408	CKMT1A	1
3409	CKMT1B	1
3410	CKMT2	7.626669e-02
3411	CKS1B	1
3412	CKS2	1
3413	CLASP1	1
3414	CLASP2	1
3415	CLC	1
3416	CLCA1	3.481750e-01
3417	CLCA2	1
3418	CLCA4	1
3419	CLCC1	1
3420	CLCF1	1.084788e-01
3421	CLCN1	1
3422	CLCN2	1
3423	CLCN3	1
3424	CLCN4	1.996276e-01
3425	CLCN5	1
3426	CLCN6	1
3427	CLCN7	1
3428	CLCNKA	1
3429	CLCNKB	1
3430	CLDN1	1
3431	CLDN10	1
3432	CLDN11	1
3433	CLDN12	1
3434	CLDN14	1
3435	CLDN15	1
3436	CLDN16	1
3437	CLDN17	1
3438	CLDN18	1
Done

Running MutSig 2:
Scatter job 38: processing genes 3348 - 3438
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CHRNB2
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: 4.766254e-02	ci left: 3.937641e-01	ci right 4.130922e-01	k: 4034	n:10000
KS ci ratio: 4.338240e-02	ci left: 4.396164e-01	ci right 4.592131e-01	k: 4494	n:10000
CHRNB2   10000 perm   3 sec   (3788 perm/sec)   p_kst 4.494000e-01   p_cons 4.034000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000038/CHRNB2.2_1533_10000_0.4494_0.4034_1.png
                gene_name: CHRNB2
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   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: 25 percent done.
CHRNB3
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: 3.092731e-02	ci left: 6.066862e-01	ci right 6.258460e-01	k: 6163	n:10000
KS ci ratio: 3.123971e-01	ci left: 1.307848e-02	ci right 1.800961e-02	k: 154	n:10000
CHRNB3   10000 perm   3 sec   (3418 perm/sec)   p_kst 1.540000e-02   p_cons 6.163000e-01   p_joint 1.478000e-01

Joint ci ratio: 8.615353e-02	ci left: 8.974462e-02	ci right 9.787391e-02	k: 1875	n:20000
Cons ci ratio: 2.265684e-02	ci left: 5.926199e-01	ci right 6.062512e-01	k: 11989	n:20000
KS ci ratio: 2.257608e-01	ci left: 1.317232e-02	ci right 1.657086e-02	k: 296	n:20000
CHRNB3   20000 perm   6 sec   (3089 perm/sec)   p_kst 1.480000e-02   p_cons 5.994500e-01   p_joint 9.375000e-02

Joint ci ratio: 7.023441e-02	ci left: 9.075327e-02	ci right 9.739225e-02	k: 2821	n:30000
Cons ci ratio: 1.782816e-02	ci left: 6.115382e-01	ci right 6.225724e-01	k: 18512	n:30000
KS ci ratio: 1.867970e-01	ci left: 1.311422e-02	ci right 1.584766e-02	k: 433	n:30000
CHRNB3   30000 perm   10 sec   (2982 perm/sec)   p_kst 1.443333e-02   p_cons 6.170667e-01   p_joint 9.403333e-02

Joint ci ratio: 4.705903e-02	ci left: 1.443352e-01	ci right 1.513160e-01	k: 5912	n:40000
Cons ci ratio: 1.534409e-02	ci left: 6.152222e-01	ci right 6.247603e-01	k: 24800	n:40000
KS ci ratio: 1.618662e-01	ci left: 1.327937e-02	ci right 1.564189e-02	k: 577	n:40000
CHRNB3   40000 perm   14 sec   (2843 perm/sec)   p_kst 1.442500e-02   p_cons 6.200000e-01   p_joint 1.478000e-01

Joint ci ratio: 4.238493e-02	ci left: 1.429750e-01	ci right 1.491861e-01	k: 7303	n:50000
Cons ci ratio: 1.364805e-02	ci left: 6.183542e-01	ci right 6.268716e-01	k: 31131	n:50000
KS ci ratio: 1.462744e-01	ci left: 1.312339e-02	ci right 1.521358e-02	k: 707	n:50000
CHRNB3   50000 perm   17 sec   (2963 perm/sec)   p_kst 1.414000e-02   p_cons 6.226200e-01   p_joint 1.460600e-01

Joint ci ratio: 3.876403e-02	ci left: 1.427867e-01	ci right 1.484476e-01	k: 8736	n:60000
Cons ci ratio: 1.244048e-02	ci left: 6.194253e-01	ci right 6.271961e-01	k: 37399	n:60000
KS ci ratio: 1.338981e-01	ci left: 1.313959e-02	ci right 1.504117e-02	k: 844	n:60000
CHRNB3   60000 perm   19 sec   (3112 perm/sec)   p_kst 1.406667e-02   p_cons 6.233167e-01   p_joint 1.456000e-01

Joint ci ratio: 5.599840e-05	ci left: 9.999473e-01	ci right 1	k: 70000	n:70000
Cons ci ratio: 1.155280e-02	ci left: 6.182813e-01	ci right 6.254800e-01	k: 43532	n:70000
KS ci ratio: 1.229471e-01	ci left: 1.343353e-02	ci right 1.520707e-02	k: 1001	n:70000
CHRNB3   70000 perm   23 sec   (3079 perm/sec)   p_kst 1.430000e-02   p_cons 6.218857e-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: 1.082617e-02	ci left: 6.176652e-01	ci right 6.244010e-01	k: 49683	n:80000
KS ci ratio: 1.158898e-01	ci left: 1.328225e-02	ci right 1.492826e-02	k: 1127	n:80000
CHRNB3   80000 perm   26 sec   (3047 perm/sec)   p_kst 1.408750e-02   p_cons 6.210375e-01   p_joint 1

Joint ci ratio: 3.144950e-02	ci left: 1.448911e-01	ci right 1.495317e-01	k: 13248	n:90000
Cons ci ratio: 1.019363e-02	ci left: 6.184777e-01	ci right 6.248256e-01	k: 55949	n:90000
KS ci ratio: 1.091748e-01	ci left: 1.335066e-02	ci right 1.490311e-02	k: 1270	n:90000
CHRNB3   90000 perm   29 sec   (3113 perm/sec)   p_kst 1.411111e-02   p_cons 6.216556e-01   p_joint 1.472000e-01

Joint ci ratio: 3.919922e-05	ci left: 9.999631e-01	ci right 1	k: 100000	n:100000
Cons ci ratio: 9.692043e-03	ci left: 6.175941e-01	ci right 6.236189e-01	k: 62061	n:100000
KS ci ratio: 1.034321e-01	ci left: 1.342708e-02	ci right 1.490129e-02	k: 1415	n:100000
CHRNB3   100000 perm   32 sec   (3157 perm/sec)   p_kst 1.415000e-02   p_cons 6.206100e-01   p_joint 1

Joint ci ratio: 3.563572e-05	ci left: 9.999665e-01	ci right 1	k: 110000	n:110000
Cons ci ratio: 9.238172e-03	ci left: 6.178796e-01	ci right 6.236232e-01	k: 68283	n:110000
KS ci ratio: 9.892843e-02	ci left: 1.337606e-02	ci right 1.477701e-02	k: 1547	n:110000
CHRNB3   110000 perm   34 sec   (3189 perm/sec)   p_kst 1.406364e-02   p_cons 6.207545e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000038/CHRNB3.2_1401_110000_0.014064_0.62075_1.png
                gene_name: CHRNB3
               theta_stop: 0.099 
                    nperm: 110000 
                     p_ks: 0.014 
        ci_ks_bounds_left: 0.013 
       ci_ks_bounds_right: 0.015 
                   p_cons: 0.62 
      ci_cons_bounds_left: 0.62 
     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.
CIZ1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.550381e-02	ci left: 4.161812e-01	ci right 4.356620e-01	k: 4259	n:10000
Cons ci ratio: 4.333861e-02	ci left: 4.401153e-01	ci right 4.597139e-01	k: 4499	n:10000
KS ci ratio: 3.038716e-02	ci left: 6.150242e-01	ci right 6.341032e-01	k: 6246	n:10000
CIZ1   10000 perm   2 sec   (5234 perm/sec)   p_kst 6.246000e-01   p_cons 4.499000e-01   p_joint 4.259000e-01

Outputting figure to mutsig2_images.part000000000038/CIZ1.2_2761_10000_0.6246_0.4499_0.4259.png
                gene_name: CIZ1
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 75 percent done.
CLCA1
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: 2.058822e-02	ci left: 7.755997e-01	ci right 7.918347e-01	k: 7838	n:10000
KS ci ratio: 3.877317e-02	ci left: 4.955504e-01	ci right 5.152465e-01	k: 5054	n:10000
CLCA1   10000 perm   2 sec   (5366 perm/sec)   p_kst 5.054000e-01   p_cons 7.838000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000038/CLCA1.2_2801_10000_0.5054_0.7838_1.png
                gene_name: CLCA1
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.52 
                   p_cons: 0.78 
      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.165.3896/
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/181708/iteration1/scatter.0000000038
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 38 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1537>
Subject: Job 1119689: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1537>, 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/181708/iteration1/scatter.0000000039> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:44:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000039.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000039.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 39  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    132.23 sec.
    Max Memory :      1130 MB
    Max Swap   :      3769 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.165.3896/
-whichjob
39
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 39: processing genes 3439 - 3528
Calculating significance of each gene.
Using projection method.
3439	CLDN19	1
3440	CLDN2	7.340362e-02
3441	CLDN20	1
3442	CLDN22	1
3443	CLDN25	1.085593e-01
3444	CLDN3	1
3445	CLDN4	9.266200e-02
3446	CLDN5	1
3447	CLDN6	1
3448	CLDN7	1
3449	CLDN8	1
3450	CLDN9	1
3451	CLDND1	1
3452	CLDND2	1
3453	CLEC10A	1
3454	CLEC11A	1
3455	CLEC12A	1
3456	CLEC12B	1
3457	CLEC14A	1.162103e-01
3458	CLEC16A	1
3459	CLEC17A	1
3460	CLEC18A	1
3461	CLEC18B	1
3462	CLEC18C	1
3463	CLEC1A	1
3464	CLEC1B	1.880121e-02
3465	CLEC2B	1
3466	CLEC2D	1
3467	CLEC2L	1
3468	CLEC3A	1
3469	CLEC3B	1
3470	CLEC4A	1
3471	CLEC4C	3.835973e-02
3472	CLEC4D	3.792405e-02
3473	CLEC4E	1
3474	CLEC4F	1
3475	CLEC4G	1
3476	CLEC4M	1
3477	CLEC5A	1
3478	CLEC6A	1
3479	CLEC7A	1
3480	CLEC9A	6.347976e-02
3481	CLECL1	1
3482	CLGN	2.058982e-01
3483	CLIC1	1
3484	CLIC2	1
3485	CLIC3	1
3486	CLIC4	1
3487	CLIC5	1
3488	CLIC6	1.085009e-01
3489	CLINT1	1.919662e-01
3490	CLIP1	3.588214e-01
3491	CLIP2	1
3492	CLIP3	1
3493	CLIP4	1
3494	CLK1	4.528996e-02
3495	CLK2	1
3496	CLK3	1
3497	CLK4	1
3498	CLLU1	1
3499	CLLU1OS	1
3500	CLMN	1
3501	CLN3	1
3502	CLN5	1
3503	CLN6	1
3504	CLN8	1.329295e-01
3505	CLNK	1
3506	CLNS1A	1
3507	CLOCK	1
3508	CLP1	1
3509	CLPB	1
3510	CLPP	1
3511	CLPS	1
3512	CLPTM1	1
3513	CLPTM1L	1
3514	CLPX	1
3515	CLRN1	1
3516	CLRN2	1
3517	CLRN3	1
3518	CLSPN	1
3519	CLSTN1	4.270474e-01
3520	CLSTN2	1
3521	CLSTN3	1
3522	CLTA	1
3523	CLTB	1
3524	CLTC	1
3525	CLTCL1	1
3526	CLU	1
3527	CLUAP1	1.195584e-02
3528	CLUL1	1
Done

Running MutSig 2:
Scatter job 39: processing genes 3439 - 3528
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CLUAP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.042345e-01	ci left: 1.174050e-01	ci right 1.304149e-01	k: 1238	n:10000
Cons ci ratio: 2.831816e-01	ci left: 1.613586e-02	ci right 2.154960e-02	k: 187	n:10000
KS ci ratio: 3.021250e-02	ci left: 6.177371e-01	ci right 6.367887e-01	k: 6273	n:10000
CLUAP1   10000 perm   2 sec   (5423 perm/sec)   p_kst 6.273000e-01   p_cons 1.870000e-02   p_joint 1.238000e-01

Joint ci ratio: 1.421072e-01	ci left: 3.404014e-02	ci right 3.929568e-02	k: 732	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: 2.128005e-02	ci left: 6.224122e-01	ci right 6.358502e-01	k: 12583	n:20000
CLUAP1   20000 perm   9 sec   (2228 perm/sec)   p_kst 6.291500e-01   p_cons 1.820000e-02   p_joint 3.660000e-02

Joint ci ratio: 1.203893e-01	ci left: 3.207488e-02	ci right 3.621597e-02	k: 1023	n:30000
Cons ci ratio: 1.673200e-01	ci left: 1.646177e-02	ci right 1.949927e-02	k: 538	n:30000
KS ci ratio: 1.731646e-02	ci left: 6.252431e-01	ci right 6.361982e-01	k: 18922	n:30000
CLUAP1   30000 perm   11 sec   (2691 perm/sec)   p_kst 6.307333e-01   p_cons 1.793333e-02   p_joint 3.410000e-02

Joint ci ratio: 9.509402e-02	ci left: 3.880895e-02	ci right 4.270808e-02	k: 1629	n:40000
Cons ci ratio: 1.436538e-01	ci left: 1.696081e-02	ci right 1.960978e-02	k: 730	n:40000
KS ci ratio: 1.498802e-02	ci left: 6.262494e-01	ci right 6.357316e-01	k: 25240	n:40000
CLUAP1   40000 perm   13 sec   (2989 perm/sec)   p_kst 6.310000e-01   p_cons 1.825000e-02   p_joint 4.072500e-02

Joint ci ratio: 1.117934e-01	ci left: 2.265673e-02	ci right 2.535892e-02	k: 1199	n:50000
Cons ci ratio: 1.263738e-01	ci left: 1.768566e-02	ci right 2.009066e-02	k: 943	n:50000
KS ci ratio: 1.344263e-02	ci left: 6.254700e-01	ci right 6.339549e-01	k: 31486	n:50000
CLUAP1   50000 perm   16 sec   (3178 perm/sec)   p_kst 6.297200e-01   p_cons 1.886000e-02   p_joint 2.398000e-02

Joint ci ratio: 9.027676e-02	ci left: 2.908958e-02	ci right 3.185608e-02	k: 1827	n:60000
Cons ci ratio: 1.154047e-01	ci left: 1.777682e-02	ci right 1.997007e-02	k: 1131	n:60000
KS ci ratio: 1.224872e-02	ci left: 6.267068e-01	ci right 6.344472e-01	k: 37835	n:60000
CLUAP1   60000 perm   18 sec   (3306 perm/sec)   p_kst 6.305833e-01   p_cons 1.885000e-02   p_joint 3.045000e-02

Joint ci ratio: 8.373550e-02	ci left: 2.908453e-02	ci right 3.164031e-02	k: 2124	n:70000
Cons ci ratio: 1.063391e-01	ci left: 1.802929e-02	ci right 2.006800e-02	k: 1332	n:70000
KS ci ratio: 1.131297e-02	ci left: 6.281143e-01	ci right 6.352748e-01	k: 44219	n:70000
CLUAP1   70000 perm   21 sec   (3393 perm/sec)   p_kst 6.317000e-01   p_cons 1.902857e-02   p_joint 3.034286e-02

Joint ci ratio: 8.184500e-02	ci left: 2.673294e-02	ci right 2.902647e-02	k: 2229	n:80000
Cons ci ratio: 9.898969e-02	ci left: 1.827249e-02	ci right 2.018760e-02	k: 1537	n:80000
KS ci ratio: 1.060025e-02	ci left: 6.275577e-01	ci right 6.342578e-01	k: 50473	n:80000
CLUAP1   80000 perm   23 sec   (3439 perm/sec)   p_kst 6.309125e-01   p_cons 1.921250e-02   p_joint 2.786250e-02

Outputting figure to mutsig2_images.part000000000039/CLUAP1.2_1290_80000_0.63091_0.019213_0.027862.png
                gene_name: CLUAP1
               theta_stop: 0.099 
                    nperm: 80000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.019 
      ci_cons_bounds_left: 0.018 
     ci_cons_bounds_right: 0.020 
                  p_joint: 0.028 
     ci_joint_bounds_left: 0.027 
    ci_joint_bounds_right: 0.029 

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.165.3896/
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/181708/iteration1/scatter.0000000039
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 39 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1706>
Subject: Job 1119694: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1706>, 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/181708/iteration1/scatter.0000000040> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:45:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000040.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000040.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 40  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    224.59 sec.
    Max Memory :      1564 MB
    Max Swap   :      3930 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.165.3896/
-whichjob
40
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 40: processing genes 3529 - 3619
Calculating significance of each gene.
Using projection method.
3529	CLVS1	1.003174e-01
3530	CLVS2	1
3531	CLYBL	1
3532	CMA1	1
3533	CMAS	1
3534	CMBL	1
3535	CMC1	1
3536	CMIP	1
3537	CMKLR1	1
3538	CMPK1	1
3539	CMPK2	1
3540	CMTM1	1
3541	CMTM2	9.364573e-02
3542	CMTM3	1
3543	CMTM4	1
3544	CMTM5	1
3545	CMTM6	1
3546	CMTM7	1
3547	CMTM8	1
3548	CMYA5	8.919594e-01
3549	CNBD1	1.621004e-02
3550	CNBP	1
3551	CNDP1	1
3552	CNDP2	1
3553	CNFN	1
3554	CNGA1	1.631446e-01
3555	CNGA2	1
3556	CNGA3	1
3557	CNGA4	1
3558	CNGB1	1.288339e-01
3559	CNGB3	1
3560	CNIH	1
3561	CNIH2	1
3562	CNIH3	1
3563	CNIH4	1
3564	CNKSR1	1
3565	CNKSR2	1
3566	CNKSR3	2.412004e-01
3567	CNN1	1
3568	CNN2	1
3569	CNN3	8.820426e-02
3570	CNNM1	1
3571	CNNM2	1.338840e-01
3572	CNNM3	2.673741e-02
3573	CNNM4	1
3574	CNO	1
3575	CNOT1	1
3576	CNOT10	1
3577	CNOT2	6.906009e-02
3578	CNOT3	3.148593e-01
3579	CNOT4	1
3580	CNOT6	1
3581	CNOT6L	7.103997e-02
3582	CNOT7	1
3583	CNOT8	1
3584	CNP	1
3585	CNPY1	1
3586	CNPY2	1
3587	CNPY3	1
3588	CNPY4	1
3589	CNR1	2.296033e-01
3590	CNR2	1
3591	CNRIP1	1
3592	CNST	1.727036e-01
3593	CNTD1	1
3594	CNTD2	1
3595	CNTF	1
3596	CNTFR	1
3597	CNTLN	3.651001e-01
3598	CNTN1	4.109192e-02
3599	CNTN2	1
3600	CNTN3	1.087585e-01
3601	CNTN4	1
3602	CNTN5	2.650456e-01
3603	CNTN6	3.424228e-02
3604	CNTNAP1	1
3605	CNTNAP2	1.738881e-01
3606	CNTNAP3	1
3607	CNTNAP4	2.362269e-01
3608	CNTNAP5	1
3609	CNTROB	1
3610	COASY	1
3611	COBL	1
3612	COBLL1	1
3613	COBRA1	1
3614	COCH	1
3615	COG1	1
3616	COG2	6.851798e-03
3617	COG3	1
3618	COG4	1
3619	COG5	1
Done

Running MutSig 2:
Scatter job 40: processing genes 3529 - 3619
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
COG2
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: 8.263127e-02	ci left: 1.760548e-01	ci right 1.913299e-01	k: 1836	n:10000
KS ci ratio: 3.177704e-02	ci left: 5.937330e-01	ci right 6.130067e-01	k: 6034	n:10000
COG2   10000 perm   2 sec   (4379 perm/sec)   p_kst 6.034000e-01   p_cons 1.836000e-01   p_joint 3.819000e-01

Outputting figure to mutsig2_images.part000000000040/COG2.3_2289_10000_0.6034_0.1836_0.3819.png
                gene_name: COG2
               theta_stop: 0.083 
                    nperm: 10000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 12 percent done.
CNGB1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.263190e-02	ci left: 3.473041e-01	ci right 3.661794e-01	k: 3567	n:10000
Cons ci ratio: 6.585772e-02	ci left: 2.529073e-01	ci right 2.702318e-01	k: 2615	n:10000
KS ci ratio: 6.340926e-02	ci left: 2.676508e-01	ci right 2.852796e-01	k: 2764	n:10000
CNGB1   10000 perm   2 sec   (5292 perm/sec)   p_kst 2.764000e-01   p_cons 2.615000e-01   p_joint 3.567000e-01

Outputting figure to mutsig2_images.part000000000040/CNGB1.2_3914_10000_0.2764_0.2615_0.3567.png
                gene_name: CNGB1
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 25 percent done.
CNN3
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: 5.470120e-02	ci left: 3.299187e-01	ci right 3.485750e-01	k: 3392	n:10000
KS ci ratio: 2.121886e-01	ci left: 2.949052e-02	ci right 3.658492e-02	k: 329	n:10000
CNN3   10000 perm   2 sec   (5586 perm/sec)   p_kst 3.290000e-02   p_cons 3.392000e-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: 3.857627e-02	ci left: 3.338813e-01	ci right 3.470651e-01	k: 6809	n:20000
KS ci ratio: 1.496921e-01	ci left: 3.066372e-02	ci right 3.567321e-02	k: 662	n:20000
CNN3   20000 perm   5 sec   (3886 perm/sec)   p_kst 3.310000e-02   p_cons 3.404500e-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: 3.155592e-02	ci left: 3.342734e-01	ci right 3.450243e-01	k: 10189	n:30000
KS ci ratio: 1.212501e-01	ci left: 3.162187e-02	ci right 3.573575e-02	k: 1009	n:30000
CNN3   30000 perm   9 sec   (3380 perm/sec)   p_kst 3.363333e-02   p_cons 3.396333e-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: 3.047364e-02	ci left: 2.881442e-01	ci right 2.970859e-01	k: 11704	n:40000
KS ci ratio: 1.054390e-01	ci left: 3.163626e-02	ci right 3.518190e-02	k: 1335	n:40000
CNN3   40000 perm   12 sec   (3231 perm/sec)   p_kst 3.337500e-02   p_cons 2.926000e-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: 2.725942e-02	ci left: 2.885745e-01	ci right 2.965696e-01	k: 14628	n:50000
KS ci ratio: 9.543683e-02	ci left: 3.108013e-02	ci right 3.421444e-02	k: 1631	n:50000
CNN3   50000 perm   16 sec   (3214 perm/sec)   p_kst 3.262000e-02   p_cons 2.925600e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000040/CNN3.2_1018_50000_0.03262_0.29256_1.png
                gene_name: CNN3
               theta_stop: 0.095 
                    nperm: 50000 
                     p_ks: 0.033 
        ci_ks_bounds_left: 0.031 
       ci_ks_bounds_right: 0.034 
                   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: 38 percent done.
CNNM3
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: 2.350084e-02	ci left: 7.268385e-01	ci right 7.442241e-01	k: 7356	n:10000
KS ci ratio: 2.686446e-02	ci left: 6.711587e-01	ci right 6.895361e-01	k: 6804	n:10000
CNNM3   10000 perm   2 sec   (4035 perm/sec)   p_kst 6.804000e-01   p_cons 7.356000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000040/CNNM3.2_2156_10000_0.6804_0.7356_1.png
                gene_name: CNNM3
               theta_stop: 0.027 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.74 
      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: 50 percent done.
CNOT3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.486677e-01	ci left: 6.014890e-02	ci right 6.990637e-02	k: 649	n:10000
Cons ci ratio: 1.229981e-01	ci left: 8.650182e-02	ci right 9.793702e-02	k: 921	n:10000
KS ci ratio: 2.650703e-01	ci left: 1.856024e-02	ci right 2.432325e-02	k: 213	n:10000
CNOT3   10000 perm   2 sec   (5746 perm/sec)   p_kst 2.130000e-02   p_cons 9.210000e-02   p_joint 6.490000e-02

Joint ci ratio: 1.038504e-01	ci left: 6.303638e-02	ci right 6.999029e-02	k: 1329	n:20000
Cons ci ratio: 8.728774e-02	ci left: 8.758778e-02	ci right 9.563141e-02	k: 1831	n:20000
KS ci ratio: 1.777090e-01	ci left: 2.163632e-02	ci right 2.590368e-02	k: 474	n:20000
CNOT3   20000 perm   4 sec   (5066 perm/sec)   p_kst 2.370000e-02   p_cons 9.155000e-02   p_joint 6.645000e-02

Joint ci ratio: 1.052837e-02	ci left: 8.177247e-01	ci right 8.264128e-01	k: 24663	n:30000
Cons ci ratio: 7.078956e-02	ci left: 8.944116e-02	ci right 9.603796e-02	k: 2781	n:30000
KS ci ratio: 1.457825e-01	ci left: 2.181541e-02	ci right 2.527771e-02	k: 705	n:30000
CNOT3   30000 perm   6 sec   (4927 perm/sec)   p_kst 2.350000e-02   p_cons 9.270000e-02   p_joint 8.221000e-01

Joint ci ratio: 3.173663e-02	ci left: 2.716978e-01	ci right 2.804847e-01	k: 11043	n:40000
Cons ci ratio: 6.120881e-02	ci left: 9.014628e-02	ci right 9.586297e-02	k: 3719	n:40000
KS ci ratio: 1.252562e-01	ci left: 2.240110e-02	ci right 2.541856e-02	k: 955	n:40000
CNOT3   40000 perm   8 sec   (4833 perm/sec)   p_kst 2.387500e-02   p_cons 9.297500e-02   p_joint 2.760750e-01

Joint ci ratio: 8.162413e-03	ci left: 8.184574e-01	ci right 8.251852e-01	k: 41092	n:50000
Cons ci ratio: 5.474693e-02	ci left: 9.044822e-02	ci right 9.555915e-02	k: 4649	n:50000
KS ci ratio: 1.109438e-01	ci left: 2.300693e-02	ci right 2.572868e-02	k: 1217	n:50000
CNOT3   50000 perm   11 sec   (4747 perm/sec)   p_kst 2.434000e-02   p_cons 9.298000e-02   p_joint 8.218400e-01

Joint ci ratio: 6.324642e-03	ci left: 8.621557e-01	ci right 8.676423e-01	k: 51895	n:60000
Cons ci ratio: 4.984901e-02	ci left: 9.109947e-02	ci right 9.577327e-02	k: 5605	n:60000
KS ci ratio: 1.007349e-01	ci left: 2.337524e-02	ci right 2.587103e-02	k: 1476	n:60000
CNOT3   60000 perm   13 sec   (4597 perm/sec)   p_kst 2.460000e-02   p_cons 9.341667e-02   p_joint 8.649167e-01

Joint ci ratio: 5.855518e-03	ci left: 8.623599e-01	ci right 8.674384e-01	k: 60544	n:70000
Cons ci ratio: 4.607101e-02	ci left: 9.156510e-02	ci right 9.589721e-02	k: 6560	n:70000
KS ci ratio: 9.258083e-02	ci left: 2.381412e-02	ci right 2.613977e-02	k: 1747	n:70000
CNOT3   70000 perm   16 sec   (4497 perm/sec)   p_kst 2.495714e-02   p_cons 9.371429e-02   p_joint 8.649143e-01

Outputting figure to mutsig2_images.part000000000040/CNOT3.2_2330_70000_0.024957_0.093714_0.86491.png
                gene_name: CNOT3
               theta_stop: 0.093 
                    nperm: 70000 
                     p_ks: 0.025 
        ci_ks_bounds_left: 0.024 
       ci_ks_bounds_right: 0.026 
                   p_cons: 0.094 
      ci_cons_bounds_left: 0.092 
     ci_cons_bounds_right: 0.096 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

Current progress: 62 percent done.
CNST
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.142107e-01	ci left: 2.892165e-02	ci right 3.595419e-02	k: 323	n:10000
Cons ci ratio: 4.023926e-01	ci left: 7.512676e-03	ci right 1.138119e-02	k: 93	n:10000
KS ci ratio: 3.817613e-03	ci left: 9.886188e-01	ci right 9.924873e-01	k: 9907	n:10000
CNST   10000 perm   2 sec   (4703 perm/sec)   p_kst 9.907000e-01   p_cons 9.300000e-03   p_joint 3.230000e-02

Joint ci ratio: 2.050195e-01	ci left: 1.610780e-02	ci right 1.983423e-02	k: 358	n:20000
Cons ci ratio: 2.868611e-01	ci left: 7.923549e-03	ci right 1.062202e-02	k: 184	n:20000
KS ci ratio: 2.573737e-03	ci left: 9.901286e-01	ci right 9.927254e-01	k: 19830	n:20000
CNST   20000 perm   4 sec   (4653 perm/sec)   p_kst 9.915000e-01   p_cons 9.200000e-03   p_joint 1.790000e-02

Joint ci ratio: 7.846694e-02	ci left: 7.377857e-02	ci right 7.983702e-02	k: 2303	n:30000
Cons ci ratio: 2.357281e-01	ci left: 8.056540e-03	ci right 1.024011e-02	k: 273	n:30000
KS ci ratio: 2.192600e-03	ci left: 9.895836e-01	ci right 9.917865e-01	k: 29722	n:30000
CNST   30000 perm   6 sec   (4617 perm/sec)   p_kst 9.907333e-01   p_cons 9.100000e-03   p_joint 7.676667e-02

Joint ci ratio: 6.600760e-02	ci left: 7.834425e-02	ci right 8.371676e-02	k: 3240	n:40000
Cons ci ratio: 1.998665e-01	ci left: 8.572620e-03	ci right 1.049959e-02	k: 380	n:40000
KS ci ratio: 1.862484e-03	ci left: 9.901043e-01	ci right 9.919734e-01	k: 39643	n:40000
CNST   40000 perm   9 sec   (4478 perm/sec)   p_kst 9.910750e-01   p_cons 9.500000e-03   p_joint 8.100000e-02

Joint ci ratio: 5.082011e-02	ci left: 1.036311e-01	ci right 1.090547e-01	k: 5316	n:50000
Cons ci ratio: 1.760346e-01	ci left: 8.955101e-03	ci right 1.070251e-02	k: 490	n:50000
KS ci ratio: 1.670566e-03	ci left: 9.901540e-01	ci right 9.918283e-01	k: 49551	n:50000
CNST   50000 perm   12 sec   (4308 perm/sec)   p_kst 9.910200e-01   p_cons 9.800000e-03   p_joint 1.063200e-01

Joint ci ratio: 4.430399e-02	ci left: 1.128538e-01	ci right 1.179835e-01	k: 6924	n:60000
Cons ci ratio: 1.611397e-01	ci left: 8.979225e-03	ci right 1.056873e-02	k: 585	n:60000
KS ci ratio: 1.542031e-03	ci left: 9.900209e-01	ci right 9.915644e-01	k: 59449	n:60000
CNST   60000 perm   14 sec   (4224 perm/sec)   p_kst 9.908167e-01   p_cons 9.750000e-03   p_joint 1.154000e-01

Joint ci ratio: 3.892322e-02	ci left: 1.240884e-01	ci right 1.290283e-01	k: 8858	n:70000
Cons ci ratio: 1.476316e-01	ci left: 9.234850e-03	ci right 1.072048e-02	k: 697	n:70000
KS ci ratio: 1.449860e-03	ci left: 9.897832e-01	ci right 9.912329e-01	k: 69337	n:70000
CNST   70000 perm   17 sec   (4121 perm/sec)   p_kst 9.905286e-01   p_cons 9.957143e-03   p_joint 1.265429e-01

Joint ci ratio: 3.631819e-02	ci left: 1.247992e-01	ci right 1.294279e-01	k: 10168	n:80000
Cons ci ratio: 1.390430e-01	ci left: 9.153092e-03	ci right 1.053280e-02	k: 786	n:80000
KS ci ratio: 1.335452e-03	ci left: 9.901270e-01	ci right 9.914620e-01	k: 79265	n:80000
CNST   80000 perm   20 sec   (4024 perm/sec)   p_kst 9.908125e-01   p_cons 9.825000e-03   p_joint 1.271000e-01

Joint ci ratio: 3.538456e-02	ci left: 1.178726e-01	ci right 1.221297e-01	k: 10799	n:90000
Cons ci ratio: 1.303038e-01	ci left: 9.306465e-03	ci right 1.061430e-02	k: 895	n:90000
KS ci ratio: 1.273581e-03	ci left: 9.899479e-01	ci right 9.912201e-01	k: 89154	n:90000
CNST   90000 perm   23 sec   (3934 perm/sec)   p_kst 9.906000e-01   p_cons 9.944444e-03   p_joint 1.199889e-01

Joint ci ratio: 3.354969e-02	ci left: 1.181011e-01	ci right 1.221409e-01	k: 12011	n:100000
Cons ci ratio: 1.234641e-01	ci left: 9.363473e-03	ci right 1.060520e-02	k: 997	n:100000
KS ci ratio: 1.205561e-03	ci left: 9.900237e-01	ci right 9.912276e-01	k: 99064	n:100000
CNST   100000 perm   27 sec   (3677 perm/sec)   p_kst 9.906400e-01   p_cons 9.970000e-03   p_joint 1.201100e-01

Joint ci ratio: 3.198454e-02	ci left: 1.182205e-01	ci right 1.220722e-01	k: 13215	n:110000
Cons ci ratio: 1.175995e-01	ci left: 9.411586e-03	ci right 1.059628e-02	k: 1099	n:110000
KS ci ratio: 1.142290e-03	ci left: 9.901713e-01	ci right 9.913117e-01	k: 108983	n:110000
CNST   110000 perm   32 sec   (3414 perm/sec)   p_kst 9.907545e-01   p_cons 9.990909e-03   p_joint 1.201364e-01

Joint ci ratio: 3.130604e-02	ci left: 1.137464e-01	ci right 1.173722e-01	k: 13866	n:120000
Cons ci ratio: 1.123097e-01	ci left: 9.485248e-03	ci right 1.062195e-02	k: 1205	n:120000
KS ci ratio: 1.101810e-03	ci left: 9.900550e-01	ci right 9.911544e-01	k: 118874	n:120000
CNST   120000 perm   37 sec   (3214 perm/sec)   p_kst 9.906167e-01   p_cons 1.004167e-02   p_joint 1.155500e-01

Joint ci ratio: 3.007287e-02	ci left: 1.138513e-01	ci right 1.173351e-01	k: 15026	n:130000
Cons ci ratio: 1.074683e-01	ci left: 9.586023e-03	ci right 1.068215e-02	k: 1316	n:130000
KS ci ratio: 1.056433e-03	ci left: 9.901158e-01	ci right 9.911698e-01	k: 128785	n:130000
CNST   130000 perm   42 sec   (3067 perm/sec)   p_kst 9.906538e-01   p_cons 1.012308e-02   p_joint 1.155846e-01

Joint ci ratio: 3.060218e-02	ci left: 1.032995e-01	ci right 1.065169e-01	k: 14686	n:140000
Cons ci ratio: 1.029851e-01	ci left: 9.715065e-03	ci right 1.077680e-02	k: 1433	n:140000
KS ci ratio: 1.018187e-03	ci left: 9.901320e-01	ci right 9.911475e-01	k: 138691	n:140000
CNST   140000 perm   46 sec   (3023 perm/sec)   p_kst 9.906500e-01   p_cons 1.023571e-02   p_joint 1.049000e-01

Joint ci ratio: 2.956460e-02	ci left: 1.033536e-01	ci right 1.064617e-01	k: 15735	n:150000
Cons ci ratio: 9.918140e-02	ci left: 9.795206e-03	ci right 1.082385e-02	k: 1545	n:150000
KS ci ratio: 9.795615e-04	ci left: 9.902287e-01	ci right 9.912056e-01	k: 148609	n:150000
CNST   150000 perm   50 sec   (3020 perm/sec)   p_kst 9.907267e-01   p_cons 1.030000e-02   p_joint 1.049000e-01

Outputting figure to mutsig2_images.part000000000040/CNST.2_2233_150000_0.99073_0.0103_0.1049.png
                gene_name: CNST
               theta_stop: 0.099 
                    nperm: 150000 
                     p_ks: 0.99 
        ci_ks_bounds_left: 0.99 
       ci_ks_bounds_right: 0.99 
                   p_cons: 0.010 
      ci_cons_bounds_left: 0.0098 
     ci_cons_bounds_right: 0.011 
                  p_joint: 0.10 
     ci_joint_bounds_left: 0.10 
    ci_joint_bounds_right: 0.11 

Current progress: 75 percent done.
CNTN1
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: 2.340422e-02	ci left: 7.284549e-01	ci right 7.458068e-01	k: 7372	n:10000
KS ci ratio: 2.940376e-02	ci left: 6.304019e-01	ci right 6.493165e-01	k: 6399	n:10000
CNTN1   10000 perm   2 sec   (5285 perm/sec)   p_kst 6.399000e-01   p_cons 7.372000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000040/CNTN1.2_3149_10000_0.6399_0.7372_1.png
                gene_name: CNTN1
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.74 
      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: 88 percent done.
CNTN6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.149215e-02	ci left: 1.801871e-01	ci right 1.955952e-01	k: 1878	n:10000
Cons ci ratio: 1.532580e-01	ci left: 5.667674e-02	ci right 6.618073e-02	k: 613	n:10000
KS ci ratio: 3.026420e-02	ci left: 6.169333e-01	ci right 6.359930e-01	k: 6265	n:10000
CNTN6   10000 perm   2 sec   (5078 perm/sec)   p_kst 6.265000e-01   p_cons 6.130000e-02   p_joint 1.878000e-01

Joint ci ratio: 5.738014e-02	ci left: 1.837429e-01	ci right 1.946476e-01	k: 3783	n:20000
Cons ci ratio: 1.079513e-01	ci left: 5.850174e-02	ci right 6.522634e-02	k: 1236	n:20000
KS ci ratio: 2.165327e-02	ci left: 6.142343e-01	ci right 6.277306e-01	k: 12420	n:20000
CNTN6   20000 perm   4 sec   (4833 perm/sec)   p_kst 6.210000e-01   p_cons 6.180000e-02   p_joint 1.891500e-01

Joint ci ratio: 1.712121e-02	ci left: 6.305258e-01	ci right 6.414479e-01	k: 19080	n:30000
Cons ci ratio: 8.787778e-02	ci left: 5.946019e-02	ci right 6.495830e-02	k: 1865	n:30000
KS ci ratio: 1.767010e-02	ci left: 6.157495e-01	ci right 6.267604e-01	k: 18638	n:30000
CNTN6   30000 perm   7 sec   (4511 perm/sec)   p_kst 6.212667e-01   p_cons 6.216667e-02   p_joint 6.360000e-01

Outputting figure to mutsig2_images.part000000000040/CNTN6.2_3175_30000_0.62127_0.062167_0.636.png
                gene_name: CNTN6
               theta_stop: 0.088 
                    nperm: 30000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.062 
      ci_cons_bounds_left: 0.059 
     ci_cons_bounds_right: 0.065 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.64 

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.165.3896/
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/181708/iteration1/scatter.0000000040
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 40 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1538>
Subject: Job 1119699: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1538>, 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/181708/iteration1/scatter.0000000041> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:46:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000041.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000041.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 41  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    249.40 sec.
    Max Memory :      1590 MB
    Max Swap   :      3854 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.165.3896/
-whichjob
41
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 41: processing genes 3620 - 3709
Calculating significance of each gene.
Using projection method.
3620	COG6	1
3621	COG7	2.065252e-01
3622	COG8	1
3623	COIL	1.067895e-01
3624	COL10A1	1
3625	COL11A1	1
3626	COL11A2	1
3627	COL12A1	1.202741e-01
3628	COL13A1	1.731628e-01
3629	COL14A1	1
3630	COL15A1	3.541455e-01
3631	COL16A1	1
3632	COL17A1	1
3633	COL18A1	3.996561e-01
3634	COL19A1	9.189458e-02
3635	COL1A1	2.107841e-01
3636	COL1A2	2.050507e-01
3637	COL20A1	1
3638	COL21A1	1
3639	COL22A1	1
3640	COL23A1	1.916033e-02
3641	COL24A1	5.673199e-02
3642	COL25A1	2.340984e-01
3643	COL27A1	1.468126e-01
3644	COL28A1	4.726850e-01
3645	COL2A1	1.756410e-01
3646	COL3A1	1
3647	COL4A1	5.193291e-01
3648	COL4A2	5.547288e-01
3649	COL4A3	6.038605e-01
3650	COL4A3BP	2.675008e-01
3651	COL4A4	2.191133e-01
3652	COL4A5	4.673393e-01
3653	COL4A6	4.855921e-01
3654	COL5A1	1.779245e-02
3655	COL5A2	1.619529e-02
3656	COL5A3	1
3657	COL6A1	1
3658	COL6A2	1
3659	COL6A3	1.546820e-01
3660	COL6A5	1
3661	COL6A6	2.579211e-01
3662	COL7A1	1.522061e-01
3663	COL8A1	1
3664	COL8A2	1
3665	COL9A1	1
3666	COL9A2	1.345499e-02
3667	COL9A3	1
3668	COLEC10	1
3669	COLEC11	1
3670	COLEC12	1
3671	COLQ	1
3672	COMMD1	1
3673	COMMD10	1
3674	COMMD2	1.070762e-01
3675	COMMD3	1
3676	COMMD4	1
3677	COMMD5	1
3678	COMMD6	2.277075e-02
3679	COMMD7	1
3680	COMMD8	1
3681	COMMD9	1
3682	COMP	2.801875e-02
3683	COMT	1
3684	COMTD1	1
3685	COPA	3.074897e-01
3686	COPB1	8.729891e-02
3687	COPB2	1.653321e-01
3688	COPE	1
3689	COPG	3.086007e-01
3690	COPG2	1
3691	COPS2	1
3692	COPS3	1
3693	COPS4	9.475797e-03
3694	COPS5	1
3695	COPS6	1
3696	COPS7A	3.882906e-02
3697	COPS7B	1
3698	COPS8	1
3699	COPZ1	1
3700	COPZ2	1
3701	COQ10A	1
3702	COQ10B	1
3703	COQ2	1
3704	COQ3	1
3705	COQ4	1
3706	COQ5	6.726311e-02
3707	COQ6	1
3708	COQ7	2.378126e-02
3709	COQ9	1
Done

Running MutSig 2:
Scatter job 41: processing genes 3620 - 3709
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
COL6A3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.154559e-02	ci left: 1.799903e-01	ci right 1.953921e-01	k: 1876	n:10000
Cons ci ratio: 2.482671e-02	ci left: 7.047290e-01	ci right 7.225464e-01	k: 7137	n:10000
KS ci ratio: 1.191234e-01	ci left: 9.185115e-02	ci right 1.035844e-01	k: 976	n:10000
COL6A3   10000 perm   4 sec   (2767 perm/sec)   p_kst 9.760000e-02   p_cons 7.137000e-01   p_joint 1.876000e-01

Joint ci ratio: 5.716596e-02	ci left: 1.848801e-01	ci right 1.958101e-01	k: 3806	n:20000
Cons ci ratio: 1.712885e-02	ci left: 7.173951e-01	ci right 7.298398e-01	k: 14473	n:20000
KS ci ratio: 8.656147e-02	ci left: 8.896023e-02	ci right 9.705854e-02	k: 1859	n:20000
COL6A3   20000 perm   13 sec   (1520 perm/sec)   p_kst 9.295000e-02   p_cons 7.236500e-01   p_joint 1.903000e-01

Outputting figure to mutsig2_images.part000000000041/COL6A3.4_9753_20000_0.09295_0.72365_0.1903.png
                gene_name: COL6A3
               theta_stop: 0.087 
                    nperm: 20000 
                     p_ks: 0.093 
        ci_ks_bounds_left: 0.089 
       ci_ks_bounds_right: 0.097 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.73 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.20 

Current progress: 7 percent done.
COL7A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.202812e-02	ci left: 2.202021e-01	ci right 2.367564e-01	k: 2284	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: 6.058452e-02	ci left: 2.860725e-01	ci right 3.040471e-01	k: 2950	n:10000
COL7A1   10000 perm   4 sec   (2826 perm/sec)   p_kst 2.950000e-01   p_cons 9.260000e-02   p_joint 2.284000e-01

Joint ci ratio: 7.096984e-02	ci left: 1.276330e-01	ci right 1.370741e-01	k: 2646	n:20000
Cons ci ratio: 8.694855e-02	ci left: 8.822495e-02	ci right 9.629404e-02	k: 1844	n:20000
KS ci ratio: 4.364641e-02	ci left: 2.810847e-01	ci right 2.936772e-01	k: 5747	n:20000
COL7A1   20000 perm   7 sec   (2728 perm/sec)   p_kst 2.873500e-01   p_cons 9.220000e-02   p_joint 1.323000e-01

Outputting figure to mutsig2_images.part000000000041/COL7A1.4_9307_20000_0.28735_0.0922_0.1323.png
                gene_name: COL7A1
               theta_stop: 0.087 
                    nperm: 20000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.092 
      ci_cons_bounds_left: 0.088 
     ci_cons_bounds_right: 0.096 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 14 percent done.
COL24A1
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: 8.195533e-03	ci left: 9.540918e-01	ci right 9.620385e-01	k: 9582	n:10000
KS ci ratio: 4.231157e-02	ci left: 4.519911e-01	ci right 4.716311e-01	k: 4618	n:10000
COL24A1   10000 perm   3 sec   (3529 perm/sec)   p_kst 4.618000e-01   p_cons 9.582000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000041/COL24A1.3_5385_10000_0.4618_0.9582_1.png
                gene_name: COL24A1
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   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: 21 percent done.
COL27A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.526021e-02	ci left: 5.428906e-01	ci right 5.624787e-01	k: 5527	n:10000
Cons ci ratio: 7.021289e-03	ci left: 9.654135e-01	ci right 9.723098e-01	k: 9690	n:10000
KS ci ratio: 7.774266e-02	ci left: 1.947597e-01	ci right 2.106139e-01	k: 2026	n:10000
COL27A1   10000 perm   2 sec   (4071 perm/sec)   p_kst 2.026000e-01   p_cons 9.690000e-01   p_joint 5.527000e-01

Outputting figure to mutsig2_images.part000000000041/COL27A1.3_5826_10000_0.2026_0.969_0.5527.png
                gene_name: COL27A1
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.55 
     ci_joint_bounds_left: 0.54 
    ci_joint_bounds_right: 0.56 

Current progress: 29 percent done.
COL5A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.653175e-02	ci left: 3.154251e-01	ci right 3.338771e-01	k: 3246	n:10000
Cons ci ratio: 2.729774e-02	ci left: 6.641089e-01	ci right 6.825900e-01	k: 6734	n:10000
KS ci ratio: 7.361654e-02	ci left: 2.127026e-01	ci right 2.290604e-01	k: 2208	n:10000
COL5A1   10000 perm   3 sec   (3494 perm/sec)   p_kst 2.208000e-01   p_cons 6.734000e-01   p_joint 3.246000e-01

Outputting figure to mutsig2_images.part000000000041/COL5A1.3_5781_10000_0.2208_0.6734_0.3246.png
                gene_name: COL5A1
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.33 

Current progress: 36 percent done.
COL5A2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.395808e-01	ci left: 6.797633e-02	ci right 7.827401e-02	k: 730	n:10000
Cons ci ratio: 2.286102e-02	ci left: 7.375496e-01	ci right 7.547068e-01	k: 7462	n:10000
KS ci ratio: 1.573961e-01	ci left: 5.378678e-02	ci right 6.307254e-02	k: 583	n:10000
COL5A2   10000 perm   3 sec   (3903 perm/sec)   p_kst 5.830000e-02   p_cons 7.462000e-01   p_joint 7.300000e-02

Joint ci ratio: 9.880999e-02	ci left: 6.933431e-02	ci right 7.659043e-02	k: 1458	n:20000
Cons ci ratio: 1.621442e-02	ci left: 7.389494e-01	ci right 7.510793e-01	k: 14901	n:20000
KS ci ratio: 1.118587e-01	ci left: 5.460525e-02	ci right 6.112403e-02	k: 1156	n:20000
COL5A2   20000 perm   5 sec   (3731 perm/sec)   p_kst 5.780000e-02   p_cons 7.450500e-01   p_joint 7.290000e-02

Joint ci ratio: 6.868689e-02	ci left: 9.455954e-02	ci right 1.013185e-01	k: 2937	n:30000
Cons ci ratio: 1.332095e-02	ci left: 7.377133e-01	ci right 7.476397e-01	k: 22281	n:30000
KS ci ratio: 9.115190e-02	ci left: 5.541384e-02	ci right 6.073881e-02	k: 1741	n:30000
COL5A2   30000 perm   8 sec   (3647 perm/sec)   p_kst 5.803333e-02   p_cons 7.427000e-01   p_joint 9.790000e-02

Outputting figure to mutsig2_images.part000000000041/COL5A2.3_4716_30000_0.058033_0.7427_0.0979.png
                gene_name: COL5A2
               theta_stop: 0.091 
                    nperm: 30000 
                     p_ks: 0.058 
        ci_ks_bounds_left: 0.055 
       ci_ks_bounds_right: 0.061 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.74 
     ci_cons_bounds_right: 0.75 
                  p_joint: 0.098 
     ci_joint_bounds_left: 0.095 
    ci_joint_bounds_right: 0.10 

Current progress: 43 percent done.
COL12A1
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: 2.566713e-02	ci left: 6.908102e-01	ci right 7.088733e-01	k: 6999	n:10000
KS ci ratio: 3.430777e-02	ci left: 5.564183e-01	ci right 5.759431e-01	k: 5662	n:10000
COL12A1   10000 perm   4 sec   (2851 perm/sec)   p_kst 5.662000e-01   p_cons 6.999000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000041/COL12A1.2_9452_10000_0.5662_0.6999_1.png
                gene_name: COL12A1
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.70 
      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: 50 percent done.
COL19A1
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: 3.408486e-02	ci left: 5.596260e-01	ci right 5.791336e-01	k: 5694	n:10000
KS ci ratio: 1.667539e-02	ci left: 8.395897e-01	ci right 8.538077e-01	k: 8468	n:10000
COL19A1   10000 perm   2 sec   (4439 perm/sec)   p_kst 8.468000e-01   p_cons 5.694000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000041/COL19A1.2_3629_10000_0.8468_0.5694_1.png
                gene_name: COL19A1
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.85 
                   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: 57 percent done.
COL2A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.707269e-02	ci left: 5.179584e-01	ci right 5.376254e-01	k: 5278	n:10000
Cons ci ratio: 6.112769e-02	ci left: 2.824065e-01	ci right 3.003152e-01	k: 2913	n:10000
KS ci ratio: 6.049727e-02	ci left: 2.866670e-01	ci right 3.046522e-01	k: 2956	n:10000
COL2A1   10000 perm   2 sec   (4275 perm/sec)   p_kst 2.956000e-01   p_cons 2.913000e-01   p_joint 5.278000e-01

Outputting figure to mutsig2_images.part000000000041/COL2A1.2_4680_10000_0.2956_0.2913_0.5278.png
                gene_name: COL2A1
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.28 
     ci_cons_bounds_right: 0.30 
                  p_joint: 0.53 
     ci_joint_bounds_left: 0.52 
    ci_joint_bounds_right: 0.54 

Current progress: 64 percent done.
COL4A4
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: 2.621813e-02	ci left: 6.817379e-01	ci right 6.999508e-01	k: 6909	n:10000
KS ci ratio: 3.073802e-02	ci left: 6.095991e-01	ci right 6.287314e-01	k: 6192	n:10000
COL4A4   10000 perm   2 sec   (4283 perm/sec)   p_kst 6.192000e-01   p_cons 6.909000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000041/COL4A4.2_5261_10000_0.6192_0.6909_1.png
                gene_name: COL4A4
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.69 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.70 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 71 percent done.
COL6A6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.597573e-02	ci left: 8.505966e-01	ci right 8.643944e-01	k: 8576	n:10000
Cons ci ratio: 8.464158e-02	ci left: 1.690728e-01	ci right 1.841161e-01	k: 1765	n:10000
KS ci ratio: 1.118988e-01	ci left: 1.031515e-01	ci right 1.154771e-01	k: 1092	n:10000
COL6A6   10000 perm   3 sec   (3739 perm/sec)   p_kst 1.092000e-01   p_cons 1.765000e-01   p_joint 8.576000e-01

Joint ci ratio: 4.078071e-02	ci left: 3.095092e-01	ci right 3.224444e-01	k: 6319	n:20000
Cons ci ratio: 6.206165e-02	ci left: 1.611140e-01	ci right 1.714832e-01	k: 3325	n:20000
KS ci ratio: 7.828409e-02	ci left: 1.070221e-01	ci right 1.157912e-01	k: 2227	n:20000
COL6A6   20000 perm   6 sec   (3261 perm/sec)   p_kst 1.113500e-01   p_cons 1.662500e-01   p_joint 3.159500e-01

Outputting figure to mutsig2_images.part000000000041/COL6A6.2_6936_20000_0.11135_0.16625_0.31595.png
                gene_name: COL6A6
               theta_stop: 0.078 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.32 

Current progress: 79 percent done.
COL9A2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.706602e-03	ci left: 9.375495e-01	ci right 9.467908e-01	k: 9423	n:10000
Cons ci ratio: 4.852541e-03	ci left: 9.824212e-01	ci right 9.872903e-01	k: 9850	n:10000
KS ci ratio: 1.901722e-02	ci left: 8.016636e-01	ci right 8.171557e-01	k: 8095	n:10000
COL9A2   10000 perm   2 sec   (5868 perm/sec)   p_kst 8.095000e-01   p_cons 9.850000e-01   p_joint 9.423000e-01

Outputting figure to mutsig2_images.part000000000041/COL9A2.2_2198_10000_0.8095_0.985_0.9423.png
                gene_name: COL9A2
               theta_stop: 0.019 
                    nperm: 10000 
                     p_ks: 0.81 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.94 
    ci_joint_bounds_right: 0.95 

Current progress: 86 percent done.
COMP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.757246e-01	ci left: 4.322176e-02	ci right 5.164440e-02	k: 473	n:10000
Cons ci ratio: 1.816359e-01	ci left: 4.044604e-02	ci right 4.862195e-02	k: 444	n:10000
KS ci ratio: 1.157396e-01	ci left: 9.691393e-02	ci right 1.089185e-01	k: 1028	n:10000
COMP   10000 perm   2 sec   (4950 perm/sec)   p_kst 1.028000e-01   p_cons 4.440000e-02   p_joint 4.730000e-02

Joint ci ratio: 1.957807e-01	ci left: 1.772392e-02	ci right 2.161749e-02	k: 392	n:20000
Cons ci ratio: 1.263723e-01	ci left: 4.299245e-02	ci right 4.884048e-02	k: 917	n:20000
KS ci ratio: 8.133614e-02	ci left: 9.980216e-02	ci right 1.083133e-01	k: 2080	n:20000
COMP   20000 perm   4 sec   (4642 perm/sec)   p_kst 1.040000e-01   p_cons 4.585000e-02   p_joint 1.960000e-02

Joint ci ratio: 1.603418e-01	ci left: 1.796530e-02	ci right 2.112871e-02	k: 585	n:30000
Cons ci ratio: 1.042188e-01	ci left: 4.268167e-02	ci right 4.740695e-02	k: 1350	n:30000
KS ci ratio: 6.647649e-02	ci left: 1.004033e-01	ci right 1.073403e-01	k: 3115	n:30000
COMP   30000 perm   7 sec   (4540 perm/sec)   p_kst 1.038333e-01   p_cons 4.500000e-02   p_joint 1.950000e-02

Joint ci ratio: 1.384395e-01	ci left: 1.828815e-02	ci right 2.103221e-02	k: 785	n:40000
Cons ci ratio: 9.082104e-02	ci left: 4.247542e-02	ci right 4.654104e-02	k: 1779	n:40000
KS ci ratio: 5.718473e-02	ci left: 1.021108e-01	ci right 1.081467e-01	k: 4204	n:40000
COMP   40000 perm   9 sec   (4461 perm/sec)   p_kst 1.051000e-01   p_cons 4.447500e-02   p_joint 1.962500e-02

Joint ci ratio: 1.302973e-01	ci left: 1.662037e-02	ci right 1.895610e-02	k: 888	n:50000
Cons ci ratio: 8.066550e-02	ci left: 4.327785e-02	ci right 4.693520e-02	k: 2254	n:50000
KS ci ratio: 5.136223e-02	ci left: 1.016537e-01	ci right 1.070323e-01	k: 5216	n:50000
COMP   50000 perm   11 sec   (4379 perm/sec)   p_kst 1.043200e-01   p_cons 4.508000e-02   p_joint 1.776000e-02

Joint ci ratio: 1.178142e-01	ci left: 1.704832e-02	ci right 1.919866e-02	k: 1086	n:60000
Cons ci ratio: 9.876448e-02	ci left: 2.431837e-02	ci right 2.686113e-02	k: 1534	n:60000
KS ci ratio: 4.701891e-02	ci left: 1.013704e-01	ci right 1.062680e-01	k: 6228	n:60000
COMP   60000 perm   14 sec   (4291 perm/sec)   p_kst 1.038000e-01   p_cons 2.556667e-02   p_joint 1.810000e-02

Joint ci ratio: 1.086034e-01	ci left: 1.727823e-02	ci right 1.927627e-02	k: 1278	n:70000
Cons ci ratio: 9.106925e-02	ci left: 2.461016e-02	ci right 2.697223e-02	k: 1804	n:70000
KS ci ratio: 4.350827e-02	ci left: 1.016489e-01	ci right 1.061840e-01	k: 7273	n:70000
COMP   70000 perm   17 sec   (4198 perm/sec)   p_kst 1.039000e-01   p_cons 2.577143e-02   p_joint 1.825714e-02

Joint ci ratio: 9.286485e-02	ci left: 2.077477e-02	ci right 2.281012e-02	k: 1742	n:80000
Cons ci ratio: 8.497337e-02	ci left: 2.481030e-02	ci right 2.702426e-02	k: 2072	n:80000
KS ci ratio: 4.089107e-02	ci left: 1.009267e-01	ci right 1.051522e-01	k: 8242	n:80000
COMP   80000 perm   19 sec   (4125 perm/sec)   p_kst 1.030250e-01   p_cons 2.590000e-02   p_joint 2.177500e-02

Outputting figure to mutsig2_images.part000000000041/COMP.2_2350_80000_0.10303_0.0259_0.021775.png
                gene_name: COMP
               theta_stop: 0.093 
                    nperm: 80000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.026 
      ci_cons_bounds_left: 0.025 
     ci_cons_bounds_right: 0.027 
                  p_joint: 0.022 
     ci_joint_bounds_left: 0.021 
    ci_joint_bounds_right: 0.023 

Current progress: 93 percent done.
COPS4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.871987e-02	ci left: 2.369909e-01	ci right 2.539576e-01	k: 2454	n:10000
Cons ci ratio: 1.044305e-02	ci left: 9.287493e-01	ci right 9.385962e-01	k: 9338	n:10000
KS ci ratio: 9.727431e-02	ci left: 1.328630e-01	ci right 1.465476e-01	k: 1396	n:10000
COPS4   10000 perm   2 sec   (6504 perm/sec)   p_kst 1.396000e-01   p_cons 9.338000e-01   p_joint 2.454000e-01

Outputting figure to mutsig2_images.part000000000041/COPS4.2_1261_10000_0.1396_0.9338_0.2454.png
                gene_name: COPS4
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.25 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.25 

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.165.3896/
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/181708/iteration1/scatter.0000000041
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 41 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1541>
Subject: Job 1119726: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1541>, 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/181708/iteration1/scatter.0000000042> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:44:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000042.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000042.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 42  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    119.85 sec.
    Max Memory :       927 MB
    Max Swap   :      3737 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.165.3896/
-whichjob
42
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 42: processing genes 3710 - 3800
Calculating significance of each gene.
Using projection method.
3710	CORIN	1
3711	CORO1A	1
3712	CORO1B	1
3713	CORO1C	1
3714	CORO2A	1
3715	CORO2B	1.389025e-01
3716	CORO6	1.684602e-02
3717	CORO7	2.204075e-01
3718	CORT	1
3719	COTL1	1
3720	COX10	1
3721	COX11	1
3722	COX15	1
3723	COX16	1
3724	COX17	1
3725	COX18	1
3726	COX19	1
3727	COX4I1	1
3728	COX4I2	1
3729	COX4NB	1
3730	COX5A	1
3731	COX5B	1
3732	COX6A1	1
3733	COX6A2	1
3734	COX6B1	1
3735	COX6B2	1
3736	COX6C	2.844351e-02
3737	COX7A1	1
3738	COX7A2	1
3739	COX7A2L	1
3740	COX7B	1
3741	COX7B2	1
3742	COX7C	1
3743	COX8A	1
3744	COX8C	1
3745	CP	3.283585e-01
3746	CP110	1
3747	CPA1	1
3748	CPA2	5.120999e-02
3749	CPA3	1
3750	CPA4	1
3751	CPA5	1
3752	CPA6	1
3753	CPAMD8	1
3754	CPB1	1
3755	CPB2	1.040530e-01
3756	CPD	1.650348e-01
3757	CPE	6.043925e-02
3758	CPEB1	1.763000e-01
3759	CPEB2	1
3760	CPEB3	1
3761	CPEB4	1
3762	CPLX1	1
3763	CPLX2	1
3764	CPLX3	1
3765	CPLX4	1
3766	CPM	1
3767	CPN1	1
3768	CPN2	1
3769	CPNE1	2.697786e-02
3770	CPNE2	1
3771	CPNE3	1
3772	CPNE4	1
3773	CPNE5	1
3774	CPNE6	1
3775	CPNE7	1
3776	CPNE8	1
3777	CPNE9	1.434173e-01
3778	CPO	1
3779	CPOX	1
3780	CPPED1	1
3781	CPS1	3.511270e-01
3782	CPSF1	4.551586e-01
3783	CPSF2	1
3784	CPSF3	1.437916e-01
3785	CPSF3L	1
3786	CPSF4	1
3787	CPSF6	1
3788	CPSF7	1
3789	CPT1A	3.250838e-01
3790	CPT1B	1.500545e-01
3791	CPT1C	3.624120e-01
3792	CPT2	1
3793	CPVL	1
3794	CPXCR1	1
3795	CPXM1	1.291827e-01
3796	CPXM2	1
3797	CPZ	2.601268e-01
3798	CR1	1
3799	CR1L	1
3800	CR2	1
Done

Running MutSig 2:
Scatter job 42: processing genes 3710 - 3800
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CORO6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.931551e-02	ci left: 3.775373e-01	ci right 3.967285e-01	k: 3871	n:10000
Cons ci ratio: 5.875724e-02	ci left: 2.988593e-01	ci right 3.170527e-01	k: 3079	n:10000
KS ci ratio: 5.655754e-02	ci left: 3.152266e-01	ci right 3.336757e-01	k: 3244	n:10000
CORO6   10000 perm   2 sec   (5065 perm/sec)   p_kst 3.244000e-01   p_cons 3.079000e-01   p_joint 3.871000e-01

Outputting figure to mutsig2_images.part000000000042/CORO6.2_1459_10000_0.3244_0.3079_0.3871.png
                gene_name: CORO6
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 50 percent done.
CPNE1
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: 1.050197e-02	ci left: 9.280257e-01	ci right 9.379203e-01	k: 9331	n:10000
KS ci ratio: 1.120740e-02	ci left: 9.191472e-01	ci right 9.296040e-01	k: 9245	n:10000
CPNE1   10000 perm   2 sec   (5936 perm/sec)   p_kst 9.245000e-01   p_cons 9.331000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000042/CPNE1.2_1693_10000_0.9245_0.9331_1.png
                gene_name: CPNE1
               theta_stop: 0.011 
                    nperm: 10000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   p_cons: 0.93 
      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.165.3896/
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/181708/iteration1/scatter.0000000042
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 42 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1702>
Subject: Job 1119732: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1702>, 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/181708/iteration1/scatter.0000000043> was used as the working directory.
Started at Wed Oct 10 10:42:29 2012
Results reported at Wed Oct 10 10:46:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000043.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000043.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 43  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    238.29 sec.
    Max Memory :      1427 MB
    Max Swap   :      3922 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.165.3896/
-whichjob
43
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 43: processing genes 3801 - 3890
Calculating significance of each gene.
Using projection method.
3801	CRABP1	1
3802	CRABP2	1
3803	CRADD	1
3804	CRAMP1L	1
3805	CRAT	1.661350e-02
3806	CRB1	9.529563e-02
3807	CRB2	1
3808	CRB3	1
3809	CRBN	1
3810	CRCP	1
3811	CRCT1	1
3812	CREB1	1
3813	CREB3	1
3814	CREB3L1	1
3815	CREB3L2	1
3816	CREB3L3	1.122540e-02
3817	CREB3L4	1
3818	CREB5	1
3819	CREBBP	1.581371e-03
3820	CREBL2	1
3821	CREBZF	1
3822	CREG1	1
3823	CREG2	1
3824	CRELD1	1
3825	CRELD2	1
3826	CREM	1
3827	CRH	1
3828	CRHBP	1
3829	CRHR1	1
3830	CRHR2	1
3831	CRIM1	5.712903e-02
3832	CRIP1	1
3833	CRIP2	1
3834	CRIP3	1
3835	CRIPAK	1.859430e-02
3836	CRIPT	1
3837	CRISP1	1
3838	CRISP2	1
3839	CRISP3	1
3840	CRISPLD1	1.996328e-01
3841	CRISPLD2	1
3842	CRK	1
3843	CRKL	1
3844	CRLF1	1
3845	CRLF2	1
3846	CRLF3	1
3847	CRLS1	1
3848	CRMP1	1
3849	CRNKL1	2.040222e-03
3850	CRNN	1
3851	CROCC	4.888276e-01
3852	CROT	1
3853	CRP	1
3854	CRTAC1	1.487782e-01
3855	CRTAM	1
3856	CRTAP	1
3857	CRTC1	1
3858	CRTC2	1
3859	CRTC3	2.792339e-01
3860	CRX	5.692847e-02
3861	CRY1	1
3862	CRY2	1
3863	CRYAA	1
3864	CRYAB	1
3865	CRYBA1	1
3866	CRYBA2	2.036396e-02
3867	CRYBA4	1.003336e-01
3868	CRYBB1	1.953315e-02
3869	CRYBB2	1
3870	CRYBB3	1
3871	CRYBG3	1
3872	CRYGA	1
3873	CRYGB	1
3874	CRYGC	1
3875	CRYGD	1
3876	CRYGN	1
3877	CRYGS	1
3878	CRYL1	1
3879	CRYM	1
3880	CRYZ	1
3881	CRYZL1	8.295202e-02
3882	CS	1
3883	CSAD	1
3884	CSAG1	1
3885	CSDA	1
3886	CSDC2	1
3887	CSDE1	1
3888	CSE1L	3.171312e-01
3889	CSF1	9.116201e-02
3890	CSF1R	1.149418e-02
Done

Running MutSig 2:
Scatter job 43: processing genes 3801 - 3890
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CREBBP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.288571e-01	ci left: 7.921726e-02	ci right 9.022608e-02	k: 846	n:10000
Cons ci ratio: 6.903667e-02	ci left: 2.353112e-01	ci right 2.522383e-01	k: 2437	n:10000
KS ci ratio: 1.814227e-01	ci left: 4.054168e-02	ci right 4.872625e-02	k: 445	n:10000
CREBBP   10000 perm   3 sec   (3333 perm/sec)   p_kst 4.450000e-02   p_cons 2.437000e-01   p_joint 8.460000e-02

Joint ci ratio: 1.062673e-01	ci left: 6.030523e-02	ci right 6.712229e-02	k: 1273	n:20000
Cons ci ratio: 4.898946e-02	ci left: 2.365233e-01	ci right 2.484517e-01	k: 4849	n:20000
KS ci ratio: 1.279133e-01	ci left: 4.197441e-02	ci right 4.775885e-02	k: 896	n:20000
CREBBP   20000 perm   9 sec   (2274 perm/sec)   p_kst 4.480000e-02   p_cons 2.424500e-01   p_joint 6.365000e-02

Joint ci ratio: 1.294329e-01	ci left: 2.774345e-02	ci right 3.161501e-02	k: 889	n:30000
Cons ci ratio: 4.042167e-02	ci left: 2.338188e-01	ci right 2.434985e-01	k: 7159	n:30000
KS ci ratio: 1.067247e-01	ci left: 4.073218e-02	ci right 4.535684e-02	k: 1290	n:30000
CREBBP   30000 perm   12 sec   (2540 perm/sec)   p_kst 4.300000e-02   p_cons 2.386333e-01   p_joint 2.963333e-02

Joint ci ratio: 8.902986e-02	ci left: 4.416335e-02	ci right 4.830285e-02	k: 1848	n:40000
Cons ci ratio: 3.502954e-02	ci left: 2.342309e-01	ci right 2.426072e-01	k: 9536	n:40000
KS ci ratio: 9.235189e-02	ci left: 4.110612e-02	ci right 4.511056e-02	k: 1723	n:40000
CREBBP   40000 perm   15 sec   (2585 perm/sec)   p_kst 4.307500e-02   p_cons 2.384000e-01   p_joint 4.620000e-02

Outputting figure to mutsig2_images.part000000000043/CREBBP.5_7453_40000_0.043075_0.2384_0.0462.png
                gene_name: CREBBP
               theta_stop: 0.092 
                    nperm: 40000 
                     p_ks: 0.043 
        ci_ks_bounds_left: 0.041 
       ci_ks_bounds_right: 0.045 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.046 
     ci_joint_bounds_left: 0.044 
    ci_joint_bounds_right: 0.048 

Current progress: 14 percent done.
CREB3L3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.963012e-01	ci left: 1.465041e-02	ci right 1.983629e-02	k: 171	n:10000
Cons ci ratio: 4.539792e-01	ci left: 5.726273e-03	ci right 9.170022e-03	k: 73	n:10000
KS ci ratio: 1.771017e-01	ci left: 4.255135e-02	ci right 5.091525e-02	k: 466	n:10000
CREB3L3   10000 perm   2 sec   (6569 perm/sec)   p_kst 4.660000e-02   p_cons 7.300000e-03   p_joint 1.710000e-02

Joint ci ratio: 2.194697e-01	ci left: 1.397554e-02	ci right 1.746732e-02	k: 313	n:20000
Cons ci ratio: 3.126171e-01	ci left: 6.581657e-03	ci right 9.064647e-03	k: 155	n:20000
KS ci ratio: 1.229707e-01	ci left: 4.536948e-02	ci right 5.136270e-02	k: 966	n:20000
CREB3L3   20000 perm   4 sec   (5609 perm/sec)   p_kst 4.830000e-02   p_cons 7.750000e-03   p_joint 1.565000e-02

Joint ci ratio: 3.317134e-01	ci left: 3.865922e-03	ci right 5.432388e-03	k: 138	n:30000
Cons ci ratio: 2.547049e-01	ci left: 6.835746e-03	ci right 8.861311e-03	k: 234	n:30000
KS ci ratio: 1.027927e-01	ci left: 4.385197e-02	ci right 4.863640e-02	k: 1386	n:30000
CREB3L3   30000 perm   7 sec   (4528 perm/sec)   p_kst 4.620000e-02   p_cons 7.800000e-03   p_joint 4.600000e-03

Joint ci ratio: 2.404589e-01	ci left: 5.806474e-03	ci right 7.416412e-03	k: 263	n:40000
Cons ci ratio: 2.217739e-01	ci left: 6.890396e-03	ci right 8.632207e-03	k: 309	n:40000
KS ci ratio: 8.890390e-02	ci left: 4.428569e-02	ci right 4.843049e-02	k: 1853	n:40000
CREB3L3   40000 perm   10 sec   (3840 perm/sec)   p_kst 4.632500e-02   p_cons 7.725000e-03   p_joint 6.575000e-03

Joint ci ratio: 1.362716e-01	ci left: 1.516958e-02	ci right 1.740709e-02	k: 813	n:50000
Cons ci ratio: 1.977193e-01	ci left: 7.028568e-03	ci right 8.589391e-03	k: 389	n:50000
KS ci ratio: 8.027484e-02	ci left: 4.368978e-02	ci right 4.736322e-02	k: 2275	n:50000
CREB3L3   50000 perm   13 sec   (3705 perm/sec)   p_kst 4.550000e-02   p_cons 7.780000e-03   p_joint 1.626000e-02

Joint ci ratio: 1.269871e-01	ci left: 1.463973e-02	ci right 1.664085e-02	k: 937	n:60000
Cons ci ratio: 1.797200e-01	ci left: 7.159405e-03	ci right 8.588814e-03	k: 471	n:60000
KS ci ratio: 7.355194e-02	ci left: 4.353507e-02	ci right 4.687577e-02	k: 2711	n:60000
CREB3L3   60000 perm   16 sec   (3786 perm/sec)   p_kst 4.518333e-02   p_cons 7.850000e-03   p_joint 1.561667e-02

Joint ci ratio: 9.279886e-02	ci left: 2.370242e-02	ci right 2.602291e-02	k: 1739	n:70000
Cons ci ratio: 1.663379e-01	ci left: 7.216403e-03	ci right 8.539165e-03	k: 550	n:70000
KS ci ratio: 6.827694e-02	ci left: 4.343388e-02	ci right 4.651826e-02	k: 3147	n:70000
CREB3L3   70000 perm   18 sec   (3817 perm/sec)   p_kst 4.495714e-02   p_cons 7.857143e-03   p_joint 2.484286e-02

Joint ci ratio: 8.745187e-02	ci left: 2.342751e-02	ci right 2.558216e-02	k: 1959	n:80000
Cons ci ratio: 1.554351e-01	ci left: 7.274142e-03	ci right 8.511946e-03	k: 630	n:80000
KS ci ratio: 6.380894e-02	ci left: 4.361068e-02	ci right 4.649743e-02	k: 3603	n:80000
CREB3L3   80000 perm   21 sec   (3841 perm/sec)   p_kst 4.503750e-02   p_cons 7.875000e-03   p_joint 2.448750e-02

Joint ci ratio: 7.751057e-02	ci left: 2.656120e-02	ci right 2.871384e-02	k: 2486	n:90000
Cons ci ratio: 1.460154e-01	ci left: 7.364086e-03	ci right 8.534629e-03	k: 714	n:90000
KS ci ratio: 6.014027e-02	ci left: 4.372047e-02	ci right 4.644228e-02	k: 4056	n:90000
CREB3L3   90000 perm   23 sec   (3862 perm/sec)   p_kst 4.506667e-02   p_cons 7.933333e-03   p_joint 2.762222e-02

Joint ci ratio: 7.705068e-02	ci left: 2.425700e-02	ci right 2.621067e-02	k: 2522	n:100000
Cons ci ratio: 1.381238e-01	ci left: 7.437854e-03	ci right 8.550968e-03	k: 798	n:100000
KS ci ratio: 5.719894e-02	ci left: 4.357540e-02	ci right 4.615108e-02	k: 4485	n:100000
CREB3L3   100000 perm   26 sec   (3866 perm/sec)   p_kst 4.485000e-02   p_cons 7.980000e-03   p_joint 2.522000e-02

Joint ci ratio: 7.058609e-02	ci left: 2.630920e-02	ci right 2.824310e-02	k: 2999	n:110000
Cons ci ratio: 1.320676e-01	ci left: 7.420461e-03	ci right 8.478457e-03	k: 873	n:110000
KS ci ratio: 5.448853e-02	ci left: 4.371062e-02	ci right 4.616799e-02	k: 4942	n:110000
CREB3L3   110000 perm   28 sec   (3862 perm/sec)   p_kst 4.492727e-02   p_cons 7.936364e-03   p_joint 2.726364e-02

Joint ci ratio: 7.120592e-02	ci left: 2.375547e-02	ci right 2.551760e-02	k: 2955	n:120000
Cons ci ratio: 1.271497e-01	ci left: 7.358433e-03	ci right 8.365569e-03	k: 942	n:120000
KS ci ratio: 5.219600e-02	ci left: 4.371871e-02	ci right 4.607001e-02	k: 5386	n:120000
CREB3L3   120000 perm   31 sec   (3846 perm/sec)   p_kst 4.488333e-02   p_cons 7.850000e-03   p_joint 2.462500e-02

Joint ci ratio: 6.049863e-02	ci left: 3.033733e-02	ci right 3.223750e-02	k: 4066	n:130000
Cons ci ratio: 1.226820e-01	ci left: 7.314027e-03	ci right 8.277354e-03	k: 1012	n:130000
KS ci ratio: 5.032425e-02	ci left: 4.346901e-02	ci right 4.572059e-02	k: 5796	n:130000
CREB3L3   130000 perm   34 sec   (3800 perm/sec)   p_kst 4.458462e-02   p_cons 7.784615e-03   p_joint 3.127692e-02

Joint ci ratio: 6.003083e-02	ci left: 2.866913e-02	ci right 3.045043e-02	k: 4137	n:140000
Cons ci ratio: 1.180517e-01	ci left: 7.352759e-03	ci right 8.282085e-03	k: 1093	n:140000
KS ci ratio: 4.855852e-02	ci left: 4.339749e-02	ci right 4.556428e-02	k: 6226	n:140000
CREB3L3   140000 perm   39 sec   (3607 perm/sec)   p_kst 4.447143e-02   p_cons 7.807143e-03   p_joint 2.955000e-02

Joint ci ratio: 5.912888e-02	ci left: 2.762430e-02	ci right 2.931399e-02	k: 4269	n:150000
Cons ci ratio: 1.142032e-01	ci left: 7.348052e-03	ci right 8.244464e-03	k: 1168	n:150000
KS ci ratio: 4.694804e-02	ci left: 4.336968e-02	ci right 4.546131e-02	k: 6661	n:150000
CREB3L3   150000 perm   44 sec   (3426 perm/sec)   p_kst 4.440667e-02   p_cons 7.786667e-03   p_joint 2.846000e-02

Joint ci ratio: 6.202478e-02	ci left: 2.360026e-02	ci right 2.511704e-02	k: 3896	n:160000
Cons ci ratio: 1.103956e-01	ci left: 7.386912e-03	ci right 8.256065e-03	k: 1250	n:160000
KS ci ratio: 4.523829e-02	ci left: 4.381006e-02	ci right 4.584397e-02	k: 7171	n:160000
CREB3L3   160000 perm   49 sec   (3269 perm/sec)   p_kst 4.481875e-02   p_cons 7.812500e-03   p_joint 2.435000e-02

Joint ci ratio: 5.948125e-02	ci left: 2.417026e-02	ci right 2.565777e-02	k: 4234	n:170000
Cons ci ratio: 1.066230e-01	ci left: 7.467450e-03	ci right 8.314168e-03	k: 1340	n:170000
KS ci ratio: 4.386124e-02	ci left: 4.389132e-02	ci right 4.586541e-02	k: 7628	n:170000
CREB3L3   170000 perm   53 sec   (3233 perm/sec)   p_kst 4.487059e-02   p_cons 7.882353e-03   p_joint 2.490588e-02

Joint ci ratio: 7.235592e-02	ci left: 1.546357e-02	ci right 1.662987e-02	k: 2887	n:180000
Cons ci ratio: 1.041706e-01	ci left: 7.398760e-03	ci right 8.217211e-03	k: 1404	n:180000
KS ci ratio: 4.263863e-02	ci left: 4.389290e-02	ci right 4.581068e-02	k: 8072	n:180000
CREB3L3   180000 perm   56 sec   (3188 perm/sec)   p_kst 4.484444e-02   p_cons 7.800000e-03   p_joint 1.603889e-02

Joint ci ratio: 7.217157e-02	ci left: 1.473735e-02	ci right 1.584593e-02	k: 2904	n:190000
Cons ci ratio: 1.012223e-01	ci left: 7.434981e-03	ci right 8.232777e-03	k: 1487	n:190000
KS ci ratio: 4.156400e-02	ci left: 4.379078e-02	ci right 4.565472e-02	k: 8496	n:190000
CREB3L3   190000 perm   62 sec   (3053 perm/sec)   p_kst 4.471579e-02   p_cons 7.826316e-03   p_joint 1.528421e-02

Joint ci ratio: 6.781939e-02	ci left: 1.587247e-02	ci right 1.699161e-02	k: 3285	n:200000
Cons ci ratio: 9.873289e-02	ci left: 7.433730e-03	ci right 8.210637e-03	k: 1563	n:200000
KS ci ratio: 4.051208e-02	ci left: 4.381332e-02	ci right 4.562991e-02	k: 8943	n:200000
CREB3L3   200000 perm   68 sec   (2938 perm/sec)   p_kst 4.471500e-02   p_cons 7.815000e-03   p_joint 1.642500e-02

Outputting figure to mutsig2_images.part000000000043/CREB3L3.3_1426_200000_0.044715_0.007815_0.016425.png
                gene_name: CREB3L3
               theta_stop: 0.099 
                    nperm: 200000 
                     p_ks: 0.045 
        ci_ks_bounds_left: 0.044 
       ci_ks_bounds_right: 0.046 
                   p_cons: 0.0078 
      ci_cons_bounds_left: 0.0074 
     ci_cons_bounds_right: 0.0082 
                  p_joint: 0.016 
     ci_joint_bounds_left: 0.016 
    ci_joint_bounds_right: 0.017 

Current progress: 29 percent done.
CRNKL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.333963e-02	ci left: 2.139851e-01	ci right 2.303771e-01	k: 2221	n:10000
Cons ci ratio: 9.935064e-02	ci left: 1.279678e-01	ci right 1.414457e-01	k: 1346	n:10000
KS ci ratio: 8.429399e-02	ci left: 1.702525e-01	ci right 1.853357e-01	k: 1777	n:10000
CRNKL1   10000 perm   2 sec   (5187 perm/sec)   p_kst 1.777000e-01   p_cons 1.346000e-01   p_joint 2.221000e-01

Outputting figure to mutsig2_images.part000000000043/CRNKL1.3_2607_10000_0.1777_0.1346_0.2221.png
                gene_name: CRNKL1
               theta_stop: 0.099 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.23 

Current progress: 43 percent done.
CSF1R
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: 3.752127e-02	ci left: 5.119543e-01	ci right 5.316330e-01	k: 5218	n:10000
KS ci ratio: 1.657893e-02	ci left: 8.411177e-01	ci right 8.552788e-01	k: 8483	n:10000
CSF1R   10000 perm   2 sec   (5588 perm/sec)   p_kst 8.483000e-01   p_cons 5.218000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000043/CSF1R.3_3003_10000_0.8483_0.5218_1.png
                gene_name: CSF1R
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.86 
                   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: 57 percent done.
CRAT
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.063072e-02	ci left: 7.748905e-01	ci right 7.911443e-01	k: 7831	n:10000
Cons ci ratio: 4.523504e-02	ci left: 4.190720e-01	ci right 4.385695e-01	k: 4288	n:10000
KS ci ratio: 4.010601e-02	ci left: 4.786573e-01	ci right 4.983494e-01	k: 4885	n:10000
CRAT   10000 perm   2 sec   (5389 perm/sec)   p_kst 4.885000e-01   p_cons 4.288000e-01   p_joint 7.831000e-01

Outputting figure to mutsig2_images.part000000000043/CRAT.2_1937_10000_0.4885_0.4288_0.7831.png
                gene_name: CRAT
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.79 

Current progress: 71 percent done.
CRB1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.196988e-02	ci left: 5.908220e-01	ci right 6.101194e-01	k: 6005	n:10000
Cons ci ratio: 1.242219e-02	ci left: 9.029877e-01	ci right 9.143730e-01	k: 9088	n:10000
KS ci ratio: 1.712220e-01	ci left: 4.552219e-02	ci right 5.414247e-02	k: 497	n:10000
CRB1   10000 perm   2 sec   (4559 perm/sec)   p_kst 4.970000e-02   p_cons 9.088000e-01   p_joint 6.005000e-01

Joint ci ratio: 1.403687e-02	ci left: 7.902464e-01	ci right 8.014675e-01	k: 15918	n:20000
Cons ci ratio: 8.750502e-03	ci left: 9.053372e-01	ci right 9.133434e-01	k: 18188	n:20000
KS ci ratio: 1.184690e-01	ci left: 4.881745e-02	ci right 5.501365e-02	k: 1037	n:20000
CRB1   20000 perm   5 sec   (3785 perm/sec)   p_kst 5.185000e-02   p_cons 9.094000e-01   p_joint 7.959000e-01

Joint ci ratio: 2.735257e-02	ci left: 4.008015e-01	ci right 4.119500e-01	k: 12191	n:30000
Cons ci ratio: 7.099466e-03	ci left: 9.071454e-01	ci right 9.136415e-01	k: 27313	n:30000
KS ci ratio: 9.617773e-02	ci left: 4.993781e-02	ci right 5.501597e-02	k: 1573	n:30000
CRB1   30000 perm   8 sec   (3744 perm/sec)   p_kst 5.243333e-02   p_cons 9.104333e-01   p_joint 4.063667e-01

Outputting figure to mutsig2_images.part000000000043/CRB1.2_4269_30000_0.052433_0.91043_0.40637.png
                gene_name: CRB1
               theta_stop: 0.096 
                    nperm: 30000 
                     p_ks: 0.052 
        ci_ks_bounds_left: 0.050 
       ci_ks_bounds_right: 0.055 
                   p_cons: 0.91 
      ci_cons_bounds_left: 0.91 
     ci_cons_bounds_right: 0.91 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.41 

Current progress: 86 percent done.
CRIM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.138054e-02	ci left: 2.233609e-01	ci right 2.399957e-01	k: 2316	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: 4.333861e-02	ci left: 4.401153e-01	ci right 4.597139e-01	k: 4499	n:10000
CRIM1   10000 perm   3 sec   (3574 perm/sec)   p_kst 4.499000e-01   p_cons 8.710000e-02   p_joint 2.316000e-01

Joint ci ratio: 1.902071e-02	ci left: 6.733335e-01	ci right 6.863142e-01	k: 13597	n:20000
Cons ci ratio: 9.082502e-02	ci left: 8.131738e-02	ci right 8.910371e-02	k: 1703	n:20000
KS ci ratio: 3.110364e-02	ci left: 4.357001e-01	ci right 4.495166e-01	k: 8852	n:20000
CRIM1   20000 perm   6 sec   (3093 perm/sec)   p_kst 4.426000e-01   p_cons 8.515000e-02   p_joint 6.798500e-01

Outputting figure to mutsig2_images.part000000000043/CRIM1.2_3179_20000_0.4426_0.08515_0.67985.png
                gene_name: CRIM1
               theta_stop: 0.091 
                    nperm: 20000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.085 
      ci_cons_bounds_left: 0.081 
     ci_cons_bounds_right: 0.089 
                  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.165.3896/
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/181708/iteration1/scatter.0000000043
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 43 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119739: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000044> was used as the working directory.
Started at Wed Oct 10 10:42:32 2012
Results reported at Wed Oct 10 10:44:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000044.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000044.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 44  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    129.90 sec.
    Max Memory :      1338 MB
    Max Swap   :      3848 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.165.3896/
-whichjob
44
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 44: processing genes 3891 - 3981
Calculating significance of each gene.
Using projection method.
3891	CSF2	1
3892	CSF2RA	1
3893	CSF2RB	1
3894	CSF3	1
3895	CSF3R	1
3896	CSGALNACT1	1
3897	CSGALNACT2	1
3898	CSH1	1
3899	CSH2	1
3900	CSHL1	1
3901	CSK	1
3902	CSMD1	1.774407e-01
3903	CSMD2	6.703529e-01
3904	CSMD3	6.453370e-03
3905	CSN1S1	1
3906	CSN2	1
3907	CSN3	1
3908	CSNK1A1	1
3909	CSNK1A1L	1
3910	CSNK1D	1
3911	CSNK1E	4.797915e-03
3912	CSNK1G1	5.264393e-02
3913	CSNK1G2	1
3914	CSNK1G3	1
3915	CSNK2A1	1.659149e-01
3916	CSNK2A2	1
3917	CSNK2B	7.764925e-02
3918	CSPG4	1
3919	CSPG5	7.539924e-02
3920	CSPP1	3.358061e-01
3921	CSRNP1	1
3922	CSRNP2	1.830011e-01
3923	CSRNP3	1
3924	CSRP1	1
3925	CSRP2	1
3926	CSRP2BP	1
3927	CSRP3	1
3928	CST1	1
3929	CST11	1
3930	CST2	1
3931	CST3	1
3932	CST4	1
3933	CST5	1
3934	CST6	1
3935	CST7	1
3936	CST8	1
3937	CST9	1
3938	CST9L	1
3939	CSTA	1
3940	CSTB	1
3941	CSTF1	1
3942	CSTF2	1
3943	CSTF2T	1
3944	CSTF3	1
3945	CSTL1	1
3946	CT45A5	1
3947	CT47B1	1
3948	CT62	1
3949	CTAG2	1
3950	CTAGE1	1
3951	CTAGE5	5.509689e-02
3952	CTAGE6P	1
3953	CTAGE9	1
3954	CTBP1	1.816950e-02
3955	CTBP2	1
3956	CTBS	1
3957	CTCF	1
3958	CTCFL	8.402915e-02
3959	CTDP1	1.344888e-01
3960	CTDSP1	1
3961	CTDSP2	1
3962	CTDSPL	1
3963	CTDSPL2	1
3964	CTGF	1
3965	CTH	8.418611e-02
3966	CTHRC1	1
3967	CTLA4	1
3968	CTNNA1	1
3969	CTNNA2	2.298007e-02
3970	CTNNA3	1
3971	CTNNAL1	2.331207e-01
3972	CTNNB1	1
3973	CTNNBIP1	1
3974	CTNNBL1	1
3975	CTNND1	1
3976	CTNND2	4.958188e-02
3977	CTNS	1
3978	CTPS	1
3979	CTPS2	1
3980	CTR9	1
3981	CTRC	1
Done

Running MutSig 2:
Scatter job 44: processing genes 3891 - 3981
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CSMD3
Processing conservation and coverage...
87% 
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: 2.904749e-02	ci left: 6.360330e-01	ci right 6.548822e-01	k: 6455	n:10000
KS ci ratio: 5.532926e-02	ci left: 3.248548e-01	ci right 3.434420e-01	k: 3341	n:10000
CSMD3   10000 perm   3 sec   (3500 perm/sec)   p_kst 3.341000e-01   p_cons 6.455000e-01   p_joint 4.761000e-01

Outputting figure to mutsig2_images.part000000000044/CSMD3.5_11470_10000_0.3341_0.6455_0.4761.png
                gene_name: CSMD3
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 17 percent done.
CSMD1
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: 5.066151e-02	ci left: 3.649021e-01	ci right 3.839711e-01	k: 3744	n:10000
KS ci ratio: 4.182965e-02	ci left: 4.576816e-01	ci right 4.773374e-01	k: 4675	n:10000
CSMD1   10000 perm   4 sec   (2493 perm/sec)   p_kst 4.675000e-01   p_cons 3.744000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000044/CSMD1.2_10788_10000_0.4675_0.3744_1.png
                gene_name: CSMD1
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   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: 33 percent done.
CSNK1E
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.338209e-02	ci left: 2.137878e-01	ci right 2.301745e-01	k: 2219	n:10000
Cons ci ratio: 7.834908e-02	ci left: 1.922969e-01	ci right 2.080782e-01	k: 2001	n:10000
KS ci ratio: 8.458342e-02	ci left: 1.692694e-01	ci right 1.843194e-01	k: 1767	n:10000
CSNK1E   10000 perm   3 sec   (3557 perm/sec)   p_kst 1.767000e-01   p_cons 2.001000e-01   p_joint 2.219000e-01

Outputting figure to mutsig2_images.part000000000044/CSNK1E.2_1287_10000_0.1767_0.2001_0.2219.png
                gene_name: CSNK1E
               theta_stop: 0.085 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.23 

Current progress: 50 percent done.
CTAGE5
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: 1.577910e-02	ci left: 8.536564e-01	ci right 8.673329e-01	k: 8606	n:10000
KS ci ratio: 2.907287e-02	ci left: 6.356307e-01	ci right 6.544847e-01	k: 6451	n:10000
CTAGE5   10000 perm   2 sec   (5912 perm/sec)   p_kst 6.451000e-01   p_cons 8.606000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000044/CTAGE5.2_2542_10000_0.6451_0.8606_1.png
                gene_name: CTAGE5
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.87 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 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: 7.612086e-02	ci left: 2.015594e-01	ci right 2.176102e-01	k: 2095	n:10000
KS ci ratio: 6.095056e-02	ci left: 2.835954e-01	ci right 3.015256e-01	k: 2925	n:10000
CTNNA2   10000 perm   2 sec   (5756 perm/sec)   p_kst 2.925000e-01   p_cons 2.095000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000044/CTNNA2.2_2578_10000_0.2925_0.2095_1.png
                gene_name: CTNNA2
               theta_stop: 0.076 
                    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: 0.20 
     ci_cons_bounds_right: 0.22 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 83 percent done.
CTNND2
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: 6.851645e-02	ci left: 2.380779e-01	ci right 2.550700e-01	k: 2465	n:10000
KS ci ratio: 3.212332e-02	ci left: 5.885136e-01	ci right 6.078292e-01	k: 5982	n:10000
CTNND2   10000 perm   2 sec   (5497 perm/sec)   p_kst 5.982000e-01   p_cons 2.465000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000044/CTNND2.2_3766_10000_0.5982_0.2465_1.png
                gene_name: CTNND2
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.61 
                   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.165.3896/
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/181708/iteration1/scatter.0000000044
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 44 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119748: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000045> was used as the working directory.
Started at Wed Oct 10 10:42:32 2012
Results reported at Wed Oct 10 10:46:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000045.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000045.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 45  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    281.54 sec.
    Max Memory :      1369 MB
    Max Swap   :      3849 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.165.3896/
-whichjob
45
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 45: processing genes 3982 - 4071
Calculating significance of each gene.
Using projection method.
3982	CTRL	9.959140e-02
3983	CTSA	1.155753e-01
3984	CTSB	1
3985	CTSC	1
3986	CTSD	1
3987	CTSE	1
3988	CTSF	1
3989	CTSG	1
3990	CTSH	1
3991	CTSK	1
3992	CTSL1	1
3993	CTSL2	1
3994	CTSO	1
3995	CTSS	1.221192e-01
3996	CTSW	1
3997	CTSZ	1
3998	CTTN	1
3999	CTTNBP2	1
4000/18094 4000	CTTNBP2NL	1.941159e-01
4001	CTU2	1
4002	CTXN1	1
4003	CTXN3	1
4004	CUBN	1.002191e-01
4005	CUEDC1	1
4006	CUEDC2	1
4007	CUL1	4.425633e-04
4008	CUL2	2.368430e-02
4009	CUL3	1
4010	CUL4A	1
4011	CUL4B	2.685006e-01
4012	CUL5	1
4013	CUL7	5.745560e-01
4014	CUL9	1.272730e-01
4015	CUTA	1
4016	CUTC	1
4017	CUX1	1.377374e-01
4018	CUX2	2.106450e-01
4019	CUZD1	1
4020	CWC15	1
4021	CWC22	1
4022	CWC25	1
4023	CWC27	1
4024	CWF19L1	1
4025	CWF19L2	1
4026	CWH43	6.361603e-02
4027	CX3CL1	1
4028	CX3CR1	3.380742e-02
4029	CXADR	1
4030	CXCL1	1
4031	CXCL10	1
4032	CXCL11	1
4033	CXCL12	1
4034	CXCL13	1
4035	CXCL14	1
4036	CXCL16	1
4037	CXCL17	1
4038	CXCL2	1
4039	CXCL3	1
4040	CXCL5	4.622972e-02
4041	CXCL6	1
4042	CXCL9	1
4043	CXCR1	1
4044	CXCR2	1
4045	CXCR3	1
4046	CXCR4	6.103875e-02
4047	CXCR5	1
4048	CXCR6	1
4049	CXCR7	1
4050	CXXC1	1
4051	CXXC4	4.626028e-02
4052	CXXC5	1
4053	CXorf1	1
4054	CXorf21	1.896736e-02
4055	CXorf22	1
4056	CXorf23	1
4057	CXorf26	1
4058	CXorf27	1
4059	CXorf36	1
4060	CXorf38	1.158722e-01
4061	CXorf40A	1
4062	CXorf40B	1
4063	CXorf41	1
4064	CXorf48	1
4065	CXorf56	1
4066	CXorf57	1
4067	CXorf58	1
4068	CXorf59	1
4069	CXorf61	1
4070	CXorf65	1
4071	CXorf66	1
Done

Running MutSig 2:
Scatter job 45: processing genes 3982 - 4071
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: 5.104208e-02	ci left: 3.614212e-01	ci right 3.804540e-01	k: 3709	n:10000
Cons ci ratio: 1.922036e-02	ci left: 7.983141e-01	ci right 8.139072e-01	k: 8062	n:10000
KS ci ratio: 1.179233e-01	ci left: 9.360310e-02	ci right 1.054314e-01	k: 994	n:10000
CUBN   10000 perm   3 sec   (3360 perm/sec)   p_kst 9.940000e-02   p_cons 8.062000e-01   p_joint 3.709000e-01

Joint ci ratio: 5.384246e-02	ci left: 2.038281e-01	ci right 2.151565e-01	k: 4189	n:20000
Cons ci ratio: 1.356879e-02	ci left: 8.011578e-01	ci right 8.121529e-01	k: 16134	n:20000
KS ci ratio: 8.385469e-02	ci left: 9.435467e-02	ci right 1.026625e-01	k: 1969	n:20000
CUBN   20000 perm   9 sec   (2128 perm/sec)   p_kst 9.845000e-02   p_cons 8.067000e-01   p_joint 2.094500e-01

Outputting figure to mutsig2_images.part000000000045/CUBN.4_11140_20000_0.09845_0.8067_0.20945.png
                gene_name: CUBN
               theta_stop: 0.084 
                    nperm: 20000 
                     p_ks: 0.098 
        ci_ks_bounds_left: 0.094 
       ci_ks_bounds_right: 0.10 
                   p_cons: 0.81 
      ci_cons_bounds_left: 0.80 
     ci_cons_bounds_right: 0.81 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.22 

Current progress: 20 percent done.
CUL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.925331e-01	ci left: 3.595770e-02	ci right 4.371330e-02	k: 397	n:10000
Cons ci ratio: 4.962703e-01	ci left: 4.669135e-03	ci right 7.828899e-03	k: 61	n:10000
KS ci ratio: 3.264705e-02	ci left: 5.806865e-01	ci right 6.000608e-01	k: 5904	n:10000
CUL1   10000 perm   2 sec   (5612 perm/sec)   p_kst 5.904000e-01   p_cons 6.100000e-03   p_joint 3.970000e-02

Joint ci ratio: 1.536935e-01	ci left: 2.907449e-02	ci right 3.396297e-02	k: 629	n:20000
Cons ci ratio: 3.552752e-01	ci left: 4.977027e-03	ci right 7.170311e-03	k: 120	n:20000
KS ci ratio: 2.341228e-02	ci left: 5.767313e-01	ci right 5.904444e-01	k: 11672	n:20000
CUL1   20000 perm   4 sec   (5117 perm/sec)   p_kst 5.836000e-01   p_cons 6.000000e-03   p_joint 3.145000e-02

Joint ci ratio: 1.263217e-01	ci left: 2.913224e-02	ci right 3.309259e-02	k: 932	n:30000
Cons ci ratio: 3.006830e-01	ci left: 4.787072e-03	ci right 6.510790e-03	k: 168	n:30000
KS ci ratio: 1.914658e-02	ci left: 5.772291e-01	ci right 5.884215e-01	k: 17485	n:30000
CUL1   30000 perm   6 sec   (4869 perm/sec)   p_kst 5.828333e-01   p_cons 5.600000e-03   p_joint 3.106667e-02

Joint ci ratio: 1.079731e-01	ci left: 3.017504e-02	ci right 3.364335e-02	k: 1275	n:40000
Cons ci ratio: 2.507000e-01	ci left: 5.313599e-03	ci right 6.859426e-03	k: 242	n:40000
KS ci ratio: 1.681656e-02	ci left: 5.711141e-01	ci right 5.808249e-01	k: 23039	n:40000
CUL1   40000 perm   8 sec   (4741 perm/sec)   p_kst 5.759750e-01   p_cons 6.050000e-03   p_joint 3.187500e-02

Joint ci ratio: 1.116030e-01	ci left: 2.273454e-02	ci right 2.544110e-02	k: 1203	n:50000
Cons ci ratio: 2.267827e-01	ci left: 5.266403e-03	ci right 6.631915e-03	k: 296	n:50000
KS ci ratio: 1.503435e-02	ci left: 5.718543e-01	ci right 5.805369e-01	k: 28810	n:50000
CUL1   50000 perm   11 sec   (4553 perm/sec)   p_kst 5.762000e-01   p_cons 5.920000e-03   p_joint 2.406000e-02

Joint ci ratio: 9.230138e-02	ci left: 2.783470e-02	ci right 3.054443e-02	k: 1750	n:60000
Cons ci ratio: 2.086195e-01	ci left: 5.239661e-03	ci right 6.475539e-03	k: 350	n:60000
KS ci ratio: 1.376432e-02	ci left: 5.708157e-01	ci right 5.787437e-01	k: 34487	n:60000
CUL1   60000 perm   14 sec   (4443 perm/sec)   p_kst 5.747833e-01   p_cons 5.833333e-03   p_joint 2.916667e-02

Joint ci ratio: 1.027067e-01	ci left: 1.933770e-02	ci right 2.144518e-02	k: 1426	n:70000
Cons ci ratio: 1.909292e-01	ci left: 5.414102e-03	ci right 6.570281e-03	k: 418	n:70000
KS ci ratio: 1.271758e-02	ci left: 5.721000e-01	ci right 5.794366e-01	k: 40304	n:70000
CUL1   70000 perm   16 sec   (4254 perm/sec)   p_kst 5.757714e-01   p_cons 5.971429e-03   p_joint 2.037143e-02

Joint ci ratio: 9.640146e-02	ci left: 1.927292e-02	ci right 2.123709e-02	k: 1619	n:80000
Cons ci ratio: 1.761819e-01	ci left: 5.608017e-03	ci right 6.703261e-03	k: 491	n:80000
KS ci ratio: 1.189006e-02	ci left: 5.725916e-01	ci right 5.794529e-01	k: 46082	n:80000
CUL1   80000 perm   19 sec   (4202 perm/sec)   p_kst 5.760250e-01   p_cons 6.137500e-03   p_joint 2.023750e-02

Joint ci ratio: 9.022101e-02	ci left: 1.961674e-02	ci right 2.148101e-02	k: 1848	n:90000
Cons ci ratio: 1.642501e-01	ci left: 5.772172e-03	ci right 6.815589e-03	k: 565	n:90000
KS ci ratio: 1.119612e-02	ci left: 5.733973e-01	ci right 5.798644e-01	k: 51897	n:90000
CUL1   90000 perm   22 sec   (4156 perm/sec)   p_kst 5.766333e-01   p_cons 6.277778e-03   p_joint 2.053333e-02

Joint ci ratio: 8.524121e-02	ci left: 1.982647e-02	ci right 2.160148e-02	k: 2070	n:100000
Cons ci ratio: 1.558075e-01	ci left: 5.799743e-03	ci right 6.789221e-03	k: 628	n:100000
KS ci ratio: 1.063450e-02	ci left: 5.729699e-01	ci right 5.791057e-01	k: 57604	n:100000
CUL1   100000 perm   24 sec   (4104 perm/sec)   p_kst 5.760400e-01   p_cons 6.280000e-03   p_joint 2.070000e-02

Joint ci ratio: 8.105841e-02	ci left: 1.997364e-02	ci right 2.166993e-02	k: 2289	n:110000
Cons ci ratio: 1.487624e-01	ci left: 5.805916e-03	ci right 6.747673e-03	k: 689	n:110000
KS ci ratio: 1.025488e-02	ci left: 5.675775e-01	ci right 5.734370e-01	k: 62756	n:110000
CUL1   110000 perm   27 sec   (4053 perm/sec)   p_kst 5.705091e-01   p_cons 6.263636e-03   p_joint 2.080909e-02

Joint ci ratio: 7.664463e-02	ci left: 2.051504e-02	ci right 2.215820e-02	k: 2559	n:120000
Cons ci ratio: 1.422133e-01	ci left: 5.844053e-03	ci right 6.746723e-03	k: 754	n:120000
KS ci ratio: 9.822500e-03	ci left: 5.674933e-01	ci right 5.731033e-01	k: 68436	n:120000
CUL1   120000 perm   30 sec   (4001 perm/sec)   p_kst 5.703000e-01   p_cons 6.283333e-03   p_joint 2.132500e-02

Joint ci ratio: 7.372387e-02	ci left: 2.049933e-02	ci right 2.207597e-02	k: 2766	n:130000
Cons ci ratio: 1.366272e-01	ci left: 5.862229e-03	ci right 6.729246e-03	k: 817	n:130000
KS ci ratio: 9.432421e-03	ci left: 5.678500e-01	ci right 5.732392e-01	k: 74171	n:130000
CUL1   130000 perm   33 sec   (3949 perm/sec)   p_kst 5.705462e-01   p_cons 6.284615e-03   p_joint 2.127692e-02

Joint ci ratio: 7.161945e-02	ci left: 2.019914e-02	ci right 2.170650e-02	k: 2932	n:140000
Cons ci ratio: 1.332592e-01	ci left: 5.733345e-03	ci right 6.558739e-03	k: 859	n:140000
KS ci ratio: 9.087521e-03	ci left: 5.680450e-01	ci right 5.732378e-01	k: 79890	n:140000
CUL1   140000 perm   36 sec   (3895 perm/sec)   p_kst 5.706429e-01   p_cons 6.135714e-03   p_joint 2.094286e-02

Joint ci ratio: 6.993913e-02	ci left: 1.979540e-02	ci right 2.123656e-02	k: 3076	n:150000
Cons ci ratio: 1.284205e-01	ci left: 5.776730e-03	ci right 6.575872e-03	k: 925	n:150000
KS ci ratio: 8.773465e-03	ci left: 5.684640e-01	ci right 5.734800e-01	k: 85646	n:150000
CUL1   150000 perm   39 sec   (3843 perm/sec)   p_kst 5.709733e-01   p_cons 6.166667e-03   p_joint 2.050667e-02

Joint ci ratio: 7.019453e-02	ci left: 1.844720e-02	ci right 1.979530e-02	k: 3058	n:160000
Cons ci ratio: 1.252216e-01	ci left: 5.706154e-03	ci right 6.474409e-03	k: 973	n:160000
KS ci ratio: 8.484556e-03	ci left: 5.691396e-01	ci right 5.739953e-01	k: 91451	n:160000
CUL1   160000 perm   42 sec   (3791 perm/sec)   p_kst 5.715687e-01   p_cons 6.081250e-03   p_joint 1.911250e-02

Joint ci ratio: 6.831532e-02	ci left: 1.835050e-02	ci right 1.965421e-02	k: 3229	n:170000
Cons ci ratio: 1.217717e-01	ci left: 5.689731e-03	ci right 6.433148e-03	k: 1029	n:170000
KS ci ratio: 8.236937e-03	ci left: 5.688727e-01	ci right 5.735837e-01	k: 97109	n:170000
CUL1   170000 perm   45 sec   (3740 perm/sec)   p_kst 5.712294e-01   p_cons 6.052941e-03   p_joint 1.899412e-02

Joint ci ratio: 6.639056e-02	ci left: 1.836881e-02	ci right 1.963564e-02	k: 3419	n:180000
Cons ci ratio: 1.189231e-01	ci left: 5.643042e-03	ci right 6.361897e-03	k: 1079	n:180000
KS ci ratio: 8.002806e-03	ci left: 5.690654e-01	ci right 5.736434e-01	k: 102844	n:180000
CUL1   180000 perm   49 sec   (3690 perm/sec)   p_kst 5.713556e-01   p_cons 5.994444e-03   p_joint 1.899444e-02

Joint ci ratio: 6.434782e-02	ci left: 1.854105e-02	ci right 1.977894e-02	k: 3639	n:190000
Cons ci ratio: 1.152438e-01	ci left: 5.703682e-03	ci right 6.406254e-03	k: 1149	n:190000
KS ci ratio: 7.792254e-03	ci left: 5.689446e-01	ci right 5.734006e-01	k: 108523	n:190000
CUL1   190000 perm   52 sec   (3630 perm/sec)   p_kst 5.711737e-01   p_cons 6.047368e-03   p_joint 1.915263e-02

Joint ci ratio: 6.043140e-02	ci left: 1.998194e-02	ci right 2.123200e-02	k: 4120	n:200000
Cons ci ratio: 1.122571e-01	ci left: 5.719681e-03	ci right 6.404754e-03	k: 1211	n:200000
KS ci ratio: 7.593382e-03	ci left: 5.691026e-01	ci right 5.734454e-01	k: 114255	n:200000
CUL1   200000 perm   56 sec   (3574 perm/sec)   p_kst 5.712750e-01   p_cons 6.055000e-03   p_joint 2.060000e-02

Joint ci ratio: 5.896841e-02	ci left: 2.000143e-02	ci right 2.122138e-02	k: 4327	n:210000
Cons ci ratio: 1.095777e-01	ci left: 5.725104e-03	ci right 6.393403e-03	k: 1271	n:210000
KS ci ratio: 7.415698e-03	ci left: 5.688036e-01	ci right 5.730421e-01	k: 119894	n:210000
CUL1   210000 perm   59 sec   (3531 perm/sec)   p_kst 5.709238e-01   p_cons 6.052381e-03   p_joint 2.060476e-02

Joint ci ratio: 5.765872e-02	ci left: 1.998362e-02	ci right 2.117451e-02	k: 4526	n:220000
Cons ci ratio: 1.071219e-01	ci left: 5.725786e-03	ci right 6.378240e-03	k: 1330	n:220000
KS ci ratio: 7.242865e-03	ci left: 5.690105e-01	ci right 5.731513e-01	k: 125638	n:220000
CUL1   220000 perm   63 sec   (3487 perm/sec)   p_kst 5.710818e-01   p_cons 6.045455e-03   p_joint 2.057273e-02

Joint ci ratio: 5.843340e-02	ci left: 1.863021e-02	ci right 1.975586e-02	k: 4413	n:230000
Cons ci ratio: 1.050907e-01	ci left: 5.696921e-03	ci right 6.333016e-03	k: 1382	n:230000
KS ci ratio: 7.082961e-03	ci left: 5.691048e-01	ci right 5.731543e-01	k: 131360	n:230000
CUL1   230000 perm   67 sec   (3443 perm/sec)   p_kst 5.711304e-01   p_cons 6.008696e-03   p_joint 1.918696e-02

Joint ci ratio: 5.716459e-02	ci left: 1.866704e-02	ci right 1.976962e-02	k: 4611	n:240000
Cons ci ratio: 1.027039e-01	ci left: 5.723349e-03	ci right 6.347004e-03	k: 1447	n:240000
KS ci ratio: 6.935972e-03	ci left: 5.689961e-01	ci right 5.729605e-01	k: 137035	n:240000
CUL1   240000 perm   71 sec   (3401 perm/sec)   p_kst 5.709792e-01   p_cons 6.029167e-03   p_joint 1.921250e-02

Joint ci ratio: 5.578608e-02	ci left: 1.882741e-02	ci right 1.991177e-02	k: 4841	n:250000
Cons ci ratio: 1.002727e-01	ci left: 5.771214e-03	ci right 6.384322e-03	k: 1518	n:250000
KS ci ratio: 6.796936e-03	ci left: 5.689570e-01	ci right 5.728413e-01	k: 142725	n:250000
CUL1   250000 perm   74 sec   (3360 perm/sec)   p_kst 5.709000e-01   p_cons 6.072000e-03   p_joint 1.936400e-02

Joint ci ratio: 5.464569e-02	ci left: 1.887707e-02	ci right 1.994137e-02	k: 5045	n:260000
Cons ci ratio: 9.853787e-02	ci left: 5.751770e-03	ci right 6.351629e-03	k: 1572	n:260000
KS ci ratio: 6.665940e-03	ci left: 5.689217e-01	ci right 5.727306e-01	k: 148415	n:260000
CUL1   260000 perm   78 sec   (3320 perm/sec)   p_kst 5.708269e-01   p_cons 6.046154e-03   p_joint 1.940385e-02

Outputting figure to mutsig2_images.part000000000045/CUL1.4_2415_260000_0.57083_0.0060462_0.019404.png
                gene_name: CUL1
               theta_stop: 0.099 
                    nperm: 260000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.0060 
      ci_cons_bounds_left: 0.0058 
     ci_cons_bounds_right: 0.0064 
                  p_joint: 0.019 
     ci_joint_bounds_left: 0.019 
    ci_joint_bounds_right: 0.020 

Current progress: 40 percent done.
CUL9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.028398e-01	ci left: 3.233938e-02	ci right 3.973408e-02	k: 359	n:10000
Cons ci ratio: 1.804930e-02	ci left: 8.175101e-01	ci right 8.325001e-01	k: 8251	n:10000
KS ci ratio: 4.420964e-01	ci left: 6.081359e-03	ci right 9.614411e-03	k: 77	n:10000
CUL9   10000 perm   2 sec   (4235 perm/sec)   p_kst 7.700000e-03   p_cons 8.251000e-01   p_joint 3.590000e-02

Joint ci ratio: 7.704429e-02	ci left: 1.101675e-01	ci right 1.190449e-01	k: 2291	n:20000
Cons ci ratio: 1.314745e-02	ci left: 8.109130e-01	ci right 8.216949e-01	k: 16327	n:20000
KS ci ratio: 2.950176e-01	ci left: 7.459769e-03	ci right 1.008604e-02	k: 174	n:20000
CUL9   20000 perm   5 sec   (3866 perm/sec)   p_kst 8.700000e-03   p_cons 8.163500e-01   p_joint 1.145500e-01

Joint ci ratio: 8.647785e-02	ci left: 6.132138e-02	ci right 6.689673e-02	k: 1922	n:30000
Cons ci ratio: 1.072818e-02	ci left: 8.121063e-01	ci right 8.208990e-01	k: 24496	n:30000
KS ci ratio: 2.488992e-01	ci left: 7.179429e-03	ci right 9.250843e-03	k: 245	n:30000
CUL9   30000 perm   8 sec   (3734 perm/sec)   p_kst 8.166667e-03   p_cons 8.165333e-01   p_joint 6.406667e-02

Joint ci ratio: 9.232391e-02	ci left: 4.113056e-02	ci right 4.513611e-02	k: 1724	n:40000
Cons ci ratio: 9.277905e-03	ci left: 8.131249e-01	ci right 8.207291e-01	k: 32678	n:40000
KS ci ratio: 2.123145e-01	ci left: 7.552622e-03	ci right 9.369820e-03	k: 337	n:40000
CUL9   40000 perm   11 sec   (3631 perm/sec)   p_kst 8.425000e-03   p_cons 8.169500e-01   p_joint 4.310000e-02

Joint ci ratio: 8.106156e-02	ci left: 4.286597e-02	ci right 4.650713e-02	k: 2233	n:50000
Cons ci ratio: 8.255908e-03	ci left: 8.150730e-01	ci right 8.218500e-01	k: 40924	n:50000
KS ci ratio: 1.869118e-01	ci left: 7.904622e-03	ci right 9.553176e-03	k: 435	n:50000
CUL9   50000 perm   14 sec   (3551 perm/sec)   p_kst 8.700000e-03   p_cons 8.184800e-01   p_joint 4.466000e-02

Joint ci ratio: 8.118845e-02	ci left: 3.587953e-02	ci right 3.893209e-02	k: 2243	n:60000
Cons ci ratio: 7.533519e-03	ci left: 8.154929e-01	ci right 8.216762e-01	k: 49116	n:60000
KS ci ratio: 1.719915e-01	ci left: 7.844769e-03	ci right 9.336682e-03	k: 514	n:60000
CUL9   60000 perm   17 sec   (3436 perm/sec)   p_kst 8.566667e-03   p_cons 8.186000e-01   p_joint 3.738333e-02

Joint ci ratio: 7.344884e-02	ci left: 3.766205e-02	ci right 4.054775e-02	k: 2736	n:70000
Cons ci ratio: 6.974673e-03	ci left: 8.157250e-01	ci right 8.214485e-01	k: 57302	n:70000
KS ci ratio: 1.607012e-01	ci left: 7.750918e-03	ci right 9.118870e-03	k: 589	n:70000
CUL9   70000 perm   21 sec   (3296 perm/sec)   p_kst 8.414286e-03   p_cons 8.186000e-01   p_joint 3.908571e-02

Joint ci ratio: 7.519999e-02	ci left: 3.161330e-02	ci right 3.409573e-02	k: 2627	n:80000
Cons ci ratio: 6.512391e-03	ci left: 8.164525e-01	ci right 8.217993e-01	k: 65531	n:80000
KS ci ratio: 1.518382e-01	ci left: 7.634831e-03	ci right 8.901218e-03	k: 660	n:80000
CUL9   80000 perm   25 sec   (3251 perm/sec)   p_kst 8.250000e-03   p_cons 8.191375e-01   p_joint 3.283750e-02

Joint ci ratio: 7.537135e-02	ci left: 2.807694e-02	ci right 3.028688e-02	k: 2625	n:90000
Cons ci ratio: 6.139331e-03	ci left: 8.166363e-01	ci right 8.216764e-01	k: 73725	n:90000
KS ci ratio: 1.431181e-01	ci left: 7.674739e-03	ci right 8.868392e-03	k: 743	n:90000
CUL9   90000 perm   28 sec   (3230 perm/sec)   p_kst 8.255556e-03   p_cons 8.191667e-01   p_joint 2.916667e-02

Joint ci ratio: 7.058412e-02	ci left: 2.886290e-02	ci right 3.098448e-02	k: 2991	n:100000
Cons ci ratio: 5.847788e-03	ci left: 8.155642e-01	ci right 8.203574e-01	k: 81797	n:100000
KS ci ratio: 1.357463e-01	ci left: 7.708333e-03	ci right 8.840467e-03	k: 826	n:100000
CUL9   100000 perm   31 sec   (3207 perm/sec)   p_kst 8.260000e-03   p_cons 8.179700e-01   p_joint 2.991000e-02

Joint ci ratio: 6.853488e-02	ci left: 2.789108e-02	ci right 2.987932e-02	k: 3176	n:110000
Cons ci ratio: 5.579337e-03	ci left: 8.154786e-01	ci right 8.200501e-01	k: 89955	n:110000
KS ci ratio: 1.289085e-01	ci left: 7.798706e-03	ci right 8.882002e-03	k: 916	n:110000
CUL9   110000 perm   35 sec   (3180 perm/sec)   p_kst 8.327273e-03   p_cons 8.177727e-01   p_joint 2.887273e-02

Joint ci ratio: 6.816927e-02	ci left: 2.590173e-02	ci right 2.773790e-02	k: 3217	n:120000
Cons ci ratio: 5.335342e-03	ci left: 8.159390e-01	ci right 8.203123e-01	k: 98176	n:120000
KS ci ratio: 1.231332e-01	ci left: 7.859050e-03	ci right 8.898252e-03	k: 1004	n:120000
CUL9   120000 perm   38 sec   (3152 perm/sec)   p_kst 8.366667e-03   p_cons 8.181333e-01   p_joint 2.680833e-02

Joint ci ratio: 6.389470e-02	ci left: 2.723864e-02	ci right 2.904403e-02	k: 3657	n:130000
Cons ci ratio: 5.132829e-03	ci left: 8.156289e-01	ci right 8.198338e-01	k: 106306	n:130000
KS ci ratio: 1.188403e-01	ci left: 7.806500e-03	ci right 8.800235e-03	k: 1078	n:130000
CUL9   130000 perm   42 sec   (3123 perm/sec)   p_kst 8.292308e-03   p_cons 8.177385e-01   p_joint 2.813077e-02

Joint ci ratio: 5.782834e-02	ci left: 3.085883e-02	ci right 3.270349e-02	k: 4448	n:140000
Cons ci ratio: 4.946280e-03	ci left: 8.156961e-01	ci right 8.197479e-01	k: 114482	n:140000
KS ci ratio: 1.154732e-01	ci left: 7.692614e-03	ci right 8.642212e-03	k: 1142	n:140000
CUL9   140000 perm   45 sec   (3092 perm/sec)   p_kst 8.157143e-03   p_cons 8.177286e-01   p_joint 3.177143e-02

Joint ci ratio: 5.933660e-02	ci left: 2.743375e-02	ci right 2.911789e-02	k: 4240	n:150000
Cons ci ratio: 4.779658e-03	ci left: 8.156965e-01	ci right 8.196112e-01	k: 122649	n:150000
KS ci ratio: 1.120963e-01	ci left: 7.633145e-03	ci right 8.546023e-03	k: 1212	n:150000
CUL9   150000 perm   49 sec   (3062 perm/sec)   p_kst 8.080000e-03   p_cons 8.176600e-01   p_joint 2.826667e-02

Joint ci ratio: 4.874442e-02	ci left: 3.790222e-02	ci right 3.980204e-02	k: 6215	n:160000
Cons ci ratio: 4.627941e-03	ci left: 8.157554e-01	ci right 8.195456e-01	k: 130825	n:160000
KS ci ratio: 1.106633e-01	ci left: 7.350442e-03	ci right 8.217537e-03	k: 1244	n:160000
CUL9   160000 perm   53 sec   (3029 perm/sec)   p_kst 7.775000e-03   p_cons 8.176562e-01   p_joint 3.884375e-02

Joint ci ratio: 5.066777e-02	ci left: 3.314933e-02	ci right 3.487837e-02	k: 5781	n:170000
Cons ci ratio: 4.488660e-03	ci left: 8.158858e-01	ci right 8.195621e-01	k: 139014	n:170000
KS ci ratio: 1.074744e-01	ci left: 7.347203e-03	ci right 8.187361e-03	k: 1319	n:170000
CUL9   170000 perm   57 sec   (2996 perm/sec)   p_kst 7.758824e-03   p_cons 8.177294e-01   p_joint 3.400588e-02

Joint ci ratio: 5.056391e-02	ci left: 3.149351e-02	ci right 3.313271e-02	k: 5815	n:180000
Cons ci ratio: 4.362460e-03	ci left: 8.159196e-01	ci right 8.194923e-01	k: 147188	n:180000
KS ci ratio: 1.046976e-01	ci left: 7.322999e-03	ci right 8.137420e-03	k: 1390	n:180000
CUL9   180000 perm   61 sec   (2965 perm/sec)   p_kst 7.722222e-03   p_cons 8.177111e-01   p_joint 3.230556e-02

Joint ci ratio: 5.034992e-02	ci left: 3.013683e-02	ci right 3.169858e-02	k: 5873	n:190000
Cons ci ratio: 4.246864e-03	ci left: 8.159142e-01	ci right 8.193919e-01	k: 155355	n:190000
KS ci ratio: 1.014977e-01	ci left: 7.393935e-03	ci right 8.189614e-03	k: 1479	n:190000
CUL9   190000 perm   65 sec   (2935 perm/sec)   p_kst 7.784211e-03   p_cons 8.176579e-01   p_joint 3.091053e-02

Joint ci ratio: 4.846434e-02	ci left: 3.090681e-02	ci right 3.244680e-02	k: 6334	n:200000
Cons ci ratio: 4.138815e-03	ci left: 8.159958e-01	ci right 8.193850e-01	k: 163539	n:200000
KS ci ratio: 9.876472e-02	ci left: 7.428852e-03	ci right 8.205515e-03	k: 1562	n:200000
CUL9   200000 perm   69 sec   (2908 perm/sec)   p_kst 7.810000e-03   p_cons 8.176950e-01   p_joint 3.167000e-02

Outputting figure to mutsig2_images.part000000000045/CUL9.3_7714_200000_0.00781_0.81769_0.03167.png
                gene_name: CUL9
               theta_stop: 0.099 
                    nperm: 200000 
                     p_ks: 0.0078 
        ci_ks_bounds_left: 0.0074 
       ci_ks_bounds_right: 0.0082 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.82 
                  p_joint: 0.032 
     ci_joint_bounds_left: 0.031 
    ci_joint_bounds_right: 0.032 

Current progress: 60 percent done.
CUL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.427063e-03	ci left: 9.851247e-01	ci right 9.895847e-01	k: 9875	n:10000
Cons ci ratio: 8.036185e-02	ci left: 1.844192e-01	ci right 1.999605e-01	k: 1921	n:10000
KS ci ratio: 1.436189e-02	ci left: 8.752086e-01	ci right 8.879681e-01	k: 8817	n:10000
CUL2   10000 perm   2 sec   (5288 perm/sec)   p_kst 8.817000e-01   p_cons 1.921000e-01   p_joint 9.875000e-01

Outputting figure to mutsig2_images.part000000000045/CUL2.2_2318_10000_0.8817_0.1921_0.9875.png
                gene_name: CUL2
               theta_stop: 0.080 
                    nperm: 10000 
                     p_ks: 0.88 
        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: 0.20 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 80 percent done.
CUX1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.928828e-02	ci left: 4.889518e-01	ci right 5.086489e-01	k: 4988	n:10000
Cons ci ratio: 4.336488e-02	ci left: 4.398160e-01	ci right 4.594134e-01	k: 4496	n:10000
KS ci ratio: 1.289403e-01	ci left: 7.912021e-02	ci right 9.012318e-02	k: 845	n:10000
CUX1   10000 perm   2 sec   (4632 perm/sec)   p_kst 8.450000e-02   p_cons 4.496000e-01   p_joint 4.988000e-01

Joint ci ratio: 5.254407e-02	ci left: 2.119475e-01	ci right 2.234347e-01	k: 4353	n:20000
Cons ci ratio: 3.074377e-02	ci left: 4.414405e-01	ci right 4.552745e-01	k: 8967	n:20000
KS ci ratio: 9.204076e-02	ci left: 7.931024e-02	ci right 8.701145e-02	k: 1662	n:20000
CUX1   20000 perm   4 sec   (4460 perm/sec)   p_kst 8.310000e-02   p_cons 4.483500e-01   p_joint 2.176500e-01

Outputting figure to mutsig2_images.part000000000045/CUX1.2_5499_20000_0.0831_0.44835_0.21765.png
                gene_name: CUX1
               theta_stop: 0.092 
                    nperm: 20000 
                     p_ks: 0.083 
        ci_ks_bounds_left: 0.079 
       ci_ks_bounds_right: 0.087 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  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.165.3896/
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/181708/iteration1/scatter.0000000045
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 45 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119755: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000046> was used as the working directory.
Started at Wed Oct 10 10:42:38 2012
Results reported at Wed Oct 10 10:44:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000046.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000046.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 46  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     97.14 sec.
    Max Memory :       614 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.165.3896/
-whichjob
46
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 46: processing genes 4072 - 4162
Calculating significance of each gene.
Using projection method.
4072	CYB561	1
4073	CYB561D1	1
4074	CYB561D2	5.380696e-02
4075	CYB5A	1
4076	CYB5B	1
4077	CYB5D1	1
4078	CYB5D2	1
4079	CYB5R1	1
4080	CYB5R2	1
4081	CYB5R3	1
4082	CYB5R4	1
4083	CYB5RL	1.563387e-01
4084	CYBA	1
4085	CYBASC3	1
4086	CYBB	1
4087	CYBRD1	1
4088	CYC1	1
4089	CYCS	1
4090	CYFIP1	4.210084e-01
4091	CYFIP2	1
4092	CYGB	1
4093	CYHR1	1
4094	CYLC1	1
4095	CYLC2	1
4096	CYLD	1
4097	CYP11A1	1
4098	CYP11B1	1
4099	CYP11B2	1
4100	CYP17A1	1
4101	CYP19A1	1
4102	CYP1A1	1
4103	CYP1A2	1
4104	CYP1B1	1
4105	CYP20A1	1
4106	CYP21A2	1
4107	CYP24A1	1
4108	CYP26A1	1.427911e-02
4109	CYP26B1	1
4110	CYP26C1	1
4111	CYP27A1	1
4112	CYP27B1	3.708336e-02
4113	CYP27C1	1
4114	CYP2A13	1
4115	CYP2A6	1
4116	CYP2A7	1.257032e-01
4117	CYP2B6	1
4118	CYP2C18	1
4119	CYP2C19	2.453688e-01
4120	CYP2C8	1
4121	CYP2C9	6.540764e-02
4122	CYP2D6	1
4123	CYP2E1	1
4124	CYP2F1	1
4125	CYP2J2	1
4126	CYP2R1	3.293132e-02
4127	CYP2S1	1
4128	CYP2U1	9.366716e-02
4129	CYP2W1	1
4130	CYP39A1	1
4131	CYP3A4	1
4132	CYP3A43	1
4133	CYP3A5	1
4134	CYP3A7	1
4135	CYP46A1	1
4136	CYP4A11	1
4137	CYP4A22	2.641412e-01
4138	CYP4B1	1
4139	CYP4F11	1
4140	CYP4F12	2.065127e-01
4141	CYP4F2	1
4142	CYP4F22	1
4143	CYP4F3	1
4144	CYP4F8	1
4145	CYP4V2	1
4146	CYP4X1	1
4147	CYP4Z1	1
4148	CYP51A1	1
4149	CYP7A1	1.188903e-01
4150	CYP7B1	1
4151	CYP8B1	1
4152	CYR61	1
4153	CYSLTR1	1
4154	CYSLTR2	1
4155	CYTH1	1
4156	CYTH2	1
4157	CYTH3	6.769727e-02
4158	CYTH4	1
4159	CYTIP	1
4160	CYTL1	1
4161	CYTSA	1.642641e-01
4162	CYTSB	1
Done

Running MutSig 2:
Scatter job 46: processing genes 4072 - 4162
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
CYP26A1
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: 8.866392e-02	ci left: 1.562022e-01	ci right 1.707944e-01	k: 1634	n:10000
KS ci ratio: 7.108113e-02	ci left: 2.248418e-01	ci right 2.415139e-01	k: 2331	n:10000
CYP26A1   10000 perm   2 sec   (5771 perm/sec)   p_kst 2.331000e-01   p_cons 1.634000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000046/CYP26A1.2_1522_10000_0.2331_0.1634_1.png
                gene_name: CYP26A1
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  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.165.3896/
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/181708/iteration1/scatter.0000000046
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 46 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119761: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000047> was used as the working directory.
Started at Wed Oct 10 10:42:38 2012
Results reported at Wed Oct 10 10:46:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000047.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000047.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 47  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    259.65 sec.
    Max Memory :      1241 MB
    Max Swap   :      3852 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.165.3896/
-whichjob
47
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 47: processing genes 4163 - 4252
Calculating significance of each gene.
Using projection method.
4163	CYYR1	1
4164	CYorf15A	1
4165	CYorf15B	1
4166	D2HGDH	2.239486e-01
4167	D4S234E	1
4168	DAAM1	2.943646e-01
4169	DAAM2	1
4170	DAB1	5.758668e-02
4171	DAB2	1
4172	DAB2IP	1
4173	DACH1	6.173425e-02
4174	DACH2	1
4175	DACT1	1
4176	DAD1	1
4177	DAG1	1
4178	DAGLA	1
4179	DAGLB	3.322369e-02
4180	DAK	1
4181	DALRD3	1
4182	DAND5	1
4183	DAO	1
4184	DAOA	1
4185	DAP	1
4186	DAP3	1.468763e-01
4187	DAPK1	1
4188	DAPK2	1
4189	DAPK3	1
4190	DAPL1	1
4191	DAPP1	1
4192	DARC	1
4193	DARS	2.736836e-02
4194	DARS2	5.705651e-02
4195	DAXX	3.426233e-01
4196	DAZAP1	1
4197	DAZAP2	1.149898e-01
4198	DAZL	1
4199	DBC1	1.843820e-01
4200	DBF4	1
4201	DBF4B	1
4202	DBH	1
4203	DBI	1
4204	DBN1	1
4205	DBNDD1	1
4206	DBNDD2	1
4207	DBNL	1
4208	DBP	1
4209	DBR1	1
4210	DBT	1
4211	DBX1	1
4212	DBX2	1
4213	DCAF10	1
4214	DCAF11	1
4215	DCAF12	1
4216	DCAF12L1	5.636317e-03
4217	DCAF12L2	1
4218	DCAF13	1
4219	DCAF15	1
4220	DCAF16	1
4221	DCAF17	1
4222	DCAF4	1
4223	DCAF4L1	1
4224	DCAF4L2	1.150923e-01
4225	DCAF5	1
4226	DCAF6	2.784243e-01
4227	DCAF7	1
4228	DCAF8	1
4229	DCAF8L1	1.302103e-01
4230	DCAF8L2	1
4231	DCAKD	1
4232	DCBLD1	1
4233	DCBLD2	1
4234	DCC	6.514320e-03
4235	DCD	1
4236	DCDC1	1
4237	DCDC2	1
4238	DCDC2B	1
4239	DCHS1	7.883851e-02
4240	DCHS2	5.628870e-01
4241	DCI	1
4242	DCK	1
4243	DCLK1	1.552082e-01
4244	DCLK2	1
4245	DCLK3	1
4246	DCLRE1A	1.891294e-01
4247	DCLRE1B	1
4248	DCLRE1C	1
4249	DCN	1
4250	DCP1A	1
4251	DCP1B	1
4252	DCP2	1
Done

Running MutSig 2:
Scatter job 47: processing genes 4163 - 4252
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DCC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.827128e-01	ci left: 3.996794e-02	ci right 4.810038e-02	k: 439	n:10000
Cons ci ratio: 3.805205e-01	ci left: 8.505237e-03	ci right 1.258745e-02	k: 104	n:10000
KS ci ratio: 5.075896e-02	ci left: 3.640070e-01	ci right 3.830667e-01	k: 3735	n:10000
DCC   10000 perm   3 sec   (3977 perm/sec)   p_kst 3.735000e-01   p_cons 1.040000e-02   p_joint 4.390000e-02

Joint ci ratio: 1.219798e-01	ci left: 4.609757e-02	ci right 5.213438e-02	k: 981	n:20000
Cons ci ratio: 2.807961e-01	ci left: 8.295294e-03	ci right 1.105008e-02	k: 192	n:20000
KS ci ratio: 3.557950e-02	ci left: 3.709243e-01	ci right 3.844112e-01	k: 7553	n:20000
DCC   20000 perm   8 sec   (2427 perm/sec)   p_kst 3.776500e-01   p_cons 9.600000e-03   p_joint 4.905000e-02

Joint ci ratio: 8.461250e-02	ci left: 6.393474e-02	ci right 6.961617e-02	k: 2002	n:30000
Cons ci ratio: 2.374838e-01	ci left: 7.931051e-03	ci right 1.009897e-02	k: 269	n:30000
KS ci ratio: 2.906491e-02	ci left: 3.719435e-01	ci right 3.829470e-01	k: 11323	n:30000
DCC   30000 perm   11 sec   (2703 perm/sec)   p_kst 3.774333e-01   p_cons 8.966667e-03   p_joint 6.673333e-02

Joint ci ratio: 9.834715e-02	ci left: 3.631826e-02	ci right 4.009916e-02	k: 1527	n:40000
Cons ci ratio: 2.028439e-01	ci left: 8.311372e-03	ci right 1.021090e-02	k: 369	n:40000
KS ci ratio: 2.533057e-02	ci left: 3.697288e-01	ci right 3.792395e-01	k: 14979	n:40000
DCC   40000 perm   14 sec   (2785 perm/sec)   p_kst 3.744750e-01   p_cons 9.225000e-03   p_joint 3.817500e-02

Joint ci ratio: 8.758386e-02	ci left: 3.683041e-02	ci right 4.022344e-02	k: 1925	n:50000
Cons ci ratio: 1.776867e-01	ci left: 8.783002e-03	ci right 1.051464e-02	k: 481	n:50000
KS ci ratio: 2.269507e-02	ci left: 3.694370e-01	ci right 3.779377e-01	k: 18684	n:50000
DCC   50000 perm   18 sec   (2799 perm/sec)   p_kst 3.736800e-01   p_cons 9.620000e-03   p_joint 3.850000e-02

Joint ci ratio: 7.733153e-02	ci left: 3.947635e-02	ci right 4.266823e-02	k: 2463	n:60000
Cons ci ratio: 1.638435e-01	ci left: 8.675324e-03	ci right 1.023934e-02	k: 566	n:60000
KS ci ratio: 2.072209e-02	ci left: 3.697104e-01	ci right 3.774685e-01	k: 22415	n:60000
DCC   60000 perm   22 sec   (2748 perm/sec)   p_kst 3.735833e-01   p_cons 9.433333e-03   p_joint 4.105000e-02

Joint ci ratio: 7.110222e-02	ci left: 4.013271e-02	ci right 4.310544e-02	k: 2912	n:70000
Cons ci ratio: 1.515164e-01	ci left: 8.753397e-03	ci right 1.020199e-02	k: 662	n:70000
KS ci ratio: 1.914575e-02	ci left: 3.709555e-01	ci right 3.781406e-01	k: 26218	n:70000
DCC   70000 perm   25 sec   (2795 perm/sec)   p_kst 3.745429e-01   p_cons 9.457143e-03   p_joint 4.160000e-02

Joint ci ratio: 6.750145e-02	ci left: 3.908294e-02	ci right 4.182551e-02	k: 3235	n:80000
Cons ci ratio: 1.412343e-01	ci left: 8.863518e-03	ci right 1.022241e-02	k: 762	n:80000
KS ci ratio: 1.788514e-02	ci left: 3.718183e-01	ci right 3.785408e-01	k: 30014	n:80000
DCC   80000 perm   28 sec   (2832 perm/sec)   p_kst 3.751750e-01   p_cons 9.525000e-03   p_joint 4.043750e-02

Joint ci ratio: 6.640306e-02	ci left: 3.603856e-02	ci right 3.852471e-02	k: 3354	n:90000
Cons ci ratio: 1.330300e-01	ci left: 8.919522e-03	ci right 1.020128e-02	k: 859	n:90000
KS ci ratio: 1.683707e-02	ci left: 3.727119e-01	ci right 3.790516e-01	k: 33829	n:90000
DCC   90000 perm   32 sec   (2855 perm/sec)   p_kst 3.758778e-01   p_cons 9.544444e-03   p_joint 3.726667e-02

Joint ci ratio: 5.368937e-02	ci left: 4.924959e-02	ci right 5.197655e-02	k: 5060	n:100000
Cons ci ratio: 1.166850e-01	ci left: 1.050840e-02	ci right 1.182018e-02	k: 1115	n:100000
KS ci ratio: 1.598766e-02	ci left: 3.724474e-01	ci right 3.784599e-01	k: 37545	n:100000
DCC   100000 perm   35 sec   (2834 perm/sec)   p_kst 3.754500e-01   p_cons 1.115000e-02   p_joint 5.060000e-02

Joint ci ratio: 5.450586e-02	ci left: 4.368370e-02	ci right 4.614037e-02	k: 4939	n:110000
Cons ci ratio: 1.114662e-01	ci left: 1.049807e-02	ci right 1.174609e-02	k: 1222	n:110000
KS ci ratio: 1.526540e-02	ci left: 3.719200e-01	ci right 3.776502e-01	k: 41226	n:110000
DCC   110000 perm   39 sec   (2801 perm/sec)   p_kst 3.747818e-01   p_cons 1.110909e-02   p_joint 4.490000e-02

Joint ci ratio: 5.857840e-02	ci left: 3.492018e-02	ci right 3.703565e-02	k: 4316	n:120000
Cons ci ratio: 1.058885e-01	ci left: 1.069340e-02	ci right 1.189706e-02	k: 1354	n:120000
KS ci ratio: 1.464333e-02	ci left: 3.711531e-01	ci right 3.766364e-01	k: 44867	n:120000
DCC   120000 perm   43 sec   (2786 perm/sec)   p_kst 3.738917e-01   p_cons 1.128333e-02   p_joint 3.596667e-02

Joint ci ratio: 5.473148e-02	ci left: 3.692159e-02	ci right 3.900678e-02	k: 4934	n:130000
Cons ci ratio: 1.014523e-01	ci left: 1.077749e-02	ci right 1.193677e-02	k: 1475	n:130000
KS ci ratio: 1.407788e-02	ci left: 3.709616e-01	ci right 3.762286e-01	k: 48567	n:130000
DCC   130000 perm   47 sec   (2783 perm/sec)   p_kst 3.735923e-01   p_cons 1.134615e-02   p_joint 3.795385e-02

Joint ci ratio: 5.399721e-02	ci left: 3.529811e-02	ci right 3.726402e-02	k: 5078	n:140000
Cons ci ratio: 9.777862e-02	ci left: 1.079471e-02	ci right 1.191138e-02	k: 1588	n:140000
KS ci ratio: 1.354820e-02	ci left: 3.716642e-01	ci right 3.767410e-01	k: 52388	n:140000
DCC   140000 perm   50 sec   (2774 perm/sec)   p_kst 3.742000e-01   p_cons 1.134286e-02   p_joint 3.627143e-02

Outputting figure to mutsig2_images.part000000000047/DCC.5_4460_140000_0.3742_0.011343_0.036271.png
                gene_name: DCC
               theta_stop: 0.098 
                    nperm: 140000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.011 
      ci_cons_bounds_left: 0.011 
     ci_cons_bounds_right: 0.012 
                  p_joint: 0.036 
     ci_joint_bounds_left: 0.035 
    ci_joint_bounds_right: 0.037 

Current progress: 17 percent done.
DAB1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.960612e-01	ci left: 7.782754e-03	ci right 1.171078e-02	k: 96	n:10000
Cons ci ratio: 8.397822e-02	ci left: 1.713341e-01	ci right 1.864535e-01	k: 1788	n:10000
KS ci ratio: 4.208622e-01	ci left: 6.794980e-03	ci right 1.049980e-02	k: 85	n:10000
DAB1   10000 perm   2 sec   (5708 perm/sec)   p_kst 8.500000e-03   p_cons 1.788000e-01   p_joint 9.600000e-03

Joint ci ratio: 5.011261e-01	ci left: 2.290073e-03	ci right 3.859930e-03	k: 60	n:20000
Cons ci ratio: 6.237685e-02	ci left: 1.597317e-01	ci right 1.700660e-01	k: 3297	n:20000
KS ci ratio: 3.096304e-01	ci left: 6.720018e-03	ci right 9.226206e-03	k: 158	n:20000
DAB1   20000 perm   4 sec   (5084 perm/sec)   p_kst 7.900000e-03   p_cons 1.648500e-01   p_joint 3.000000e-03

Joint ci ratio: 2.463869e-01	ci left: 7.335823e-03	ci right 9.427729e-03	k: 250	n:30000
Cons ci ratio: 5.111645e-02	ci left: 1.596941e-01	ci right 1.681045e-01	k: 4916	n:30000
KS ci ratio: 2.420484e-01	ci left: 7.617595e-03	ci right 9.745863e-03	k: 259	n:30000
DAB1   30000 perm   6 sec   (4836 perm/sec)   p_kst 8.633333e-03   p_cons 1.638667e-01   p_joint 8.333333e-03

Joint ci ratio: 1.962579e-01	ci left: 8.905409e-03	ci right 1.086673e-02	k: 394	n:40000
Cons ci ratio: 4.435324e-02	ci left: 1.597392e-01	ci right 1.670098e-01	k: 6534	n:40000
KS ci ratio: 2.028439e-01	ci left: 8.311372e-03	ci right 1.021090e-02	k: 369	n:40000
DAB1   40000 perm   9 sec   (4684 perm/sec)   p_kst 9.225000e-03   p_cons 1.633500e-01   p_joint 9.850000e-03

Joint ci ratio: 1.891120e-01	ci left: 7.713965e-03	ci right 9.343867e-03	k: 425	n:50000
Cons ci ratio: 3.982167e-02	ci left: 1.590975e-01	ci right 1.655817e-01	k: 8116	n:50000
KS ci ratio: 1.843692e-01	ci left: 8.133555e-03	ci right 9.804203e-03	k: 447	n:50000
DAB1   50000 perm   11 sec   (4538 perm/sec)   p_kst 8.940000e-03   p_cons 1.623200e-01   p_joint 8.500000e-03

Joint ci ratio: 1.812749e-01	ci left: 7.032054e-03	ci right 8.449517e-03	k: 463	n:60000
Cons ci ratio: 3.641772e-02	ci left: 1.588945e-01	ci right 1.648049e-01	k: 9710	n:60000
KS ci ratio: 1.693577e-01	ci left: 8.100132e-03	ci right 9.614615e-03	k: 530	n:60000
DAB1   60000 perm   14 sec   (4316 perm/sec)   p_kst 8.833333e-03   p_cons 1.618333e-01   p_joint 7.716667e-03

Joint ci ratio: 1.390336e-01	ci left: 1.044738e-02	ci right 1.202210e-02	k: 785	n:70000
Cons ci ratio: 3.359871e-02	ci left: 1.600578e-01	ci right 1.655416e-01	k: 11395	n:70000
KS ci ratio: 1.557207e-01	ci left: 8.272454e-03	ci right 9.682985e-03	k: 627	n:70000
DAB1   70000 perm   17 sec   (4195 perm/sec)   p_kst 8.957143e-03   p_cons 1.627857e-01   p_joint 1.121429e-02

Joint ci ratio: 1.060643e-01	ci left: 1.589637e-02	ci right 1.768892e-02	k: 1342	n:80000
Cons ci ratio: 3.144459e-02	ci left: 1.600987e-01	ci right 1.652258e-01	k: 13012	n:80000
KS ci ratio: 1.452266e-01	ci left: 8.369226e-03	ci right 9.691747e-03	k: 721	n:80000
DAB1   80000 perm   19 sec   (4105 perm/sec)   p_kst 9.012500e-03   p_cons 1.626500e-01   p_joint 1.677500e-02

Joint ci ratio: 1.097013e-01	ci left: 1.322093e-02	ci right 1.476619e-02	k: 1258	n:90000
Cons ci ratio: 2.960355e-02	ci left: 1.606364e-01	ci right 1.654743e-01	k: 14674	n:90000
KS ci ratio: 1.372839e-01	ci left: 8.361112e-03	ci right 9.604180e-03	k: 807	n:90000
DAB1   90000 perm   22 sec   (4026 perm/sec)   p_kst 8.966667e-03   p_cons 1.630444e-01   p_joint 1.397778e-02

Joint ci ratio: 1.193637e-01	ci left: 1.003272e-02	ci right 1.131590e-02	k: 1066	n:100000
Cons ci ratio: 2.810145e-02	ci left: 1.605962e-01	ci right 1.651834e-01	k: 16288	n:100000
KS ci ratio: 1.307379e-01	ci left: 8.327173e-03	ci right 9.501577e-03	k: 890	n:100000
DAB1   100000 perm   25 sec   (3946 perm/sec)   p_kst 8.900000e-03   p_cons 1.628800e-01   p_joint 1.066000e-02

Joint ci ratio: 1.190846e-01	ci left: 9.173331e-03	ci right 1.034364e-02	k: 1072	n:110000
Cons ci ratio: 2.679360e-02	ci left: 1.607040e-01	ci right 1.650774e-01	k: 17917	n:110000
KS ci ratio: 1.230858e-01	ci left: 8.573705e-03	ci right 9.706947e-03	k: 1004	n:110000
DAB1   110000 perm   28 sec   (3891 perm/sec)   p_kst 9.127273e-03   p_cons 1.628818e-01   p_joint 9.745455e-03

Joint ci ratio: 1.213794e-01	ci left: 8.093384e-03	ci right 9.147236e-03	k: 1033	n:120000
Cons ci ratio: 2.566305e-02	ci left: 1.606903e-01	ci right 1.648760e-01	k: 19533	n:120000
KS ci ratio: 1.184669e-01	ci left: 8.505741e-03	ci right 9.584853e-03	k: 1084	n:120000
DAB1   120000 perm   31 sec   (3832 perm/sec)   p_kst 9.033333e-03   p_cons 1.627750e-01   p_joint 8.608333e-03

Joint ci ratio: 1.178531e-01	ci left: 7.940895e-03	ci right 8.942756e-03	k: 1096	n:130000
Cons ci ratio: 2.462836e-02	ci left: 1.610800e-01	ci right 1.651042e-01	k: 21201	n:130000
KS ci ratio: 1.131614e-01	ci left: 8.628315e-03	ci right 9.670680e-03	k: 1188	n:130000
DAB1   130000 perm   34 sec   (3775 perm/sec)   p_kst 9.138462e-03   p_cons 1.630846e-01   p_joint 8.430769e-03

Joint ci ratio: 1.206927e-01	ci left: 7.026997e-03	ci right 7.936437e-03	k: 1046	n:140000
Cons ci ratio: 2.372623e-02	ci left: 1.612250e-01	ci right 1.651033e-01	k: 22842	n:140000
KS ci ratio: 1.088933e-01	ci left: 8.671747e-03	ci right 9.677311e-03	k: 1283	n:140000
DAB1   140000 perm   38 sec   (3721 perm/sec)   p_kst 9.164286e-03   p_cons 1.631571e-01   p_joint 7.471429e-03

Joint ci ratio: 1.172223e-01	ci left: 6.966021e-03	ci right 7.839849e-03	k: 1109	n:150000
Cons ci ratio: 2.290586e-02	ci left: 1.614790e-01	ci right 1.652273e-01	k: 24502	n:150000
KS ci ratio: 1.050744e-01	ci left: 8.710028e-03	ci right 9.682419e-03	k: 1378	n:150000
DAB1   150000 perm   41 sec   (3660 perm/sec)   p_kst 9.186667e-03   p_cons 1.633467e-01   p_joint 7.393333e-03

Joint ci ratio: 1.145277e-01	ci left: 6.852270e-03	ci right 7.690733e-03	k: 1162	n:160000
Cons ci ratio: 2.219603e-02	ci left: 1.613238e-01	ci right 1.649509e-01	k: 26101	n:160000
KS ci ratio: 1.020864e-01	ci left: 8.664864e-03	ci right 9.603053e-03	k: 1460	n:160000
DAB1   160000 perm   44 sec   (3599 perm/sec)   p_kst 9.125000e-03   p_cons 1.631313e-01   p_joint 7.262500e-03

Joint ci ratio: 1.011067e-01	ci left: 8.321344e-03	ci right 9.213177e-03	k: 1489	n:170000
Cons ci ratio: 2.154185e-02	ci left: 1.612704e-01	ci right 1.647881e-01	k: 27714	n:170000
KS ci ratio: 9.834733e-02	ci left: 8.803244e-03	ci right 9.719491e-03	k: 1573	n:170000
DAB1   170000 perm   48 sec   (3541 perm/sec)   p_kst 9.252941e-03   p_cons 1.630235e-01   p_joint 8.758824e-03

Joint ci ratio: 9.959289e-02	ci left: 8.108144e-03	ci right 8.963353e-03	k: 1535	n:180000
Cons ci ratio: 2.092993e-02	ci left: 1.613848e-01	ci right 1.648038e-01	k: 29356	n:180000
KS ci ratio: 9.573858e-02	ci left: 8.785774e-03	ci right 9.674584e-03	k: 1660	n:180000
DAB1   180000 perm   52 sec   (3492 perm/sec)   p_kst 9.222222e-03   p_cons 1.630889e-01   p_joint 8.527778e-03

Outputting figure to mutsig2_images.part000000000047/DAB1.4_1720_180000_0.0092222_0.16309_0.0085278.png
                gene_name: DAB1
               theta_stop: 0.100 
                    nperm: 180000 
                     p_ks: 0.0092 
        ci_ks_bounds_left: 0.0088 
       ci_ks_bounds_right: 0.0097 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.16 
                  p_joint: 0.0085 
     ci_joint_bounds_left: 0.0081 
    ci_joint_bounds_right: 0.0090 

Current progress: 33 percent done.
DCHS1
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: 3.668042e-02	ci left: 5.232632e-01	ci right 5.429175e-01	k: 5331	n:10000
KS ci ratio: 4.028294e-02	ci left: 4.764591e-01	ci right 4.961489e-01	k: 4863	n:10000
DCHS1   10000 perm   4 sec   (2692 perm/sec)   p_kst 4.863000e-01   p_cons 5.331000e-01   p_joint 5.775000e-01

Outputting figure to mutsig2_images.part000000000047/DCHS1.3_9977_10000_0.4863_0.5331_0.5775.png
                gene_name: DCHS1
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 50 percent done.
DAGLB
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: 3.264705e-02	ci left: 5.806865e-01	ci right 6.000608e-01	k: 5904	n:10000
KS ci ratio: 2.631022e-02	ci left: 6.802263e-01	ci right 6.984633e-01	k: 6894	n:10000
DAGLB   10000 perm   2 sec   (5598 perm/sec)   p_kst 6.894000e-01   p_cons 5.904000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000047/DAGLB.2_2079_10000_0.6894_0.5904_1.png
                gene_name: DAGLB
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.69 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.70 
                   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: 67 percent done.
DARS
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: 7.325487e-02	ci left: 2.143797e-01	ci right 2.307822e-01	k: 2225	n:10000
KS ci ratio: 4.638942e-02	ci left: 4.068133e-01	ci right 4.262354e-01	k: 4165	n:10000
DARS   10000 perm   2 sec   (6419 perm/sec)   p_kst 4.165000e-01   p_cons 2.225000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000047/DARS.2_1570_10000_0.4165_0.2225_1.png
                gene_name: DARS
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 83 percent done.
DCAF12L1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.322396e-02	ci left: 5.721598e-01	ci right 5.915924e-01	k: 5819	n:10000
Cons ci ratio: 7.008223e-02	ci left: 2.298781e-01	ci right 2.466746e-01	k: 2382	n:10000
KS ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
DCAF12L1   10000 perm   2 sec   (5910 perm/sec)   p_kst 1   p_cons 2.382000e-01   p_joint 5.819000e-01

Outputting figure to mutsig2_images.part000000000047/DCAF12L1.2_1396_10000_1_0.2382_0.5819.png
                gene_name: DCAF12L1
               theta_stop: 0.070 
                    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: 0.58 
     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.165.3896/
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/181708/iteration1/scatter.0000000047
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 47 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119765: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000048> was used as the working directory.
Started at Wed Oct 10 10:42:38 2012
Results reported at Wed Oct 10 10:44:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000048.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000048.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 48  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    137.72 sec.
    Max Memory :      1096 MB
    Max Swap   :      3842 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.165.3896/
-whichjob
48
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 48: processing genes 4253 - 4343
Calculating significance of each gene.
Using projection method.
4253	DCPS	1.120106e-01
4254	DCST1	1
4255	DCST2	1
4256	DCT	1
4257	DCTD	9.335530e-02
4258	DCTN1	1
4259	DCTN2	1
4260	DCTN3	1
4261	DCTN4	1
4262	DCTN5	9.913676e-02
4263	DCTN6	1
4264	DCTPP1	1
4265	DCUN1D1	1
4266	DCUN1D2	1
4267	DCUN1D3	1
4268	DCUN1D4	1
4269	DCUN1D5	1
4270	DCX	1
4271	DCXR	1
4272	DDA1	1
4273	DDAH1	1
4274	DDAH2	1
4275	DDB1	1
4276	DDB2	1
4277	DDC	1
4278	DDHD1	1
4279	DDHD2	3.258362e-02
4280	DDI1	1
4281	DDI2	1
4282	DDIT3	1
4283	DDIT4	3.863052e-02
4284	DDIT4L	1
4285	DDN	1
4286	DDO	1
4287	DDOST	1
4288	DDR1	1
4289	DDR2	1.071744e-01
4290	DDRGK1	1
4291	DDTL	7.402374e-03
4292	DDX1	1
4293	DDX10	1
4294	DDX11	1
4295	DDX17	1
4296	DDX18	1
4297	DDX19A	2.040179e-01
4298	DDX19B	1
4299	DDX20	1
4300	DDX21	1
4301	DDX23	3.885675e-01
4302	DDX24	3.426694e-01
4303	DDX25	1
4304	DDX26B	1
4305	DDX27	1
4306	DDX28	1
4307	DDX31	1.691907e-01
4308	DDX39	1
4309	DDX3X	7.934099e-02
4310	DDX3Y	1
4311	DDX4	1
4312	DDX41	1
4313	DDX42	1
4314	DDX43	1
4315	DDX46	1
4316	DDX47	1
4317	DDX49	1
4318	DDX5	1
4319	DDX50	1
4320	DDX51	1
4321	DDX52	1
4322	DDX53	6.917879e-02
4323	DDX54	1
4324	DDX55	1
4325	DDX56	1
4326	DDX58	1
4327	DDX59	1
4328	DDX6	1
4329	DDX60	8.411063e-02
4330	DDX60L	1
4331	DEAF1	1
4332	DEC1	1
4333	DECR1	1
4334	DECR2	1
4335	DEDD	1
4336	DEDD2	1
4337	DEF6	1
4338	DEF8	1
4339	DEFA1	1
4340	DEFA1B	1
4341	DEFA3	1
4342	DEFA4	1
4343	DEFA5	1
Done

Running MutSig 2:
Scatter job 48: processing genes 4253 - 4343
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DDX60
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: 2.353708e-02	ci left: 7.262324e-01	ci right 7.436305e-01	k: 7350	n:10000
DDX60   10000 perm   4 sec   (2492 perm/sec)   p_kst 7.350000e-01   p_cons 7.438000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000048/DDX60.3_5287_10000_0.735_0.7438_1.png
                gene_name: DDX60
               theta_stop: 0.024 
                    nperm: 10000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.74 
                   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: 25 percent done.
DDHD2
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: 9.805070e-02	ci left: 1.310025e-01	ci right 1.446093e-01	k: 1377	n:10000
KS ci ratio: 7.150104e-02	ci left: 2.227686e-01	ci right 2.393884e-01	k: 2310	n:10000
DDHD2   10000 perm   3 sec   (3575 perm/sec)   p_kst 2.310000e-01   p_cons 1.377000e-01   p_joint 2.605000e-01

Outputting figure to mutsig2_images.part000000000048/DDHD2.2_2262_10000_0.231_0.1377_0.2605.png
                gene_name: DDHD2
               theta_stop: 0.098 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.26 
     ci_joint_bounds_left: 0.25 
    ci_joint_bounds_right: 0.27 

Current progress: 50 percent done.
DDX23
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.180494e-02	ci left: 7.552478e-01	ci right 7.719984e-01	k: 7637	n:10000
Cons ci ratio: 6.639033e-02	ci left: 2.498415e-01	ci right 2.670994e-01	k: 2584	n:10000
KS ci ratio: 3.012858e-02	ci left: 6.190435e-01	ci right 6.380815e-01	k: 6286	n:10000
DDX23   10000 perm   3 sec   (3586 perm/sec)   p_kst 6.286000e-01   p_cons 2.584000e-01   p_joint 7.637000e-01

Outputting figure to mutsig2_images.part000000000048/DDX23.2_2527_10000_0.6286_0.2584_0.7637.png
                gene_name: DDX23
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.76 
     ci_joint_bounds_left: 0.76 
    ci_joint_bounds_right: 0.77 

Current progress: 75 percent done.
DDX53
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.512495e-02	ci left: 5.447941e-01	ci right 5.643741e-01	k: 5546	n:10000
Cons ci ratio: 4.745527e-02	ci left: 3.958555e-01	ci right 4.151996e-01	k: 4055	n:10000
KS ci ratio: 9.205164e-02	ci left: 1.463885e-01	ci right 1.606140e-01	k: 1534	n:10000
DDX53   10000 perm   3 sec   (3321 perm/sec)   p_kst 1.534000e-01   p_cons 4.055000e-01   p_joint 5.546000e-01

Outputting figure to mutsig2_images.part000000000048/DDX53.2_1900_10000_0.1534_0.4055_0.5546.png
                gene_name: DDX53
               theta_stop: 0.092 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.55 
     ci_joint_bounds_left: 0.54 
    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.165.3896/
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/181708/iteration1/scatter.0000000048
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 48 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119771: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000049> was used as the working directory.
Started at Wed Oct 10 10:42:38 2012
Results reported at Wed Oct 10 10:44:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000049.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000049.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 49  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    131.66 sec.
    Max Memory :       897 MB
    Max Swap   :      3756 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.165.3896/
-whichjob
49
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 49: processing genes 4344 - 4433
Calculating significance of each gene.
Using projection method.
4344	DEFA6	1
4345	DEFB1	1
4346	DEFB104A	1
4347	DEFB104B	1
4348	DEFB106A	1
4349	DEFB106B	1
4350	DEFB108B	1
4351	DEFB110	1
4352	DEFB112	1
4353	DEFB113	1
4354	DEFB114	1
4355	DEFB115	1
4356	DEFB116	1
4357	DEFB118	1
4358	DEFB119	1
4359	DEFB121	1
4360	DEFB123	1
4361	DEFB124	1
4362	DEFB125	1
4363	DEFB126	1
4364	DEFB127	1
4365	DEFB128	1
4366	DEFB129	1
4367	DEFB131	1
4368	DEFB132	1
4369	DEFB134	1
4370	DEFB135	1
4371	DEFB136	1
4372	DEFB4A	1
4373	DEGS1	1
4374	DEGS2	1
4375	DEK	1
4376	DEM1	2.978123e-03
4377	DENND1A	1
4378	DENND1B	1
4379	DENND1C	1
4380	DENND2A	1
4381	DENND2C	1
4382	DENND2D	1.614852e-01
4383	DENND3	2.223129e-01
4384	DENND4A	1.845398e-01
4385	DENND4B	1
4386	DENND4C	3.459508e-01
4387	DENND5A	3.272894e-01
4388	DENND5B	6.953083e-02
4389	DENR	3.557234e-03
4390	DEPDC1	1
4391	DEPDC1B	1
4392	DEPDC4	1.537762e-01
4393	DEPDC5	2.063944e-01
4394	DEPDC6	1
4395	DEPDC7	1
4396	DERA	1
4397	DERL1	1
4398	DERL2	1
4399	DERL3	1
4400	DES	1
4401	DET1	1.450504e-01
4402	DEXI	1
4403	DFFA	1
4404	DFFB	1
4405	DFNA5	1
4406	DFNB31	2.947762e-01
4407	DFNB59	1
4408	DGAT1	1
4409	DGAT2	1
4410	DGAT2L6	1
4411	DGCR14	1
4412	DGCR2	1
4413	DGCR6	1
4414	DGCR6L	1
4415	DGCR8	1
4416	DGKA	1
4417	DGKB	1
4418	DGKD	1
4419	DGKE	8.085026e-02
4420	DGKG	1
4421	DGKH	1
4422	DGKI	1.427940e-01
4423	DGKK	2.121965e-01
4424	DGKQ	1
4425	DGKZ	1
4426	DGUOK	1
4427	DHCR24	1
4428	DHCR7	1
4429	DHDDS	2.683541e-02
4430	DHDH	1
4431	DHDPSL	1
4432	DHFR	1
4433	DHFRL1	1
Done

Running MutSig 2:
Scatter job 49: processing genes 4344 - 4433
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DEM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.108585e-02	ci left: 3.610234e-01	ci right 3.800520e-01	k: 3705	n:10000
Cons ci ratio: 8.802117e-02	ci left: 1.581661e-01	ci right 1.728293e-01	k: 1654	n:10000
KS ci ratio: 4.934669e-02	ci left: 3.772388e-01	ci right 3.964272e-01	k: 3868	n:10000
DEM1   10000 perm   2 sec   (6175 perm/sec)   p_kst 3.868000e-01   p_cons 1.654000e-01   p_joint 3.705000e-01

Outputting figure to mutsig2_images.part000000000049/DEM1.2_1126_10000_0.3868_0.1654_0.3705.png
                gene_name: DEM1
               theta_stop: 0.088 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.17 
      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: 33 percent done.
DENND4A
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: 2.880677e-02	ci left: 6.398548e-01	ci right 6.586581e-01	k: 6493	n:10000
KS ci ratio: 2.041810e-02	ci left: 7.784370e-01	ci right 7.945958e-01	k: 7866	n:10000
DENND4A   10000 perm   3 sec   (3983 perm/sec)   p_kst 7.866000e-01   p_cons 6.493000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000049/DENND4A.2_5845_10000_0.7866_0.6493_1.png
                gene_name: DENND4A
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.79 
                   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: 67 percent done.
DENND5B
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: 4.311172e-02	ci left: 4.427095e-01	ci right 4.623181e-01	k: 4525	n:10000
KS ci ratio: 4.982851e-02	ci left: 3.726615e-01	ci right 3.918072e-01	k: 3822	n:10000
DENND5B   10000 perm   2 sec   (4760 perm/sec)   p_kst 3.822000e-01   p_cons 4.525000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000049/DENND5B.2_3909_10000_0.3822_0.4525_1.png
                gene_name: DENND5B
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.45 
      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: 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.165.3896/
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/181708/iteration1/scatter.0000000049
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 49 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119776: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000050> was used as the working directory.
Started at Wed Oct 10 10:42:38 2012
Results reported at Wed Oct 10 10:45:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000050.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000050.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 50  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    164.28 sec.
    Max Memory :      1338 MB
    Max Swap   :      3859 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.165.3896/
-whichjob
50
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 50: processing genes 4434 - 4524
Calculating significance of each gene.
Using projection method.
4434	DHH	1
4435	DHODH	1
4436	DHPS	1
4437	DHRS1	1
4438	DHRS11	1
4439	DHRS12	1.134551e-01
4440	DHRS13	1
4441	DHRS2	1
4442	DHRS3	1
4443	DHRS4	1
4444	DHRS4L1	1
4445	DHRS4L2	1
4446	DHRS7	1.121251e-01
4447	DHRS7B	4.108400e-02
4448	DHRS7C	1
4449	DHRS9	1
4450	DHRSX	1
4451	DHTKD1	1.672630e-01
4452	DHX15	1
4453	DHX16	1
4454	DHX29	4.442674e-01
4455	DHX30	1
4456	DHX32	1
4457	DHX33	1.530063e-01
4458	DHX34	3.028208e-01
4459	DHX35	6.289074e-02
4460	DHX36	3.031200e-01
4461	DHX37	1
4462	DHX38	1
4463	DHX40	1
4464	DHX57	1
4465	DHX58	1
4466	DHX8	4.535227e-01
4467	DHX9	1.104107e-01
4468	DIABLO	1
4469	DIAPH1	1
4470	DIAPH2	2.948177e-01
4471	DIAPH3	1
4472	DICER1	1
4473	DIDO1	1
4474	DIMT1L	1
4475	DIO1	1
4476	DIO2	1
4477	DIO3	1
4478	DIP2A	1
4479	DIP2B	6.210177e-02
4480	DIP2C	5.709036e-01
4481	DIRAS1	1
4482	DIRAS2	1
4483	DIRAS3	1
4484	DIRC1	1
4485	DIRC2	1
4486	DIS3	1
4487	DIS3L	2.556625e-01
4488	DIS3L2	1.940658e-01
4489	DISC1	1
4490	DISP1	1.175699e-01
4491	DISP2	1
4492	DIXDC1	1
4493	DKC1	1
4494	DKFZp761E198	1
4495	DKK1	1
4496	DKK2	1
4497	DKK3	1
4498	DKK4	1
4499	DKKL1	1
4500	DLAT	1
4501	DLC1	1
4502	DLD	1
4503	DLEC1	1
4504	DLEU7	1
4505	DLG1	4.061949e-01
4506	DLG2	2.273518e-01
4507	DLG3	3.040268e-01
4508	DLG4	1
4509	DLG5	1
4510	DLGAP1	1
4511	DLGAP2	1
4512	DLGAP3	1
4513	DLGAP4	1
4514	DLGAP5	1
4515	DLK1	1
4516	DLK2	1
4517	DLL1	8.300099e-02
4518	DLL3	1
4519	DLL4	2.881794e-01
4520	DLST	1
4521	DLX1	1
4522	DLX2	7.373270e-02
4523	DLX3	5.472569e-03
4524	DLX4	1
Done

Running MutSig 2:
Scatter job 50: processing genes 4434 - 4524
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DHX29
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.141213e-02	ci left: 1.804823e-01	ci right 1.958998e-01	k: 1881	n:10000
Cons ci ratio: 9.733309e-03	ci left: 9.372385e-01	ci right 9.465020e-01	k: 9420	n:10000
KS ci ratio: 1.612434e-01	ci left: 5.128492e-02	ci right 6.037601e-02	k: 557	n:10000
DHX29   10000 perm   2 sec   (4472 perm/sec)   p_kst 5.570000e-02   p_cons 9.420000e-01   p_joint 1.881000e-01

Joint ci ratio: 5.078088e-02	ci left: 2.236868e-01	ci right 2.353920e-01	k: 4590	n:20000
Cons ci ratio: 6.917894e-03	ci left: 9.380552e-01	ci right 9.446158e-01	k: 18828	n:20000
KS ci ratio: 1.176937e-01	ci left: 4.944921e-02	ci right 5.568168e-02	k: 1050	n:20000
DHX29   20000 perm   8 sec   (2439 perm/sec)   p_kst 5.250000e-02   p_cons 9.414000e-01   p_joint 2.295000e-01

Joint ci ratio: 3.966163e-02	ci left: 2.407373e-01	ci right 2.505120e-01	k: 7368	n:30000
Cons ci ratio: 5.471756e-03	ci left: 9.421557e-01	ci right 9.473577e-01	k: 28344	n:30000
KS ci ratio: 9.742521e-02	ci left: 4.870025e-02	ci right 5.372045e-02	k: 1535	n:30000
DHX29   30000 perm   11 sec   (2795 perm/sec)   p_kst 5.116667e-02   p_cons 9.448000e-01   p_joint 2.456000e-01

Outputting figure to mutsig2_images.part000000000050/DHX29.2_4218_30000_0.051167_0.9448_0.2456.png
                gene_name: DHX29
               theta_stop: 0.097 
                    nperm: 30000 
                     p_ks: 0.051 
        ci_ks_bounds_left: 0.049 
       ci_ks_bounds_right: 0.054 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.25 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.25 

Current progress: 20 percent done.
DHX9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.573961e-01	ci left: 5.378678e-02	ci right 6.307254e-02	k: 583	n:10000
Cons ci ratio: 3.828764e-02	ci left: 5.018507e-01	ci right 5.215425e-01	k: 5117	n:10000
KS ci ratio: 2.086194e-01	ci left: 3.053425e-02	ci right 3.774046e-02	k: 340	n:10000
DHX9   10000 perm   2 sec   (4909 perm/sec)   p_kst 3.400000e-02   p_cons 5.117000e-01   p_joint 5.830000e-02

Joint ci ratio: 1.133214e-01	ci left: 5.324249e-02	ci right 5.968722e-02	k: 1128	n:20000
Cons ci ratio: 2.735580e-02	ci left: 4.995955e-01	ci right 5.135025e-01	k: 10131	n:20000
KS ci ratio: 1.507536e-01	ci left: 3.023012e-02	ci right 3.520695e-02	k: 653	n:20000
DHX9   20000 perm   5 sec   (4421 perm/sec)   p_kst 3.265000e-02   p_cons 5.065500e-01   p_joint 5.640000e-02

Joint ci ratio: 3.679043e-02	ci left: 2.694555e-01	ci right 2.795882e-01	k: 8235	n:30000
Cons ci ratio: 2.241927e-02	ci left: 4.990254e-01	ci right 5.103737e-01	k: 15141	n:30000
KS ci ratio: 1.228966e-01	ci left: 3.078084e-02	ci right 3.484363e-02	k: 983	n:30000
DHX9   30000 perm   7 sec   (4231 perm/sec)   p_kst 3.276667e-02   p_cons 5.047000e-01   p_joint 2.745000e-01

Joint ci ratio: 4.822289e-02	ci left: 1.383455e-01	ci right 1.452066e-01	k: 5670	n:40000
Cons ci ratio: 1.932582e-02	ci left: 5.021127e-01	ci right 5.119363e-01	k: 20281	n:40000
KS ci ratio: 1.067267e-01	ci left: 3.088117e-02	ci right 3.438711e-02	k: 1304	n:40000
DHX9   40000 perm   10 sec   (4106 perm/sec)   p_kst 3.260000e-02   p_cons 5.070250e-01   p_joint 1.417500e-01

Joint ci ratio: 7.185400e-02	ci left: 5.415779e-02	ci right 5.821393e-02	k: 2808	n:50000
Cons ci ratio: 1.723474e-02	ci left: 5.041076e-01	ci right 5.128914e-01	k: 25425	n:50000
KS ci ratio: 9.516591e-02	ci left: 3.125597e-02	ci right 3.439857e-02	k: 1640	n:50000
DHX9   50000 perm   12 sec   (4002 perm/sec)   p_kst 3.280000e-02   p_cons 5.085000e-01   p_joint 5.616000e-02

Outputting figure to mutsig2_images.part000000000050/DHX9.2_3921_50000_0.0328_0.5085_0.05616.png
                gene_name: DHX9
               theta_stop: 0.095 
                    nperm: 50000 
                     p_ks: 0.033 
        ci_ks_bounds_left: 0.031 
       ci_ks_bounds_right: 0.034 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.50 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.056 
     ci_joint_bounds_left: 0.054 
    ci_joint_bounds_right: 0.058 

Current progress: 40 percent done.
DIP2B
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: 6.645966e-02	ci left: 2.494459e-01	ci right 2.666952e-01	k: 2580	n:10000
KS ci ratio: 7.474606e-03	ci left: 9.612099e-01	ci right 9.685160e-01	k: 9650	n:10000
DIP2B   10000 perm   2 sec   (4425 perm/sec)   p_kst 9.650000e-01   p_cons 2.580000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000050/DIP2B.2_4883_10000_0.965_0.258_1.png
                gene_name: DIP2B
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.96 
        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: 0.27 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
DISP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.091696e-02	ci left: 4.686667e-01	ci right 4.883458e-01	k: 4785	n:10000
Cons ci ratio: 1.429991e-02	ci left: 8.761293e-01	ci right 8.888470e-01	k: 8826	n:10000
KS ci ratio: 4.780142e-02	ci left: 3.923700e-01	ci right 4.116871e-01	k: 4020	n:10000
DISP1   10000 perm   3 sec   (3781 perm/sec)   p_kst 4.020000e-01   p_cons 8.826000e-01   p_joint 4.785000e-01

Outputting figure to mutsig2_images.part000000000050/DISP1.2_4603_10000_0.402_0.8826_0.4785.png
                gene_name: DISP1
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.40 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.41 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 80 percent done.
DLX3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.865516e-02	ci left: 6.422690e-01	ci right 6.610426e-01	k: 6517	n:10000
Cons ci ratio: 3.134726e-02	ci left: 6.002590e-01	ci right 6.194770e-01	k: 6099	n:10000
KS ci ratio: 5.119552e-02	ci left: 3.600290e-01	ci right 3.790471e-01	k: 3695	n:10000
DLX3   10000 perm   2 sec   (6589 perm/sec)   p_kst 3.695000e-01   p_cons 6.099000e-01   p_joint 6.517000e-01

Outputting figure to mutsig2_images.part000000000050/DLX3.2_876_10000_0.3695_0.6099_0.6517.png
                gene_name: DLX3
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.61 
      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.165.3896/
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/181708/iteration1/scatter.0000000050
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 50 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1543>
Subject: Job 1119781: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1543>, 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/181708/iteration1/scatter.0000000051> was used as the working directory.
Started at Wed Oct 10 10:42:38 2012
Results reported at Wed Oct 10 10:46:20 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000051.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000051.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 51  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    221.28 sec.
    Max Memory :      1567 MB
    Max Swap   :      3888 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.165.3896/
-whichjob
51
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 51: processing genes 4525 - 4614
Calculating significance of each gene.
Using projection method.
4525	DLX5	1
4526	DLX6	1.790833e-02
4527	DMAP1	1
4528	DMBT1	1.077061e-01
4529	DMBX1	5.896943e-02
4530	DMC1	1
4531	DMD	3.593619e-01
4532	DMGDH	1
4533	DMKN	1
4534	DMP1	1
4535	DMPK	9.753353e-02
4536	DMRT1	1
4537	DMRT2	1
4538	DMRT3	1
4539	DMRTA1	1
4540	DMRTA2	1
4541	DMRTB1	1
4542	DMRTC2	1
4543	DMTF1	1
4544	DMWD	1
4545	DMXL1	1
4546	DMXL2	3.235941e-01
4547	DNA2	1
4548	DNAH1	7.082716e-01
4549	DNAH10	8.291717e-01
4550	DNAH11	4.185349e-01
4551	DNAH17	7.965430e-01
4552	DNAH2	1
4553	DNAH3	7.287531e-01
4554	DNAH5	1.785712e-01
4555	DNAH7	1
4556	DNAH8	1
4557	DNAH9	1.469373e-01
4558	DNAI1	1
4559	DNAI2	2.696005e-02
4560	DNAJA1	1
4561	DNAJA2	1
4562	DNAJA3	1
4563	DNAJA4	1
4564	DNAJB1	8.320395e-02
4565	DNAJB11	5.605936e-02
4566	DNAJB12	1
4567	DNAJB13	1
4568	DNAJB14	1
4569	DNAJB2	1
4570	DNAJB3	1
4571	DNAJB4	1
4572	DNAJB5	1
4573	DNAJB6	1
4574	DNAJB7	1
4575	DNAJB8	1
4576	DNAJB9	6.180500e-02
4577	DNAJC1	1
4578	DNAJC10	1
4579	DNAJC11	1
4580	DNAJC12	1
4581	DNAJC13	4.560251e-01
4582	DNAJC14	3.629017e-02
4583	DNAJC15	1
4584	DNAJC16	1
4585	DNAJC17	1
4586	DNAJC18	1
4587	DNAJC19	1
4588	DNAJC2	1
4589	DNAJC21	1
4590	DNAJC22	1
4591	DNAJC24	1
4592	DNAJC25	1
4593	DNAJC25-GNG10	1
4594	DNAJC27	1
4595	DNAJC28	1.342109e-01
4596	DNAJC3	1.825680e-01
4597	DNAJC30	1
4598	DNAJC4	1
4599	DNAJC5	1
4600	DNAJC5B	1
4601	DNAJC5G	1
4602	DNAJC6	1
4603	DNAJC7	1
4604	DNAJC8	1
4605	DNAJC9	1
4606	DNAL1	1
4607	DNAL4	1
4608	DNALI1	1
4609	DNASE1	1
4610	DNASE1L1	1
4611	DNASE1L2	1
4612	DNASE1L3	1
4613	DNASE2	1
4614	DNASE2B	1
Done

Running MutSig 2:
Scatter job 51: processing genes 4525 - 4614
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: 3.227051e-02	ci left: 5.863057e-01	ci right 6.056384e-01	k: 5960	n:10000
Cons ci ratio: 5.117355e-02	ci left: 3.602279e-01	ci right 3.792481e-01	k: 3697	n:10000
KS ci ratio: 3.875766e-02	ci left: 4.957504e-01	ci right 5.154464e-01	k: 5056	n:10000
DNAH5   10000 perm   5 sec   (2192 perm/sec)   p_kst 5.056000e-01   p_cons 3.697000e-01   p_joint 5.960000e-01

Outputting figure to mutsig2_images.part000000000051/DNAH5.7_14191_10000_0.5056_0.3697_0.596.png
                gene_name: DNAH5
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.52 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.60 
     ci_joint_bounds_left: 0.59 
    ci_joint_bounds_right: 0.61 

Current progress: 10 percent done.
DNAH3
Processing conservation and coverage...
79% 
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: 1.955787e-02	ci left: 7.927334e-01	ci right 8.084911e-01	k: 8007	n:10000
KS ci ratio: 2.061251e-02	ci left: 7.751944e-01	ci right 7.914402e-01	k: 7834	n:10000
DNAH3   10000 perm   4 sec   (2527 perm/sec)   p_kst 7.834000e-01   p_cons 8.007000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000051/DNAH3.4_12598_10000_0.7834_0.8007_1.png
                gene_name: DNAH3
               theta_stop: 0.021 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.79 
                   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: 20 percent done.
DNAH9
Processing conservation and coverage...
72% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.917035e-02	ci left: 3.789306e-01	ci right 3.981344e-01	k: 3885	n:10000
Cons ci ratio: 7.023701e-02	ci left: 2.290880e-01	ci right 2.458652e-01	k: 2374	n:10000
KS ci ratio: 2.445056e-02	ci left: 7.109857e-01	ci right 7.286861e-01	k: 7199	n:10000
DNAH9   10000 perm   5 sec   (2190 perm/sec)   p_kst 7.199000e-01   p_cons 2.374000e-01   p_joint 3.885000e-01

Outputting figure to mutsig2_images.part000000000051/DNAH9.4_13737_10000_0.7199_0.2374_0.3885.png
                gene_name: DNAH9
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 30 percent done.
DMBT1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.842438e-02	ci left: 2.385720e-01	ci right 2.555756e-01	k: 2470	n:10000
Cons ci ratio: 7.573360e-03	ci left: 9.602659e-01	ci right 9.676606e-01	k: 9641	n:10000
KS ci ratio: 1.179891e-01	ci left: 9.350575e-02	ci right 1.053288e-01	k: 993	n:10000
DMBT1   10000 perm   3 sec   (3004 perm/sec)   p_kst 9.930000e-02   p_cons 9.641000e-01   p_joint 2.470000e-01

Joint ci ratio: 5.132526e-02	ci left: 2.199711e-01	ci right 2.316088e-01	k: 4515	n:20000
Cons ci ratio: 5.553381e-03	ci left: 9.586889e-01	ci right 9.640759e-01	k: 19229	n:20000
KS ci ratio: 8.253650e-02	ci left: 9.715154e-02	ci right 1.055648e-01	k: 2026	n:20000
DMBT1   20000 perm   7 sec   (2800 perm/sec)   p_kst 1.013000e-01   p_cons 9.614500e-01   p_joint 2.257500e-01

Outputting figure to mutsig2_images.part000000000051/DMBT1.3_7454_20000_0.1013_0.96145_0.22575.png
                gene_name: DMBT1
               theta_stop: 0.083 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.097 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.96 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.23 

Current progress: 40 percent done.
DMD
Processing conservation and coverage...
85% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.342837e-02	ci left: 7.280508e-01	ci right 7.454111e-01	k: 7368	n:10000
Cons ci ratio: 2.849757e-02	ci left: 6.447840e-01	ci right 6.635261e-01	k: 6542	n:10000
KS ci ratio: 3.270783e-02	ci left: 5.797835e-01	ci right 5.991643e-01	k: 5895	n:10000
DMD   10000 perm   4 sec   (2683 perm/sec)   p_kst 5.895000e-01   p_cons 6.542000e-01   p_joint 7.368000e-01

Outputting figure to mutsig2_images.part000000000051/DMD.2_11651_10000_0.5895_0.6542_0.7368.png
                gene_name: DMD
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  p_joint: 0.74 
     ci_joint_bounds_left: 0.73 
    ci_joint_bounds_right: 0.75 

Current progress: 50 percent done.
DMXL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.092922e-03	ci left: 9.551367e-01	ci right 9.629931e-01	k: 9592	n:10000
Cons ci ratio: 5.265484e-02	ci left: 3.471054e-01	ci right 3.659783e-01	k: 3565	n:10000
KS ci ratio: 7.243911e-02	ci left: 2.182281e-01	ci right 2.347315e-01	k: 2264	n:10000
DMXL2   10000 perm   3 sec   (3071 perm/sec)   p_kst 2.264000e-01   p_cons 3.565000e-01   p_joint 9.592000e-01

Outputting figure to mutsig2_images.part000000000051/DMXL2.2_9286_10000_0.2264_0.3565_0.9592.png
                gene_name: DMXL2
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.96 

Current progress: 60 percent done.
DNAH11
Processing conservation and coverage...
71% 
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: 3.095449e-03	ci left: 9.921711e-01	ci right 9.953309e-01	k: 9939	n:10000
KS ci ratio: 6.245627e-02	ci left: 2.736903e-01	ci right 2.914365e-01	k: 2825	n:10000
DNAH11   10000 perm   4 sec   (2487 perm/sec)   p_kst 2.825000e-01   p_cons 9.939000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000051/DNAH11.2_13901_10000_0.2825_0.9939_1.png
                gene_name: DNAH11
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 1.00 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 70 percent done.
DNAH8
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: 2.045457e-02	ci left: 7.778289e-01	ci right 7.940042e-01	k: 7860	n:10000
KS ci ratio: 4.435067e-02	ci left: 4.287437e-01	ci right 4.482921e-01	k: 4385	n:10000
DNAH8   10000 perm   4 sec   (2460 perm/sec)   p_kst 4.385000e-01   p_cons 7.860000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000051/DNAH8.2_13829_10000_0.4385_0.786_1.png
                gene_name: DNAH8
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.79 
      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: 80 percent done.
DNAI2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.969783e-02	ci left: 6.257775e-01	ci right 6.447437e-01	k: 6353	n:10000
Cons ci ratio: 9.743651e-02	ci left: 1.324713e-01	ci right 1.461396e-01	k: 1392	n:10000
KS ci ratio: 6.728524e-02	ci left: 2.447989e-01	ci right 2.619450e-01	k: 2533	n:10000
DNAI2   10000 perm   2 sec   (5484 perm/sec)   p_kst 2.533000e-01   p_cons 1.392000e-01   p_joint 6.353000e-01

Outputting figure to mutsig2_images.part000000000051/DNAI2.2_1866_10000_0.2533_0.1392_0.6353.png
                gene_name: DNAI2
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.64 

Current progress: 90 percent done.
DNAJC14
Processing conservation and coverage...
Processing mutations... 
Skipping 2 mutations outside transcript range of this gene.
Fewer than 2 mutations to analyze: skipping this gene...
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.165.3896/
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/181708/iteration1/scatter.0000000051
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 51 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119785: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000052> was used as the working directory.
Started at Wed Oct 10 10:42:38 2012
Results reported at Wed Oct 10 10:48:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000052.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000052.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 52  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    332.44 sec.
    Max Memory :      1493 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.165.3896/
-whichjob
52
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 52: processing genes 4615 - 4704
Calculating significance of each gene.
Using projection method.
4615	DND1	1
4616	DNER	3.485109e-02
4617	DNHD1	1
4618	DNLZ	1
4619	DNM1	2.483727e-02
4620	DNM1L	1
4621	DNM2	1
4622	DNM3	1.557646e-02
4623	DNMBP	1
4624	DNMT1	1
4625	DNMT3A	1
4626	DNMT3B	3.653119e-01
4627	DNMT3L	1
4628	DNPEP	1.748746e-01
4629	DNTT	2.387840e-01
4630	DNTTIP1	1
4631	DNTTIP2	1
4632	DOC2A	1
4633	DOCK1	4.100287e-01
4634	DOCK10	5.673953e-01
4635	DOCK11	5.834973e-01
4636	DOCK2	1
4637	DOCK3	4.151394e-01
4638	DOCK4	9.473766e-02
4639	DOCK5	2.941250e-01
4640	DOCK6	5.522796e-01
4641	DOCK7	6.490777e-01
4642	DOCK8	1
4643	DOCK9	4.081904e-01
4644	DOHH	1
4645	DOK1	1
4646	DOK2	1
4647	DOK3	1
4648	DOK4	1.847005e-02
4649	DOK5	1
4650	DOK6	1
4651	DOK7	1
4652	DOLK	1
4653	DOLPP1	1
4654	DOM3Z	1
4655	DONSON	1
4656	DOPEY1	3.683708e-01
4657	DOPEY2	1
4658	DOT1L	6.425814e-02
4659	DPAGT1	1
4660	DPCD	1
4661	DPEP1	1.427784e-01
4662	DPEP2	1
4663	DPEP3	1
4664	DPF1	1
4665	DPF2	1
4666	DPF3	1
4667	DPH1	1
4668	DPH2	1
4669	DPH3	1
4670	DPH3B	1
4671	DPH5	1
4672	DPM1	1
4673	DPM2	1
4674	DPM3	1
4675	DPP10	1
4676	DPP3	1
4677	DPP4	1
4678	DPP6	1
4679	DPP7	1
4680	DPP8	1.929566e-01
4681	DPP9	2.291401e-01
4682	DPPA2	1
4683	DPPA3	1
4684	DPPA4	1
4685	DPPA5	1
4686	DPRX	1
4687	DPT	1
4688	DPY19L1	1
4689	DPY19L2	3.042325e-01
4690	DPY19L3	1
4691	DPY19L4	1
4692	DPY30	1
4693	DPYD	1
4694	DPYS	1.512539e-01
4695	DPYSL2	1
4696	DPYSL3	1
4697	DPYSL4	2.258078e-01
4698	DPYSL5	1
4699	DQX1	1
4700	DR1	1
4701	DRAM1	1
4702	DRAM2	1
4703	DRAP1	1
4704	DRD1	1
Done

Running MutSig 2:
Scatter job 52: processing genes 4615 - 4704
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DOT1L
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: 3.103695e-01	ci left: 1.326304e-02	ci right 1.822489e-02	k: 156	n:10000
KS ci ratio: 4.023926e-01	ci left: 7.512676e-03	ci right 1.138119e-02	k: 93	n:10000
DOT1L   10000 perm   3 sec   (3864 perm/sec)   p_kst 9.300000e-03   p_cons 1.560000e-02   p_joint 9.700000e-03

Joint ci ratio: 2.305348e-01	ci left: 1.260619e-02	ci right 1.593723e-02	k: 284	n:20000
Cons ci ratio: 2.007894e-01	ci left: 1.682030e-02	ci right 2.062146e-02	k: 373	n:20000
KS ci ratio: 2.868611e-01	ci left: 7.923549e-03	ci right 1.062202e-02	k: 184	n:20000
DOT1L   20000 perm   10 sec   (1990 perm/sec)   p_kst 9.200000e-03   p_cons 1.865000e-02   p_joint 1.420000e-02

Joint ci ratio: 2.244287e-01	ci left: 8.936542e-03	ci right 1.122650e-02	k: 301	n:30000
Cons ci ratio: 1.604815e-01	ci left: 1.793329e-02	ci right 2.109407e-02	k: 584	n:30000
KS ci ratio: 2.340103e-01	ci left: 8.182088e-03	ci right 1.038119e-02	k: 277	n:30000
DOT1L   30000 perm   13 sec   (2235 perm/sec)   p_kst 9.233333e-03   p_cons 1.946667e-02   p_joint 1.003333e-02

Joint ci ratio: 2.224984e-01	ci left: 6.843160e-03	ci right 8.579455e-03	k: 307	n:40000
Cons ci ratio: 1.387098e-01	ci left: 1.821570e-02	ci right 2.095467e-02	k: 782	n:40000
KS ci ratio: 2.059566e-01	ci left: 8.050337e-03	ci right 9.921990e-03	k: 358	n:40000
DOT1L   40000 perm   16 sec   (2448 perm/sec)   p_kst 8.950000e-03   p_cons 1.955000e-02   p_joint 7.675000e-03

Joint ci ratio: 2.353018e-01	ci left: 4.870588e-03	ci right 6.187821e-03	k: 275	n:50000
Cons ci ratio: 1.236640e-01	ci left: 1.848047e-02	ci right 2.093574e-02	k: 984	n:50000
KS ci ratio: 1.762160e-01	ci left: 8.935976e-03	ci right 1.068164e-02	k: 489	n:50000
DOT1L   50000 perm   19 sec   (2576 perm/sec)   p_kst 9.780000e-03   p_cons 1.968000e-02   p_joint 5.500000e-03

Joint ci ratio: 2.300303e-01	ci left: 4.262702e-03	ci right 5.386019e-03	k: 288	n:60000
Cons ci ratio: 1.134290e-01	ci left: 1.840855e-02	ci right 2.063827e-02	k: 1170	n:60000
KS ci ratio: 1.597687e-01	ci left: 9.139258e-03	ci right 1.074201e-02	k: 595	n:60000
DOT1L   60000 perm   23 sec   (2656 perm/sec)   p_kst 9.916667e-03   p_cons 1.950000e-02   p_joint 4.800000e-03

Joint ci ratio: 2.221459e-01	ci left: 3.936682e-03	ci right 4.933656e-03	k: 309	n:70000
Cons ci ratio: 1.052970e-01	ci left: 1.839106e-02	ci right 2.044905e-02	k: 1358	n:70000
KS ci ratio: 1.479530e-01	ci left: 9.193563e-03	ci right 1.067606e-02	k: 694	n:70000
DOT1L   70000 perm   26 sec   (2698 perm/sec)   p_kst 9.914286e-03   p_cons 1.940000e-02   p_joint 4.414286e-03

Joint ci ratio: 2.285877e-01	ci left: 3.243954e-03	ci right 4.092667e-03	k: 292	n:80000
Cons ci ratio: 9.866315e-02	ci left: 1.839446e-02	ci right 2.031562e-02	k: 1547	n:80000
KS ci ratio: 1.377236e-01	ci left: 9.334159e-03	ci right 1.072672e-02	k: 801	n:80000
DOT1L   80000 perm   29 sec   (2715 perm/sec)   p_kst 1.001250e-02   p_cons 1.933750e-02   p_joint 3.650000e-03

Joint ci ratio: 2.382042e-01	ci left: 2.642794e-03	ci right 3.367604e-03	k: 269	n:90000
Cons ci ratio: 9.330782e-02	ci left: 1.833514e-02	ci right 2.014048e-02	k: 1730	n:90000
KS ci ratio: 1.291441e-01	ci left: 9.478527e-03	ci right 1.079778e-02	k: 911	n:90000
DOT1L   90000 perm   33 sec   (2711 perm/sec)   p_kst 1.012222e-02   p_cons 1.922222e-02   p_joint 2.988889e-03

Joint ci ratio: 2.776034e-01	ci left: 1.714018e-03	ci right 2.275497e-03	k: 198	n:100000
Cons ci ratio: 8.873941e-02	ci left: 1.828996e-02	ci right 1.999809e-02	k: 1913	n:100000
KS ci ratio: 1.229055e-01	ci left: 9.450726e-03	ci right 1.069794e-02	k: 1006	n:100000
DOT1L   100000 perm   37 sec   (2720 perm/sec)   p_kst 1.006000e-02   p_cons 1.913000e-02   p_joint 1.980000e-03

Joint ci ratio: 2.634215e-01	ci left: 1.744647e-03	ci right 2.282152e-03	k: 220	n:110000
Cons ci ratio: 8.459745e-02	ci left: 1.833489e-02	ci right 1.996333e-02	k: 2105	n:110000
KS ci ratio: 1.166393e-01	ci left: 9.570473e-03	ci right 1.076466e-02	k: 1117	n:110000
DOT1L   110000 perm   41 sec   (2708 perm/sec)   p_kst 1.015455e-02   p_cons 1.913636e-02   p_joint 2.000000e-03

Joint ci ratio: 2.582282e-01	ci left: 1.669348e-03	ci right 2.171879e-03	k: 229	n:120000
Cons ci ratio: 8.116636e-02	ci left: 1.829220e-02	ci right 1.984784e-02	k: 2287	n:120000
KS ci ratio: 1.127354e-01	ci left: 9.412339e-03	ci right 1.054486e-02	k: 1196	n:120000
DOT1L   120000 perm   44 sec   (2706 perm/sec)   p_kst 9.966667e-03   p_cons 1.905833e-02   p_joint 1.908333e-03

Joint ci ratio: 1.647027e-01	ci left: 3.981060e-03	ci right 4.702863e-03	k: 563	n:130000
Cons ci ratio: 7.794475e-02	ci left: 1.834020e-02	ci right 1.983520e-02	k: 2480	n:130000
KS ci ratio: 1.081339e-01	ci left: 9.466234e-03	ci right 1.055579e-02	k: 1300	n:130000
DOT1L   130000 perm   48 sec   (2681 perm/sec)   p_kst 1.000000e-02   p_cons 1.907692e-02   p_joint 4.330769e-03

Joint ci ratio: 1.744693e-01	ci left: 3.279356e-03	ci right 3.912906e-03	k: 502	n:140000
Cons ci ratio: 7.495013e-02	ci left: 1.844550e-02	ci right 1.988880e-02	k: 2682	n:140000
KS ci ratio: 1.040534e-01	ci left: 9.513234e-03	ci right 1.056435e-02	k: 1404	n:140000
DOT1L   140000 perm   53 sec   (2658 perm/sec)   p_kst 1.002857e-02   p_cons 1.915714e-02   p_joint 3.585714e-03

Joint ci ratio: 1.820932e-01	ci left: 2.799527e-03	ci right 3.366617e-03	k: 461	n:150000
Cons ci ratio: 7.228886e-02	ci left: 1.853116e-02	ci right 1.992751e-02	k: 2883	n:150000
KS ci ratio: 1.011500e-01	ci left: 9.411632e-03	ci right 1.042078e-02	k: 1486	n:150000
DOT1L   150000 perm   57 sec   (2648 perm/sec)   p_kst 9.906667e-03   p_cons 1.922000e-02   p_joint 3.073333e-03

Joint ci ratio: 1.381588e-01	ci left: 4.660261e-03	ci right 5.357861e-03	k: 800	n:160000
Cons ci ratio: 6.975411e-02	ci left: 1.868062e-02	ci right 2.003687e-02	k: 3096	n:160000
KS ci ratio: 9.791105e-02	ci left: 9.432853e-03	ci right 1.041003e-02	k: 1586	n:160000
DOT1L   160000 perm   61 sec   (2607 perm/sec)   p_kst 9.912500e-03   p_cons 1.935000e-02   p_joint 5.000000e-03

Joint ci ratio: 1.131407e-01	ci left: 6.614880e-03	ci right 7.413836e-03	k: 1191	n:170000
Cons ci ratio: 6.763542e-02	ci left: 1.872069e-02	ci right 2.003695e-02	k: 3293	n:170000
KS ci ratio: 9.409523e-02	ci left: 9.630114e-03	ci right 1.058670e-02	k: 1717	n:170000
DOT1L   170000 perm   66 sec   (2565 perm/sec)   p_kst 1.010000e-02   p_cons 1.937059e-02   p_joint 7.005882e-03

Joint ci ratio: 1.181008e-01	ci left: 5.723919e-03	ci right 6.447683e-03	k: 1094	n:180000
Cons ci ratio: 6.576603e-02	ci left: 1.871860e-02	ci right 1.999694e-02	k: 3483	n:180000
KS ci ratio: 9.164945e-02	ci left: 9.599767e-03	ci right 1.052723e-02	k: 1810	n:180000
DOT1L   180000 perm   70 sec   (2553 perm/sec)   p_kst 1.005556e-02   p_cons 1.935000e-02   p_joint 6.077778e-03

Joint ci ratio: 1.151431e-01	ci left: 5.713907e-03	ci right 6.417081e-03	k: 1151	n:190000
Cons ci ratio: 6.394599e-02	ci left: 1.877417e-02	ci right 2.001950e-02	k: 3684	n:190000
KS ci ratio: 8.938496e-02	ci left: 9.572904e-03	ci right 1.047372e-02	k: 1903	n:190000
DOT1L   190000 perm   75 sec   (2540 perm/sec)   p_kst 1.001579e-02   p_cons 1.938947e-02   p_joint 6.057895e-03

Joint ci ratio: 1.175982e-01	ci left: 5.199970e-03	ci right 5.854487e-03	k: 1104	n:200000
Cons ci ratio: 6.225281e-02	ci left: 1.883446e-02	ci right 2.004952e-02	k: 3887	n:200000
KS ci ratio: 8.719227e-02	ci left: 9.568549e-03	ci right 1.044574e-02	k: 2000	n:200000
DOT1L   200000 perm   79 sec   (2520 perm/sec)   p_kst 1.000000e-02   p_cons 1.943500e-02   p_joint 5.520000e-03

Joint ci ratio: 1.664753e-01	ci left: 2.414090e-03	ci right 2.856959e-03	k: 552	n:210000
Cons ci ratio: 6.088499e-02	ci left: 1.876744e-02	ci right 1.995064e-02	k: 4064	n:210000
KS ci ratio: 8.849473e-02	ci left: 8.847292e-03	ci right 9.671102e-03	k: 1943	n:210000
DOT1L   210000 perm   84 sec   (2496 perm/sec)   p_kst 9.252381e-03   p_cons 1.935238e-02   p_joint 2.628571e-03

Joint ci ratio: 1.625541e-01	ci left: 2.422034e-03	ci right 2.854872e-03	k: 579	n:220000
Cons ci ratio: 5.958204e-02	ci left: 1.872022e-02	ci right 1.987431e-02	k: 4244	n:220000
KS ci ratio: 8.640812e-02	ci left: 8.867520e-03	ci right 9.672762e-03	k: 2038	n:220000
DOT1L   220000 perm   89 sec   (2480 perm/sec)   p_kst 9.263636e-03   p_cons 1.929091e-02   p_joint 2.631818e-03

Joint ci ratio: 1.583751e-01	ci left: 2.446101e-03	ci right 2.870934e-03	k: 610	n:230000
Cons ci ratio: 5.835930e-02	ci left: 1.867735e-02	ci right 1.980437e-02	k: 4424	n:230000
KS ci ratio: 8.480408e-02	ci left: 8.813835e-03	ci right 9.598608e-03	k: 2116	n:230000
DOT1L   230000 perm   93 sec   (2462 perm/sec)   p_kst 9.200000e-03   p_cons 1.923478e-02   p_joint 2.652174e-03

Joint ci ratio: 1.225389e-01	ci left: 3.985577e-03	ci right 4.509840e-03	k: 1018	n:240000
Cons ci ratio: 5.721521e-02	ci left: 1.863417e-02	ci right 1.973581e-02	k: 4603	n:240000
KS ci ratio: 8.320967e-02	ci left: 8.781075e-03	ci right 9.547516e-03	k: 2198	n:240000
DOT1L   240000 perm   98 sec   (2438 perm/sec)   p_kst 9.158333e-03   p_cons 1.917917e-02   p_joint 4.241667e-03

Joint ci ratio: 1.360858e-01	ci left: 3.082829e-03	ci right 3.536807e-03	k: 826	n:250000
Cons ci ratio: 5.589802e-02	ci left: 1.875245e-02	ci right 1.983474e-02	k: 4822	n:250000
KS ci ratio: 8.166579e-02	ci left: 8.758900e-03	ci right 9.508546e-03	k: 2282	n:250000
DOT1L   250000 perm   103 sec   (2421 perm/sec)   p_kst 9.128000e-03   p_cons 1.928800e-02   p_joint 3.304000e-03

Joint ci ratio: 1.336053e-01	ci left: 3.079466e-03	ci right 3.524027e-03	k: 857	n:260000
Cons ci ratio: 5.480094e-02	ci left: 1.877083e-02	ci right 1.983224e-02	k: 5017	n:260000
KS ci ratio: 8.022187e-02	ci left: 8.734784e-03	ci right 9.468529e-03	k: 2365	n:260000
DOT1L   260000 perm   108 sec   (2399 perm/sec)   p_kst 9.096154e-03   p_cons 1.929615e-02   p_joint 3.296154e-03

Joint ci ratio: 1.376984e-01	ci left: 2.786481e-03	ci right 3.202079e-03	k: 807	n:270000
Cons ci ratio: 5.367161e-02	ci left: 1.885382e-02	ci right 1.989727e-02	k: 5230	n:270000
KS ci ratio: 7.883568e-02	ci left: 8.716194e-03	ci right 9.435144e-03	k: 2449	n:270000
DOT1L   270000 perm   114 sec   (2377 perm/sec)   p_kst 9.070370e-03   p_cons 1.937037e-02   p_joint 2.988889e-03

Joint ci ratio: 1.288153e-01	ci left: 3.084030e-03	ci right 3.512067e-03	k: 922	n:280000
Cons ci ratio: 5.275280e-02	ci left: 1.882886e-02	ci right 1.985255e-02	k: 5414	n:280000
KS ci ratio: 7.748810e-02	ci left: 8.706038e-03	ci right 9.411322e-03	k: 2535	n:280000
DOT1L   280000 perm   119 sec   (2355 perm/sec)   p_kst 9.053571e-03   p_cons 1.933571e-02   p_joint 3.292857e-03

Joint ci ratio: 1.263077e-01	ci left: 3.101201e-03	ci right 3.522615e-03	k: 959	n:290000
Cons ci ratio: 5.187016e-02	ci left: 1.881258e-02	ci right 1.981775e-02	k: 5600	n:290000
KS ci ratio: 7.597376e-02	ci left: 8.750813e-03	ci right 9.445258e-03	k: 2637	n:290000
DOT1L   290000 perm   124 sec   (2333 perm/sec)   p_kst 9.093103e-03   p_cons 1.931034e-02   p_joint 3.306897e-03

Joint ci ratio: 1.241285e-01	ci left: 3.107611e-03	ci right 3.522075e-03	k: 993	n:300000
Cons ci ratio: 5.109345e-02	ci left: 1.875143e-02	ci right 1.973789e-02	k: 5772	n:300000
KS ci ratio: 7.446262e-02	ci left: 8.812358e-03	ci right 9.497174e-03	k: 2745	n:300000
DOT1L   300000 perm   130 sec   (2312 perm/sec)   p_kst 9.150000e-03   p_cons 1.924000e-02   p_joint 3.310000e-03

Joint ci ratio: 1.217616e-01	ci left: 3.129305e-03	ci right 3.538131e-03	k: 1032	n:310000
Cons ci ratio: 5.027306e-02	ci left: 1.875168e-02	ci right 1.972186e-02	k: 5962	n:310000
KS ci ratio: 7.321966e-02	ci left: 8.825717e-03	ci right 9.499636e-03	k: 2839	n:310000
DOT1L   310000 perm   135 sec   (2292 perm/sec)   p_kst 9.158065e-03   p_cons 1.923226e-02   p_joint 3.329032e-03

Joint ci ratio: 1.258027e-01	ci left: 2.834650e-03	ci right 3.218187e-03	k: 967	n:320000
Cons ci ratio: 4.942549e-02	ci left: 1.880142e-02	ci right 1.975731e-02	k: 6168	n:320000
KS ci ratio: 7.209896e-02	ci left: 8.822984e-03	ci right 9.485950e-03	k: 2928	n:320000
DOT1L   320000 perm   141 sec   (2273 perm/sec)   p_kst 9.150000e-03   p_cons 1.927500e-02   p_joint 3.021875e-03

Joint ci ratio: 9.594114e-02	ci left: 4.791767e-03	ci right 5.277593e-03	k: 1660	n:330000
Cons ci ratio: 4.873253e-02	ci left: 1.876146e-02	ci right 1.970156e-02	k: 6345	n:330000
KS ci ratio: 7.090972e-02	ci left: 8.850261e-03	ci right 9.503856e-03	k: 3027	n:330000
DOT1L   330000 perm   147 sec   (2252 perm/sec)   p_kst 9.172727e-03   p_cons 1.922727e-02   p_joint 5.030303e-03

Outputting figure to mutsig2_images.part000000000052/DOT1L.5_4726_330000_0.0091727_0.019227_0.0050303.png
                gene_name: DOT1L
               theta_stop: 0.096 
                    nperm: 330000 
                     p_ks: 0.0092 
        ci_ks_bounds_left: 0.0089 
       ci_ks_bounds_right: 0.0095 
                   p_cons: 0.019 
      ci_cons_bounds_left: 0.019 
     ci_cons_bounds_right: 0.020 
                  p_joint: 0.0050 
     ci_joint_bounds_left: 0.0048 
    ci_joint_bounds_right: 0.0053 

Current progress: 20 percent done.
DOCK4
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: 1.001686e-01	ci left: 1.261085e-01	ci right 1.395062e-01	k: 1327	n:10000
KS ci ratio: 2.784546e-02	ci left: 6.552495e-01	ci right 6.738545e-01	k: 6646	n:10000
DOCK4   10000 perm   2 sec   (4189 perm/sec)   p_kst 6.646000e-01   p_cons 1.327000e-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: 7.157880e-02	ci left: 1.257128e-01	ci right 1.350949e-01	k: 2607	n:20000
KS ci ratio: 1.999601e-02	ci left: 6.510766e-01	ci right 6.642775e-01	k: 13154	n:20000
DOCK4   20000 perm   5 sec   (3728 perm/sec)   p_kst 6.577000e-01   p_cons 1.303500e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000052/DOCK4.3_6109_20000_0.6577_0.13035_1.png
                gene_name: DOCK4
               theta_stop: 0.072 
                    nperm: 20000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 40 percent done.
DNER
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.882622e-02	ci left: 2.983636e-01	ci right 3.165487e-01	k: 3074	n:10000
Cons ci ratio: 3.718438e-02	ci left: 5.164573e-01	ci right 5.361274e-01	k: 5263	n:10000
KS ci ratio: 2.037220e-01	ci left: 3.205417e-02	ci right 3.941949e-02	k: 356	n:10000
DNER   10000 perm   2 sec   (5384 perm/sec)   p_kst 3.560000e-02   p_cons 5.263000e-01   p_joint 3.074000e-01

Joint ci ratio: 4.939961e-02	ci left: 2.334993e-01	ci right 2.453765e-01	k: 4788	n:20000
Cons ci ratio: 2.638758e-02	ci left: 5.176007e-01	ci right 5.314922e-01	k: 10491	n:20000
KS ci ratio: 1.476317e-01	ci left: 3.153127e-02	ci right 3.660536e-02	k: 680	n:20000
DNER   20000 perm   4 sec   (4662 perm/sec)   p_kst 3.400000e-02   p_cons 5.245500e-01   p_joint 2.394000e-01

Joint ci ratio: 4.614528e-02	ci left: 1.894064e-01	ci right 1.983863e-01	k: 5816	n:30000
Cons ci ratio: 2.156820e-02	ci left: 5.183632e-01	ci right 5.296988e-01	k: 15721	n:30000
KS ci ratio: 1.201466e-01	ci left: 3.220433e-02	ci right 3.635316e-02	k: 1027	n:30000
DNER   30000 perm   7 sec   (4358 perm/sec)   p_kst 3.423333e-02   p_cons 5.240333e-01   p_joint 1.938667e-01

Joint ci ratio: 4.035399e-02	ci left: 1.870090e-01	ci right 1.947359e-01	k: 7634	n:40000
Cons ci ratio: 1.857550e-02	ci left: 5.218928e-01	ci right 5.317033e-01	k: 21072	n:40000
KS ci ratio: 1.043530e-01	ci left: 3.229412e-02	ci right 3.587394e-02	k: 1362	n:40000
DNER   40000 perm   9 sec   (4228 perm/sec)   p_kst 3.405000e-02   p_cons 5.268000e-01   p_joint 1.908500e-01

Joint ci ratio: 3.916405e-02	ci left: 1.636410e-01	ci right 1.701977e-01	k: 8345	n:50000
Cons ci ratio: 1.658591e-02	ci left: 5.232726e-01	ci right 5.320442e-01	k: 26383	n:50000
KS ci ratio: 9.321605e-02	ci left: 3.256543e-02	ci right 3.576895e-02	k: 1707	n:50000
DNER   50000 perm   12 sec   (4117 perm/sec)   p_kst 3.414000e-02   p_cons 5.276600e-01   p_joint 1.669000e-01

Outputting figure to mutsig2_images.part000000000052/DNER.2_2266_50000_0.03414_0.52766_0.1669.png
                gene_name: DNER
               theta_stop: 0.093 
                    nperm: 50000 
                     p_ks: 0.034 
        ci_ks_bounds_left: 0.033 
       ci_ks_bounds_right: 0.036 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.16 
    ci_joint_bounds_right: 0.17 

Current progress: 60 percent done.
DNM1
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: 7.172305e-02	ci left: 2.216827e-01	ci right 2.382749e-01	k: 2299	n:10000
KS ci ratio: 1.116695e-01	ci left: 1.035416e-01	ci right 1.158868e-01	k: 1096	n:10000
DNM1   10000 perm   2 sec   (5072 perm/sec)   p_kst 1.096000e-01   p_cons 2.299000e-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: 5.163549e-02	ci left: 2.178906e-01	ci right 2.294899e-01	k: 4473	n:20000
KS ci ratio: 7.856213e-02	ci left: 1.063343e-01	ci right 1.150793e-01	k: 2213	n:20000
DNM1   20000 perm   5 sec   (4399 perm/sec)   p_kst 1.106500e-01   p_cons 2.236500e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000052/DNM1.2_2704_20000_0.11065_0.22365_1.png
                gene_name: DNM1
               theta_stop: 0.079 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.23 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 80 percent done.
DNM3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.002574e-01	ci left: 3.319542e-02	ci right 4.067746e-02	k: 368	n:10000
Cons ci ratio: 3.313660e-01	ci left: 1.151417e-02	ci right 1.617538e-02	k: 137	n:10000
KS ci ratio: 8.458342e-02	ci left: 1.692694e-01	ci right 1.843194e-01	k: 1767	n:10000
DNM3   10000 perm   2 sec   (5106 perm/sec)   p_kst 1.767000e-01   p_cons 1.370000e-02   p_joint 3.680000e-02

Joint ci ratio: 5.478665e-02	ci left: 1.981862e-01	ci right 2.094001e-01	k: 4075	n:20000
Cons ci ratio: 2.249930e-01	ci left: 1.326674e-02	ci right 1.667640e-02	k: 298	n:20000
KS ci ratio: 5.939252e-02	ci left: 1.735114e-01	ci right 1.841821e-01	k: 3576	n:20000
DNM3   20000 perm   5 sec   (4421 perm/sec)   p_kst 1.788000e-01   p_cons 1.490000e-02   p_joint 2.037500e-01

Joint ci ratio: 3.450533e-02	ci left: 2.955801e-01	ci right 3.059918e-01	k: 9023	n:30000
Cons ci ratio: 1.799757e-01	ci left: 1.416440e-02	ci right 1.699721e-02	k: 466	n:30000
KS ci ratio: 4.871251e-02	ci left: 1.731910e-01	ci right 1.818715e-01	k: 5325	n:30000
DNM3   30000 perm   7 sec   (4331 perm/sec)   p_kst 1.775000e-01   p_cons 1.553333e-02   p_joint 3.007667e-01

Joint ci ratio: 2.628863e-02	ci left: 3.525520e-01	ci right 3.619687e-01	k: 14290	n:40000
Cons ci ratio: 1.577622e-01	ci left: 1.399978e-02	ci right 1.642135e-02	k: 607	n:40000
KS ci ratio: 4.209751e-02	ci left: 1.743864e-01	ci right 1.819104e-01	k: 7125	n:40000
DNM3   40000 perm   10 sec   (4185 perm/sec)   p_kst 1.781250e-01   p_cons 1.517500e-02   p_joint 3.572500e-01

Joint ci ratio: 3.090643e-02	ci left: 2.396435e-01	ci right 2.471863e-01	k: 12170	n:50000
Cons ci ratio: 1.408252e-01	ci left: 1.418442e-02	ci right 1.635239e-02	k: 762	n:50000
KS ci ratio: 3.771633e-02	ci left: 1.742986e-01	ci right 1.810188e-01	k: 8882	n:50000
DNM3   50000 perm   12 sec   (4013 perm/sec)   p_kst 1.776400e-01   p_cons 1.524000e-02   p_joint 2.434000e-01

Joint ci ratio: 2.880850e-02	ci left: 2.324079e-01	ci right 2.392177e-01	k: 14148	n:60000
Cons ci ratio: 1.283847e-01	ci left: 1.431689e-02	ci right 1.629706e-02	k: 917	n:60000
KS ci ratio: 3.436082e-02	ci left: 1.751784e-01	ci right 1.813195e-01	k: 10694	n:60000
DNM3   60000 perm   15 sec   (3950 perm/sec)   p_kst 1.782333e-01   p_cons 1.528333e-02   p_joint 2.358000e-01

Joint ci ratio: 2.402587e-02	ci left: 2.721926e-01	ci right 2.788260e-01	k: 19285	n:70000
Cons ci ratio: 1.193146e-01	ci left: 1.427892e-02	ci right 1.610445e-02	k: 1062	n:70000
KS ci ratio: 3.174927e-02	ci left: 1.759818e-01	ci right 1.816734e-01	k: 12517	n:70000
DNM3   70000 perm   18 sec   (3889 perm/sec)   p_kst 1.788143e-01   p_cons 1.517143e-02   p_joint 2.755000e-01

Joint ci ratio: 2.593653e-02	ci left: 2.192236e-01	ci right 2.249966e-01	k: 17768	n:80000
Cons ci ratio: 1.120713e-01	ci left: 1.421769e-02	ci right 1.591774e-02	k: 1204	n:80000
KS ci ratio: 2.972187e-02	ci left: 1.759389e-01	ci right 1.812594e-01	k: 14287	n:80000
DNM3   80000 perm   21 sec   (3841 perm/sec)   p_kst 1.785875e-01   p_cons 1.505000e-02   p_joint 2.221000e-01

Joint ci ratio: 2.592994e-02	ci left: 1.998786e-01	ci right 2.051406e-01	k: 18225	n:90000
Cons ci ratio: 1.056075e-01	ci left: 1.428091e-02	ci right 1.588390e-02	k: 1356	n:90000
KS ci ratio: 2.806245e-02	ci left: 1.756716e-01	ci right 1.806825e-01	k: 16035	n:90000
DNM3   90000 perm   24 sec   (3789 perm/sec)   p_kst 1.781667e-01   p_cons 1.506667e-02   p_joint 2.025000e-01

Joint ci ratio: 1.605674e-02	ci left: 3.704307e-01	ci right 3.764367e-01	k: 37343	n:100000
Cons ci ratio: 1.006561e-01	ci left: 1.418745e-02	ci right 1.570087e-02	k: 1493	n:100000
KS ci ratio: 2.660584e-02	ci left: 1.759817e-01	ci right 1.807369e-01	k: 17835	n:100000
DNM3   100000 perm   27 sec   (3735 perm/sec)   p_kst 1.783500e-01   p_cons 1.493000e-02   p_joint 3.734300e-01

Joint ci ratio: 1.532748e-02	ci left: 3.700230e-01	ci right 3.757474e-01	k: 41017	n:110000
Cons ci ratio: 9.551268e-02	ci left: 1.436096e-02	ci right 1.581023e-02	k: 1658	n:110000
KS ci ratio: 2.539809e-02	ci left: 1.757435e-01	ci right 1.802735e-01	k: 19580	n:110000
DNM3   110000 perm   30 sec   (3675 perm/sec)   p_kst 1.780000e-01   p_cons 1.507273e-02   p_joint 3.728818e-01

Outputting figure to mutsig2_images.part000000000052/DNM3.2_2676_110000_0.178_0.015073_0.37288.png
                gene_name: DNM3
               theta_stop: 0.096 
                    nperm: 110000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.015 
      ci_cons_bounds_left: 0.014 
     ci_cons_bounds_right: 0.016 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.37 
    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.165.3896/
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/181708/iteration1/scatter.0000000052
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 52 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119791: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000053> was used as the working directory.
Started at Wed Oct 10 10:42:38 2012
Results reported at Wed Oct 10 10:44:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000053.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000053.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 53  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    139.21 sec.
    Max Memory :      1324 MB
    Max Swap   :      3831 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.165.3896/
-whichjob
53
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 53: processing genes 4705 - 4795
Calculating significance of each gene.
Using projection method.
4705	DRD2	1
4706	DRD3	1
4707	DRD4	1
4708	DRD5	1
4709	DRG1	1
4710	DRG2	1.398951e-01
4711	DRGX	1
4712	DRP2	4.995347e-02
4713	DSC1	1
4714	DSC2	1
4715	DSC3	1.235181e-01
4716	DSCAM	5.349685e-02
4717	DSCAML1	4.714211e-01
4718	DSCC1	1
4719	DSCR3	1
4720	DSCR4	1
4721	DSCR6	1
4722	DSE	1
4723	DSEL	1
4724	DSG1	1
4725	DSG2	3.331641e-01
4726	DSG3	1
4727	DSG4	2.745000e-01
4728	DSN1	1
4729	DSP	9.900971e-02
4730	DSPP	2.493893e-01
4731	DST	9.307003e-01
4732	DSTN	1
4733	DSTYK	1
4734	DTD1	1
4735	DTL	1
4736	DTNA	1.492053e-01
4737	DTNB	1
4738	DTNBP1	1
4739	DTWD1	1
4740	DTWD2	1
4741	DTX1	1
4742	DTX2	1
4743	DTX3	1.607871e-01
4744	DTX3L	1
4745	DTX4	1
4746	DTYMK	1
4747	DULLARD	1
4748	DUOX1	1
4749	DUOX2	3.652760e-01
4750	DUOXA1	1
4751	DUOXA2	1
4752	DUPD1	4.099030e-02
4753	DUS1L	1
4754	DUS2L	1
4755	DUS3L	1
4756	DUS4L	1
4757	DUSP1	1
4758	DUSP10	7.394464e-02
4759	DUSP11	1
4760	DUSP12	1
4761	DUSP13	1
4762	DUSP14	5.022371e-02
4763	DUSP15	1
4764	DUSP16	1
4765	DUSP18	1
4766	DUSP19	1
4767	DUSP2	1
4768	DUSP21	1
4769	DUSP22	1
4770	DUSP23	1
4771	DUSP26	1
4772	DUSP27	1
4773	DUSP28	1
4774	DUSP3	1
4775	DUSP4	1
4776	DUSP5	1
4777	DUSP6	1.761955e-01
4778	DUSP7	1
4779	DUSP8	7.810073e-02
4780	DUSP9	1
4781	DUT	1
4782	DUXA	1
4783	DVL1	1
4784	DVL2	1
4785	DVL3	1
4786	DYDC1	1
4787	DYDC2	1
4788	DYM	1
4789	DYNC1H1	7.364488e-01
4790	DYNC1I1	1
4791	DYNC1I2	1
4792	DYNC1LI1	1
4793	DYNC1LI2	1
4794	DYNC2H1	6.083864e-01
4795	DYNC2LI1	1
Done

Running MutSig 2:
Scatter job 53: processing genes 4705 - 4795
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
DSP
Processing conservation and coverage...
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: 2.195589e-02	ci left: 7.527183e-01	ci right 7.695293e-01	k: 7612	n:10000
KS ci ratio: 2.145532e-01	ci left: 2.882687e-02	ci right 3.584904e-02	k: 322	n:10000
DSP   10000 perm   3 sec   (3724 perm/sec)   p_kst 3.220000e-02   p_cons 7.612000e-01   p_joint 8.480000e-02

Joint ci ratio: 8.262725e-02	ci left: 9.695524e-02	ci right 1.053611e-01	k: 2022	n:20000
Cons ci ratio: 1.533515e-02	ci left: 7.597161e-01	ci right 7.715066e-01	k: 15313	n:20000
KS ci ratio: 1.479695e-01	ci left: 3.138665e-02	ci right 3.645004e-02	k: 677	n:20000
DSP   20000 perm   9 sec   (2277 perm/sec)   p_kst 3.385000e-02   p_cons 7.656500e-01   p_joint 1.011000e-01

Joint ci ratio: 6.989320e-02	ci left: 9.157345e-02	ci right 9.823857e-02	k: 2846	n:30000
Cons ci ratio: 1.254029e-02	ci left: 7.602606e-01	ci right 7.698880e-01	k: 22953	n:30000
KS ci ratio: 1.200861e-01	ci left: 3.223670e-02	ci right 3.638746e-02	k: 1028	n:30000
DSP   30000 perm   12 sec   (2475 perm/sec)   p_kst 3.426667e-02   p_cons 7.651000e-01   p_joint 9.486667e-02

Joint ci ratio: 7.182732e-02	ci left: 6.680545e-02	ci right 7.180729e-02	k: 2771	n:40000
Cons ci ratio: 1.085341e-02	ci left: 7.611402e-01	ci right 7.694712e-01	k: 30613	n:40000
KS ci ratio: 1.034914e-01	ci left: 3.283029e-02	ci right 3.643768e-02	k: 1384	n:40000
DSP   40000 perm   15 sec   (2582 perm/sec)   p_kst 3.460000e-02   p_cons 7.653250e-01   p_joint 6.927500e-02

Joint ci ratio: 5.814760e-02	ci left: 8.089210e-02	ci right 8.575640e-02	k: 4165	n:50000
Cons ci ratio: 9.670967e-03	ci left: 7.629474e-01	ci right 7.703816e-01	k: 38334	n:50000
KS ci ratio: 9.330092e-02	ci left: 3.250678e-02	ci right 3.570761e-02	k: 1704	n:50000
DSP   50000 perm   19 sec   (2654 perm/sec)   p_kst 3.408000e-02   p_cons 7.666800e-01   p_joint 8.330000e-02

Outputting figure to mutsig2_images.part000000000053/DSP.4_8712_50000_0.03408_0.76668_0.0833.png
                gene_name: DSP
               theta_stop: 0.093 
                    nperm: 50000 
                     p_ks: 0.034 
        ci_ks_bounds_left: 0.033 
       ci_ks_bounds_right: 0.036 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.083 
     ci_joint_bounds_left: 0.081 
    ci_joint_bounds_right: 0.086 

Current progress: 25 percent done.
DSCAM
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: 2.275845e-02	ci left: 7.392680e-01	ci right 7.563874e-01	k: 7479	n:10000
KS ci ratio: 1.029041e-02	ci left: 9.306108e-01	ci right 9.403336e-01	k: 9356	n:10000
DSCAM   10000 perm   3 sec   (3961 perm/sec)   p_kst 9.356000e-01   p_cons 7.479000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000053/DSCAM.3_6171_10000_0.9356_0.7479_1.png
                gene_name: DSCAM
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   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: 50 percent done.
DRG2
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: 1.014049e-01	ci left: 1.233692e-01	ci right 1.366472e-01	k: 1299	n:10000
KS ci ratio: 8.686029e-02	ci left: 1.618004e-01	ci right 1.765928e-01	k: 1691	n:10000
DRG2   10000 perm   2 sec   (5970 perm/sec)   p_kst 1.691000e-01   p_cons 1.299000e-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: 7.178468e-02	ci left: 1.250728e-01	ci right 1.344351e-01	k: 2594	n:20000
KS ci ratio: 6.169491e-02	ci left: 1.627434e-01	ci right 1.731534e-01	k: 3358	n:20000
DRG2   20000 perm   4 sec   (5256 perm/sec)   p_kst 1.679000e-01   p_cons 1.297000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000053/DRG2.2_1147_20000_0.1679_0.1297_1.png
                gene_name: DRG2
               theta_stop: 0.072 
                    nperm: 20000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.13 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
DRP2
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: 2.392387e-02	ci left: 7.197687e-01	ci right 7.372980e-01	k: 7286	n:10000
KS ci ratio: 2.483886e-02	ci left: 7.045272e-01	ci right 7.223483e-01	k: 7135	n:10000
DRP2   10000 perm   2 sec   (5351 perm/sec)   p_kst 7.135000e-01   p_cons 7.286000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000053/DRP2.2_2962_10000_0.7135_0.7286_1.png
                gene_name: DRP2
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.74 
                  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.165.3896/
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/181708/iteration1/scatter.0000000053
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 53 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1708>
Subject: Job 1119795: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, 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/181708/iteration1/scatter.0000000054> was used as the working directory.
Started at Wed Oct 10 10:42:38 2012
Results reported at Wed Oct 10 10:44:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000054.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000054.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 54  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    128.90 sec.
    Max Memory :       951 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.165.3896/
-whichjob
54
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 54: processing genes 4796 - 4885
Calculating significance of each gene.
Using projection method.
4796	DYNLL1	1
4797	DYNLL2	1
4798	DYNLRB1	1
4799	DYNLRB2	1
4800	DYNLT1	1
4801	DYNLT3	1
4802	DYRK1A	2.595935e-01
4803	DYRK1B	1
4804	DYRK2	1.632632e-01
4805	DYRK3	1
4806	DYRK4	1.151261e-01
4807	DYSF	3.784669e-01
4808	DYSFIP1	1
4809	DYTN	1
4810	DYX1C1	1
4811	DZIP1	1
4812	DZIP1L	1
4813	DZIP3	1
4814	E2F1	1
4815	E2F2	7.182631e-02
4816	E2F3	1
4817	E2F4	1
4818	E2F5	1
4819	E2F6	1
4820	E2F7	1
4821	E2F8	1
4822	E4F1	1
4823	EAF1	1.067324e-01
4824	EAF2	1
4825	EAPP	5.508197e-02
4826	EARS2	2.449314e-01
4827	EBAG9	1
4828	EBF1	1
4829	EBF2	1
4830	EBF3	1
4831	EBI3	3.610768e-02
4832	EBLN2	1
4833	EBNA1BP2	1
4834	EBP	1
4835	EBPL	2.011156e-02
4836	ECD	1.154506e-01
4837	ECE1	1
4838	ECE2	1
4839	ECEL1	1
4840	ECH1	1
4841	ECHDC1	1
4842	ECHDC2	1
4843	ECHDC3	1
4844	ECHS1	1
4845	ECM1	1
4846	ECM2	2.096890e-01
4847	ECSCR	1
4848	ECSIT	1.446912e-01
4849	ECT2	1
4850	ECT2L	1
4851	EDA	1
4852	EDA2R	1
4853	EDAR	1
4854	EDARADD	1
4855	EDC3	1
4856	EDC4	1.274349e-02
4857	EDDM3A	1
4858	EDDM3B	1
4859	EDEM1	1.119223e-02
4860	EDEM2	1
4861	EDEM3	1
4862	EDF1	1
4863	EDIL3	1
4864	EDN1	1
4865	EDN2	1
4866	EDN3	1
4867	EDNRA	1
4868	EDNRB	1
4869	EEA1	1
4870	EED	1
4871	EEF1A1	1
4872	EEF1A2	1
4873	EEF1B2	1
4874	EEF1D	1
4875	EEF1E1	1
4876	EEF1G	1.769252e-01
4877	EEF2	2.062065e-01
4878	EEF2K	1
4879	EEFSEC	1
4880	EEPD1	1
4881	EFCAB1	8.080901e-02
4882	EFCAB2	1
4883	EFCAB3	1
4884	EFCAB4A	1
4885	EFCAB4B	1
Done

Running MutSig 2:
Scatter job 54: processing genes 4796 - 4885
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
EDC4
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: 2.750894e-02	ci left: 6.606855e-01	ci right 6.792154e-01	k: 6700	n:10000
KS ci ratio: 1.669465e-02	ci left: 8.392842e-01	ci right 8.535134e-01	k: 8465	n:10000
EDC4   10000 perm   2 sec   (4766 perm/sec)   p_kst 8.465000e-01   p_cons 6.700000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000054/EDC4.3_4322_10000_0.8465_0.67_1.png
                gene_name: EDC4
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.85 
        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: 0.68 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 25 percent done.
EDEM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.592830e-02	ci left: 5.335757e-01	ci right 5.531990e-01	k: 5434	n:10000
Cons ci ratio: 2.702516e-02	ci left: 6.685399e-01	ci right 6.869564e-01	k: 6778	n:10000
KS ci ratio: 4.558764e-02	ci left: 4.152841e-01	ci right 4.347596e-01	k: 4250	n:10000
EDEM1   10000 perm   2 sec   (5516 perm/sec)   p_kst 4.250000e-01   p_cons 6.778000e-01   p_joint 5.434000e-01

Outputting figure to mutsig2_images.part000000000054/EDEM1.3_2022_10000_0.425_0.6778_0.5434.png
                gene_name: EDEM1
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 50 percent done.
EAPP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.351584e-02	ci left: 8.875964e-01	ci right 8.997732e-01	k: 8938	n:10000
Cons ci ratio: 1.016190e-02	ci left: 9.321629e-01	ci right 9.417806e-01	k: 9371	n:10000
KS ci ratio: 7.911566e-02	ci left: 1.892437e-01	ci right 2.049332e-01	k: 1970	n:10000
EAPP   10000 perm   1 sec   (7007 perm/sec)   p_kst 1.970000e-01   p_cons 9.371000e-01   p_joint 8.938000e-01

Outputting figure to mutsig2_images.part000000000054/EAPP.2_882_10000_0.197_0.9371_0.8938.png
                gene_name: EAPP
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.89 
     ci_joint_bounds_left: 0.89 
    ci_joint_bounds_right: 0.90 

Current progress: 75 percent done.
ECE2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.092113e-02	ci left: 2.837935e-01	ci right 3.017273e-01	k: 2927	n:10000
Cons ci ratio: 8.889150e-02	ci left: 1.555149e-01	ci right 1.700821e-01	k: 1627	n:10000
KS ci ratio: 3.659211e-02	ci left: 5.244645e-01	ci right 5.441155e-01	k: 5343	n:10000
ECE2   10000 perm   2 sec   (5489 perm/sec)   p_kst 5.343000e-01   p_cons 1.627000e-01   p_joint 2.927000e-01

Outputting figure to mutsig2_images.part000000000054/ECE2.2_3292_10000_0.5343_0.1627_0.2927.png
                gene_name: ECE2
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  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.165.3896/
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/181708/iteration1/scatter.0000000054
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 54 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119800: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000055> was used as the working directory.
Started at Wed Oct 10 10:42:49 2012
Results reported at Wed Oct 10 10:44:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000055.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000055.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 55  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     74.83 sec.
    Max Memory :      1153 MB
    Max Swap   :      3895 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.165.3896/
-whichjob
55
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 55: processing genes 4886 - 4976
Calculating significance of each gene.
Using projection method.
4886	EFCAB5	6.384003e-02
4887	EFCAB6	2.427873e-01
4888	EFCAB7	1
4889	EFEMP1	1
4890	EFEMP2	1
4891	EFHA1	1
4892	EFHA2	1
4893	EFHB	2.032545e-01
4894	EFHC1	1
4895	EFHC2	8.167301e-02
4896	EFHD1	1
4897	EFHD2	1
4898	EFNA1	1
4899	EFNA2	1
4900	EFNA3	1
4901	EFNA4	1
4902	EFNA5	1
4903	EFNB1	1
4904	EFNB2	1
4905	EFNB3	1.255549e-01
4906	EFR3A	1
4907	EFS	1
4908	EFTUD1	1
4909	EFTUD2	1.344097e-01
4910	EGF	3.542916e-01
4911	EGFL6	1
4912	EGFL7	3.790432e-02
4913	EGFL8	1
4914	EGFLAM	3.100758e-01
4915	EGFR	1
4916	EGLN1	1
4917	EGLN2	1
4918	EGLN3	1
4919	EGR1	1
4920	EGR2	1
4921	EGR3	1.778289e-01
4922	EGR4	1
4923	EHBP1	1
4924	EHBP1L1	1
4925	EHD1	1
4926	EHD2	1
4927	EHD3	1
4928	EHD4	1.506558e-01
4929	EHF	1
4930	EHHADH	1
4931	EHMT1	2.977353e-01
4932	EHMT2	1
4933	EI24	1
4934	EID1	1
4935	EID2	1
4936	EID2B	5.742242e-02
4937	EID3	1
4938	EIF1	1
4939	EIF1AD	1
4940	EIF1AX	1
4941	EIF1AY	1
4942	EIF1B	1
4943	EIF2A	1
4944	EIF2AK1	1
4945	EIF2AK2	1
4946	EIF2AK3	2.819985e-01
4947	EIF2AK4	1
4948	EIF2B1	2.082835e-02
4949	EIF2B2	1
4950	EIF2B3	1
4951	EIF2B4	1
4952	EIF2B5	1.541210e-01
4953	EIF2C1	2.752155e-01
4954	EIF2C2	1
4955	EIF2C3	1
4956	EIF2C4	1
4957	EIF2S1	1
4958	EIF2S2	1
4959	EIF2S3	1
4960	EIF3A	4.056095e-02
4961	EIF3B	1
4962	EIF3D	1
4963	EIF3E	1
4964	EIF3F	1
4965	EIF3G	1
4966	EIF3H	1
4967	EIF3I	7.275556e-03
4968	EIF3J	1
4969	EIF3K	1
4970	EIF3L	2.762865e-01
4971	EIF3M	1.498520e-01
4972	EIF4A1	1
4973	EIF4A2	2.916957e-02
4974	EIF4A3	1.405605e-02
4975	EIF4B	1
4976	EIF4E	1
Done

Running MutSig 2:
Scatter job 55: processing genes 4886 - 4976
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
EIF3A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.981796e-02	ci left: 3.727610e-01	ci right 3.919076e-01	k: 3823	n:10000
Cons ci ratio: 7.786312e-02	ci left: 1.942671e-01	ci right 2.101068e-01	k: 2021	n:10000
KS ci ratio: 7.176357e-02	ci left: 2.214853e-01	ci right 2.380724e-01	k: 2297	n:10000
EIF3A   10000 perm   2 sec   (5074 perm/sec)   p_kst 2.297000e-01   p_cons 2.021000e-01   p_joint 3.823000e-01

Outputting figure to mutsig2_images.part000000000055/EIF3A.3_4237_10000_0.2297_0.2021_0.3823.png
                gene_name: EIF3A
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 25 percent done.
EFCAB5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.536816e-02	ci left: 6.957512e-01	ci right 7.137293e-01	k: 7048	n:10000
Cons ci ratio: 6.820443e-02	ci left: 2.397579e-01	ci right 2.567890e-01	k: 2482	n:10000
KS ci ratio: 3.953258e-02	ci left: 4.858530e-01	ci right 5.055495e-01	k: 4957	n:10000
EFCAB5   10000 perm   2 sec   (5222 perm/sec)   p_kst 4.957000e-01   p_cons 2.482000e-01   p_joint 7.048000e-01

Outputting figure to mutsig2_images.part000000000055/EFCAB5.2_4771_10000_0.4957_0.2482_0.7048.png
                gene_name: EFCAB5
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.70 
     ci_joint_bounds_left: 0.70 
    ci_joint_bounds_right: 0.71 

Current progress: 50 percent done.
EIF3I
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: 2.739085e-02	ci left: 6.625985e-01	ci right 6.811013e-01	k: 6719	n:10000
KS ci ratio: 5.377486e-02	ci left: 3.375666e-01	ci right 3.563226e-01	k: 3469	n:10000
EIF3I   10000 perm   1 sec   (6731 perm/sec)   p_kst 3.469000e-01   p_cons 6.719000e-01   p_joint 9.132000e-01

Outputting figure to mutsig2_images.part000000000055/EIF3I.2_1022_10000_0.3469_0.6719_0.9132.png
                gene_name: EIF3I
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.34 
       ci_ks_bounds_right: 0.36 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 75 percent done.
EIF4A3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.363646e-02	ci left: 8.858546e-01	ci right 8.981160e-01	k: 8921	n:10000
Cons ci ratio: 2.245679e-02	ci left: 7.443233e-01	ci right 7.613292e-01	k: 7529	n:10000
KS ci ratio: 1.207744e-01	ci left: 8.951617e-02	ci right 1.011208e-01	k: 952	n:10000
EIF4A3   10000 perm   1 sec   (7049 perm/sec)   p_kst 9.520000e-02   p_cons 7.529000e-01   p_joint 8.921000e-01

Joint ci ratio: 1.850269e-02	ci left: 6.852978e-01	ci right 6.981464e-01	k: 13835	n:20000
Cons ci ratio: 1.592853e-02	ci left: 7.457016e-01	ci right 7.577251e-01	k: 15035	n:20000
KS ci ratio: 8.530316e-02	ci left: 9.141174e-02	ci right 9.960629e-02	k: 1909	n:20000
EIF4A3   20000 perm   3 sec   (6143 perm/sec)   p_kst 9.545000e-02   p_cons 7.517500e-01   p_joint 6.917500e-01

Outputting figure to mutsig2_images.part000000000055/EIF4A3.2_1284_20000_0.09545_0.75175_0.69175.png
                gene_name: EIF4A3
               theta_stop: 0.085 
                    nperm: 20000 
                     p_ks: 0.095 
        ci_ks_bounds_left: 0.091 
       ci_ks_bounds_right: 0.100 
                   p_cons: 0.75 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.76 
                  p_joint: 0.69 
     ci_joint_bounds_left: 0.69 
    ci_joint_bounds_right: 0.70 

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.165.3896/
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/181708/iteration1/scatter.0000000055
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 55 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119806: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000056> was used as the working directory.
Started at Wed Oct 10 10:42:49 2012
Results reported at Wed Oct 10 10:44:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000056.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000056.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 56  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     85.21 sec.
    Max Memory :      1233 MB
    Max Swap   :      3893 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.165.3896/
-whichjob
56
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 56: processing genes 4977 - 5066
Calculating significance of each gene.
Using projection method.
4977	EIF4E1B	1
4978	EIF4E2	1
4979	EIF4E3	1
4980	EIF4EBP1	2.486296e-02
4981	EIF4EBP2	1
4982	EIF4EBP3	1
4983	EIF4ENIF1	1.738556e-01
4984	EIF4G1	1
4985	EIF4G2	1
4986	EIF4G3	8.995498e-02
4987	EIF4H	1
4988	EIF5	1
4989	EIF5A	1.106180e-02
4990	EIF5A2	1
4991	EIF5AL1	1
4992	EIF5B	1
4993	EIF6	1
4994	ELAC1	1
4995	ELAC2	1
4996	ELANE	1
4997	ELAVL1	1
4998	ELAVL2	1.469688e-01
4999	ELAVL3	1
5000/18094 5000	ELAVL4	1
5001	ELF1	1.916966e-02
5002	ELF2	1
5003	ELF3	2.014557e-04
5004	ELF4	1
5005	ELF5	1
5006	ELFN2	1
5007	ELK1	1
5008	ELK3	1
5009	ELK4	1
5010	ELL	1
5011	ELL2	1
5012	ELL3	1
5013	ELMO1	1
5014	ELMO2	1.001017e-01
5015	ELMO3	1
5016	ELMOD1	1
5017	ELMOD2	1
5018	ELMOD3	1
5019	ELN	1
5020	ELOF1	1
5021	ELOVL1	1
5022	ELOVL2	1
5023	ELOVL3	1
5024	ELOVL4	1
5025	ELOVL5	1
5026	ELOVL6	1
5027	ELOVL7	1
5028	ELP2	7.784058e-02
5029	ELP3	1
5030	ELP4	1
5031	ELSPBP1	1
5032	ELTD1	1
5033	EMB	1
5034	EMCN	1
5035	EMD	1
5036	EME1	1
5037	EME2	1
5038	EMG1	1
5039	EMID1	1
5040	EMID2	1
5041	EMILIN1	1
5042	EMILIN2	3.583835e-01
5043	EMILIN3	1.728412e-02
5044	EML1	1.431323e-01
5045	EML2	1.818951e-01
5046	EML3	1
5047	EML4	1
5048	EML5	4.843725e-01
5049	EMP1	1
5050	EMP2	1
5051	EMP3	1
5052	EMR1	1
5053	EMR2	1
5054	EMR3	1
5055	EMX1	1
5056	EMX2	1
5057	EN1	1
5058	EN2	1
5059	ENAH	1
5060	ENAM	1
5061	ENC1	1
5062	ENDOD1	1
5063	ENDOG	1
5064	ENDOU	1
5065	ENG	1
5066	ENGASE	1
Done

Running MutSig 2:
Scatter job 56: processing genes 4977 - 5066
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
EIF4G2
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: 1.556815e-02	ci left: 8.569213e-01	ci right 8.704660e-01	k: 8638	n:10000
KS ci ratio: 2.892703e-02	ci left: 6.379438e-01	ci right 6.567703e-01	k: 6474	n:10000
EIF4G2   10000 perm   2 sec   (5519 perm/sec)   p_kst 6.474000e-01   p_cons 8.638000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000056/EIF4G2.4_2808_10000_0.6474_0.8638_1.png
                gene_name: EIF4G2
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.86 
      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: 20 percent done.
ELF3
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: 4.190533e-02	ci left: 4.567830e-01	ci right 4.764365e-01	k: 4666	n:10000
KS ci ratio: 4.411732e-02	ci left: 4.313368e-01	ci right 4.508976e-01	k: 4411	n:10000
ELF3   10000 perm   2 sec   (6393 perm/sec)   p_kst 4.411000e-01   p_cons 4.666000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000056/ELF3.3_1148_10000_0.4411_0.4666_1.png
                gene_name: ELF3
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.47 
      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: 40 percent done.
EIF4G3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.824276e-02	ci left: 8.143595e-01	ci right 8.294525e-01	k: 8220	n:10000
Cons ci ratio: 2.653771e-02	ci left: 6.764980e-01	ci right 6.947937e-01	k: 6857	n:10000
KS ci ratio: 1.456935e-01	ci left: 6.256264e-02	ci right 7.249110e-02	k: 674	n:10000
EIF4G3   10000 perm   2 sec   (5080 perm/sec)   p_kst 6.740000e-02   p_cons 6.857000e-01   p_joint 8.220000e-01

Joint ci ratio: 4.605603e-02	ci left: 2.597367e-01	ci right 2.720315e-01	k: 5317	n:20000
Cons ci ratio: 1.947667e-02	ci left: 6.628813e-01	ci right 6.759694e-01	k: 13389	n:20000
KS ci ratio: 1.028597e-01	ci left: 6.420742e-02	ci right 7.121890e-02	k: 1353	n:20000
EIF4G3   20000 perm   4 sec   (4568 perm/sec)   p_kst 6.765000e-02   p_cons 6.694500e-01   p_joint 2.658500e-01

Joint ci ratio: 1.072102e-02	ci left: 8.123081e-01	ci right 8.210971e-01	k: 24502	n:30000
Cons ci ratio: 1.591301e-02	ci left: 6.638096e-01	ci right 6.744910e-01	k: 20075	n:30000
KS ci ratio: 8.380829e-02	ci left: 6.511118e-02	ci right 7.083950e-02	k: 2038	n:30000
EIF4G3   30000 perm   7 sec   (4366 perm/sec)   p_kst 6.793333e-02   p_cons 6.691667e-01   p_joint 8.167333e-01

Outputting figure to mutsig2_images.part000000000056/EIF4G3.2_4878_30000_0.067933_0.66917_0.81673.png
                gene_name: EIF4G3
               theta_stop: 0.084 
                    nperm: 30000 
                     p_ks: 0.068 
        ci_ks_bounds_left: 0.065 
       ci_ks_bounds_right: 0.071 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.67 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.82 

Current progress: 60 percent done.
ELF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.586275e-02	ci left: 6.875840e-01	ci right 7.057013e-01	k: 6967	n:10000
Cons ci ratio: 8.181399e-02	ci left: 1.790063e-01	ci right 1.943767e-01	k: 1866	n:10000
KS ci ratio: 2.766457e-02	ci left: 6.581687e-01	ci right 6.767337e-01	k: 6675	n:10000
ELF1   10000 perm   2 sec   (6188 perm/sec)   p_kst 6.675000e-01   p_cons 1.866000e-01   p_joint 6.967000e-01

Outputting figure to mutsig2_images.part000000000056/ELF1.2_1892_10000_0.6675_0.1866_0.6967.png
                gene_name: ELF1
               theta_stop: 0.082 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.68 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.70 
     ci_joint_bounds_left: 0.69 
    ci_joint_bounds_right: 0.71 

Current progress: 80 percent done.
EMILIN3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.181399e-02	ci left: 1.790063e-01	ci right 1.943767e-01	k: 1866	n:10000
Cons ci ratio: 1.096588e-01	ci left: 1.070534e-01	ci right 1.195729e-01	k: 1132	n:10000
KS ci ratio: 2.296359e-02	ci left: 7.358313e-01	ci right 7.530260e-01	k: 7445	n:10000
EMILIN3   10000 perm   2 sec   (6065 perm/sec)   p_kst 7.445000e-01   p_cons 1.132000e-01   p_joint 1.866000e-01

Joint ci ratio: 6.824597e-02	ci left: 1.367463e-01	ci right 1.464582e-01	k: 2831	n:20000
Cons ci ratio: 7.872215e-02	ci left: 1.059412e-01	ci right 1.146724e-01	k: 2205	n:20000
KS ci ratio: 1.618028e-02	ci left: 7.397556e-01	ci right 7.518729e-01	k: 14917	n:20000
EMILIN3   20000 perm   4 sec   (5362 perm/sec)   p_kst 7.458500e-01   p_cons 1.102500e-01   p_joint 1.415500e-01

Outputting figure to mutsig2_images.part000000000056/EMILIN3.2_2317_20000_0.74585_0.11025_0.14155.png
                gene_name: EMILIN3
               theta_stop: 0.079 
                    nperm: 20000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.75 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.14 
     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.165.3896/
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/181708/iteration1/scatter.0000000056
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 56 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119812: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000057> was used as the working directory.
Started at Wed Oct 10 10:42:49 2012
Results reported at Wed Oct 10 10:44:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000057.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000057.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 57  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    144.37 sec.
    Max Memory :      1258 MB
    Max Swap   :      3873 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.165.3896/
-whichjob
57
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 57: processing genes 5067 - 5157
Calculating significance of each gene.
Using projection method.
5067	ENHO	1
5068	ENKUR	1
5069	ENO1	1.347817e-01
5070	ENO2	1
5071	ENO3	1
5072	ENOPH1	1
5073	ENOSF1	1
5074	ENOX1	1
5075	ENOX2	1
5076	ENPEP	3.787437e-01
5077	ENPP1	1
5078	ENPP2	1
5079	ENPP3	1
5080	ENPP4	1
5081	ENPP5	1
5082	ENPP6	1
5083	ENPP7	1
5084	ENSA	1
5085	ENTHD1	1
5086	ENTPD1	1
5087	ENTPD2	1
5088	ENTPD3	1
5089	ENTPD4	1
5090	ENTPD5	1
5091	ENTPD6	1
5092	ENTPD7	1
5093	ENTPD8	1
5094	ENY2	1
5095	EOMES	1
5096	EP300	8.519932e-02
5097	EP400	1
5098	EPAS1	3.090861e-01
5099	EPB41	3.113016e-01
5100	EPB41L1	6.267057e-03
5101	EPB41L2	1
5102	EPB41L3	4.353240e-01
5103	EPB41L4A	1
5104	EPB41L4B	2.919020e-01
5105	EPB41L5	1
5106	EPB42	1
5107	EPB49	8.316909e-02
5108	EPC1	1.504566e-01
5109	EPC2	1
5110	EPCAM	1
5111	EPDR1	1.064335e-01
5112	EPGN	1
5113	EPHA1	8.196197e-02
5114	EPHA10	1
5115	EPHA2	2.150445e-01
5116	EPHA3	1
5117	EPHA4	1
5118	EPHA5	1
5119	EPHA6	1
5120	EPHA7	2.774686e-01
5121	EPHA8	3.176190e-01
5122	EPHB1	1
5123	EPHB2	3.103074e-01
5124	EPHB3	2.551618e-01
5125	EPHB4	1
5126	EPHB6	1
5127	EPHX1	1
5128	EPHX2	2.112739e-01
5129	EPHX3	1
5130	EPHX4	1
5131	EPM2A	1
5132	EPM2AIP1	1
5133	EPN1	1
5134	EPN2	7.181578e-02
5135	EPN3	2.173782e-01
5136	EPO	1
5137	EPOR	4.295409e-02
5138	EPPK1	1
5139	EPRS	2.633516e-02
5140	EPS15	2.681130e-01
5141	EPS15L1	1
5142	EPS8	1.569689e-01
5143	EPS8L1	1
5144	EPS8L2	1
5145	EPS8L3	1
5146	EPSTI1	1
5147	EPT1	1
5148	EPX	1
5149	EPYC	1
5150	ERAL1	1
5151	ERAP1	1
5152	ERAP2	1
5153	ERAS	1
5154	ERBB2	9.769238e-03
5155	ERBB2IP	1
5156	ERBB3	1
5157	ERBB4	2.529417e-01
Done

Running MutSig 2:
Scatter job 57: processing genes 5067 - 5157
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ERBB2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.834238e-02	ci left: 8.127337e-01	ci right 8.278793e-01	k: 8204	n:10000
Cons ci ratio: 5.086757e-02	ci left: 3.630124e-01	ci right 3.820619e-01	k: 3725	n:10000
KS ci ratio: 3.316256e-02	ci left: 5.730625e-01	ci right 5.924892e-01	k: 5828	n:10000
ERBB2   10000 perm   2 sec   (4899 perm/sec)   p_kst 5.828000e-01   p_cons 3.725000e-01   p_joint 8.204000e-01

Outputting figure to mutsig2_images.part000000000057/ERBB2.4_3876_10000_0.5828_0.3725_0.8204.png
                gene_name: ERBB2
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.58 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.59 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.83 

Current progress: 20 percent done.
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: 6.301137e-03	ci left: 9.716422e-01	ci right 9.778770e-01	k: 9749	n:10000
KS ci ratio: 2.509415e-02	ci left: 7.002900e-01	ci right 7.181879e-01	k: 7093	n:10000
EP300   10000 perm   3 sec   (2940 perm/sec)   p_kst 7.093000e-01   p_cons 9.749000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000057/EP300.3_7369_10000_0.7093_0.9749_1.png
                gene_name: EP300
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.97 
      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: 40 percent done.
EPB41L1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.630513e-02	ci left: 2.007708e-01	ci right 2.167992e-01	k: 2087	n:10000
Cons ci ratio: 4.118844e-02	ci left: 4.653707e-01	ci right 4.850438e-01	k: 4752	n:10000
KS ci ratio: 1.072707e-01	ci left: 1.114460e-01	ci right 1.241776e-01	k: 1177	n:10000
EPB41L1   10000 perm   2 sec   (5385 perm/sec)   p_kst 1.177000e-01   p_cons 4.752000e-01   p_joint 2.087000e-01

Joint ci ratio: 6.219628e-02	ci left: 1.605216e-01	ci right 1.708758e-01	k: 3313	n:20000
Cons ci ratio: 2.891467e-02	ci left: 4.719052e-01	ci right 4.858010e-01	k: 9577	n:20000
KS ci ratio: 7.514990e-02	ci left: 1.152317e-01	ci right 1.242791e-01	k: 2394	n:20000
EPB41L1   20000 perm   4 sec   (4874 perm/sec)   p_kst 1.197000e-01   p_cons 4.788500e-01   p_joint 1.656500e-01

Outputting figure to mutsig2_images.part000000000057/EPB41L1.3_2730_20000_0.1197_0.47885_0.16565.png
                gene_name: EPB41L1
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.16 
    ci_joint_bounds_right: 0.17 

Current progress: 60 percent done.
EPHA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.122612e-02	ci left: 1.811711e-01	ci right 1.966105e-01	k: 1888	n:10000
Cons ci ratio: 8.857514e-03	ci left: 9.471062e-01	ci right 9.556284e-01	k: 9515	n:10000
KS ci ratio: 1.799496e-01	ci left: 4.121131e-02	ci right 4.945618e-02	k: 452	n:10000
EPHA1   10000 perm   2 sec   (6010 perm/sec)   p_kst 4.520000e-02   p_cons 9.515000e-01   p_joint 1.888000e-01

Joint ci ratio: 7.123371e-02	ci left: 1.267960e-01	ci right 1.362115e-01	k: 2629	n:20000
Cons ci ratio: 6.321372e-03	ci left: 9.475056e-01	ci right 9.535626e-01	k: 19012	n:20000
KS ci ratio: 1.271729e-01	ci left: 4.245914e-02	ci right 4.827396e-02	k: 906	n:20000
EPHA1   20000 perm   6 sec   (3635 perm/sec)   p_kst 4.530000e-02   p_cons 9.506000e-01   p_joint 1.314500e-01

Joint ci ratio: 5.950708e-02	ci left: 1.225936e-01	ci right 1.301456e-01	k: 3790	n:30000
Cons ci ratio: 5.193546e-03	ci left: 9.474732e-01	ci right 9.524392e-01	k: 28500	n:30000
KS ci ratio: 1.055343e-01	ci left: 4.164178e-02	ci right 4.631372e-02	k: 1318	n:30000
EPHA1   30000 perm   9 sec   (3454 perm/sec)   p_kst 4.393333e-02   p_cons 9.500000e-01   p_joint 1.263333e-01

Joint ci ratio: 5.357883e-02	ci left: 1.148538e-01	ci right 1.212018e-01	k: 4720	n:40000
Cons ci ratio: 4.473735e-03	ci left: 9.483289e-01	ci right 9.526054e-01	k: 38020	n:40000
KS ci ratio: 8.786528e-02	ci left: 4.531355e-02	ci right 4.950247e-02	k: 1895	n:40000
EPHA1   40000 perm   11 sec   (3515 perm/sec)   p_kst 4.737500e-02   p_cons 9.505000e-01   p_joint 1.180000e-01

Outputting figure to mutsig2_images.part000000000057/EPHA1.3_3003_40000_0.047375_0.9505_0.118.png
                gene_name: EPHA1
               theta_stop: 0.088 
                    nperm: 40000 
                     p_ks: 0.047 
        ci_ks_bounds_left: 0.045 
       ci_ks_bounds_right: 0.050 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.12 

Current progress: 80 percent done.
EPRS
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.991251e-02	ci left: 7.868508e-01	ci right 8.027771e-01	k: 7949	n:10000
Cons ci ratio: 3.511073e-02	ci left: 5.449944e-01	ci right 5.645736e-01	k: 5548	n:10000
KS ci ratio: 2.836544e-02	ci left: 6.468968e-01	ci right 6.656121e-01	k: 6563	n:10000
EPRS   10000 perm   2 sec   (4666 perm/sec)   p_kst 6.563000e-01   p_cons 5.548000e-01   p_joint 7.949000e-01

Outputting figure to mutsig2_images.part000000000057/EPRS.3_4667_10000_0.6563_0.5548_0.7949.png
                gene_name: EPRS
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.55 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.79 
    ci_joint_bounds_right: 0.80 

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.165.3896/
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/181708/iteration1/scatter.0000000057
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 57 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119815: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000058> was used as the working directory.
Started at Wed Oct 10 10:42:49 2012
Results reported at Wed Oct 10 10:45:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000058.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000058.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 58  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    151.17 sec.
    Max Memory :      1242 MB
    Max Swap   :      3861 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.165.3896/
-whichjob
58
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 58: processing genes 5158 - 5247
Calculating significance of each gene.
Using projection method.
5158	ERC1	3.963484e-01
5159	ERC2	1.873560e-01
5160	ERCC1	1
5161	ERCC2	1.231620e-04
5162	ERCC3	1
5163	ERCC4	1
5164	ERCC5	2.374906e-01
5165	ERCC6	3.595911e-01
5166	ERCC6L	1
5167	ERCC8	1
5168	EREG	1
5169	ERF	1
5170	ERG	1.989393e-02
5171	ERGIC1	1
5172	ERGIC2	1.555907e-01
5173	ERGIC3	1
5174	ERH	1
5175	ERI1	1
5176	ERI2	1
5177	ERI3	1.567763e-01
5178	ERICH1	1
5179	ERLEC1	2.058815e-01
5180	ERLIN1	1
5181	ERLIN2	1
5182	ERMAP	1
5183	ERMN	1
5184	ERMP1	1
5185	ERN1	1
5186	ERN2	3.986665e-01
5187	ERO1L	1
5188	ERO1LB	1.840558e-01
5189	ERP27	1
5190	ERP29	1
5191	ERP44	1
5192	ERRFI1	1
5193	ERV3	1
5194	ERVFRDE1	1
5195	ESAM	1
5196	ESCO1	1
5197	ESCO2	2.242256e-01
5198	ESD	1
5199	ESF1	1
5200	ESM1	1
5201	ESPL1	2.469429e-01
5202	ESPN	1
5203	ESPNL	1
5204	ESR1	1
5205	ESR2	1
5206	ESRP1	8.005115e-02
5207	ESRP2	1
5208	ESRRA	1
5209	ESRRB	1
5210	ESRRG	4.709251e-02
5211	ESX1	1
5212	ESYT1	1
5213	ESYT2	1
5214	ESYT3	2.582384e-01
5215	ETAA1	3.033717e-01
5216	ETF1	1.342575e-01
5217	ETFA	1
5218	ETFB	1
5219	ETFDH	1
5220	ETHE1	1
5221	ETNK1	1.984835e-01
5222	ETNK2	1
5223	ETS1	1
5224	ETS2	1
5225	ETV1	1
5226	ETV2	1
5227	ETV3	1
5228	ETV3L	1
5229	ETV4	1
5230	ETV5	1
5231	ETV6	5.105266e-02
5232	ETV7	1
5233	EVC	1
5234	EVC2	6.450342e-02
5235	EVI2A	1
5236	EVI2B	3.677815e-02
5237	EVI5	1
5238	EVI5L	1
5239	EVL	6.618296e-03
5240	EVPL	1
5241	EVPLL	1
5242	EVX1	1
5243	EVX2	1
5244	EWSR1	1.870476e-01
5245	EXD1	1
5246	EXD2	1
5247	EXD3	1
Done

Running MutSig 2:
Scatter job 58: processing genes 5158 - 5247
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ERCC2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.056010e-01	ci left: 1.146691e-01	ci right 1.275526e-01	k: 1210	n:10000
Cons ci ratio: 3.325900e-01	ci left: 1.142242e-02	ci right 1.606722e-02	k: 136	n:10000
KS ci ratio: 1.183680e-02	ci left: 9.109059e-01	ci right 9.218501e-01	k: 9165	n:10000
ERCC2   10000 perm   2 sec   (5366 perm/sec)   p_kst 9.165000e-01   p_cons 1.360000e-02   p_joint 1.210000e-01

Joint ci ratio: 3.653300e-02	ci left: 3.586217e-01	ci right 3.720175e-01	k: 7306	n:20000
Cons ci ratio: 1.906485e-01	ci left: 1.872403e-02	ci right 2.271702e-02	k: 413	n:20000
KS ci ratio: 8.468921e-03	ci left: 9.106922e-01	ci right 9.184868e-01	k: 18293	n:20000
ERCC2   20000 perm   6 sec   (3274 perm/sec)   p_kst 9.146500e-01   p_cons 2.065000e-02   p_joint 3.653000e-01

Joint ci ratio: 4.397121e-02	ci left: 2.048074e-01	ci right 2.140489e-01	k: 6282	n:30000
Cons ci ratio: 1.887932e-01	ci left: 1.282815e-02	ci right 1.553381e-02	k: 424	n:30000
KS ci ratio: 6.962257e-03	ci left: 9.103300e-01	ci right 9.167230e-01	k: 27407	n:30000
ERCC2   30000 perm   8 sec   (3573 perm/sec)   p_kst 9.135667e-01   p_cons 1.413333e-02   p_joint 2.094000e-01

Joint ci ratio: 4.303372e-02	ci left: 1.680901e-01	ci right 1.755076e-01	k: 6871	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: 6.025168e-03	ci left: 9.108802e-01	ci right 9.164096e-01	k: 36547	n:40000
ERCC2   40000 perm   11 sec   (3728 perm/sec)   p_kst 9.136750e-01   p_cons 1.362500e-02   p_joint 1.717750e-01

Joint ci ratio: 3.523322e-02	ci left: 1.949319e-01	ci right 2.019431e-01	k: 9921	n:50000
Cons ci ratio: 1.491868e-01	ci left: 1.260310e-02	ci right 1.465395e-02	k: 680	n:50000
KS ci ratio: 5.402453e-03	ci left: 9.107792e-01	ci right 9.157327e-01	k: 45664	n:50000
ERCC2   50000 perm   13 sec   (3803 perm/sec)   p_kst 9.132800e-01   p_cons 1.360000e-02   p_joint 1.984200e-01

Joint ci ratio: 3.252577e-02	ci left: 1.917203e-01	ci right 1.980759e-01	k: 11693	n:60000
Cons ci ratio: 1.368008e-01	ci left: 1.257576e-02	ci right 1.443841e-02	k: 809	n:60000
KS ci ratio: 4.933134e-03	ci left: 9.109526e-01	ci right 9.154740e-01	k: 54794	n:60000
ERCC2   60000 perm   16 sec   (3818 perm/sec)   p_kst 9.132333e-01   p_cons 1.348333e-02   p_joint 1.948833e-01

Joint ci ratio: 3.266344e-02	ci left: 1.678484e-01	ci right 1.734361e-01	k: 11944	n:70000
Cons ci ratio: 1.277539e-01	ci left: 1.242294e-02	ci right 1.413204e-02	k: 928	n:70000
KS ci ratio: 4.577164e-03	ci left: 9.107724e-01	ci right 9.149648e-01	k: 63902	n:70000
ERCC2   70000 perm   18 sec   (3814 perm/sec)   p_kst 9.128857e-01   p_cons 1.325714e-02   p_joint 1.706286e-01

Joint ci ratio: 3.127683e-02	ci left: 1.615519e-01	ci right 1.666975e-01	k: 13129	n:80000
Cons ci ratio: 1.198301e-01	ci left: 1.240844e-02	ci right 1.400215e-02	k: 1055	n:80000
KS ci ratio: 4.285504e-03	ci left: 9.107606e-01	ci right 9.146844e-01	k: 73019	n:80000
ERCC2   80000 perm   21 sec   (3800 perm/sec)   p_kst 9.127375e-01   p_cons 1.318750e-02   p_joint 1.641125e-01

Joint ci ratio: 2.741249e-02	ci left: 1.826004e-01	ci right 1.876866e-01	k: 16662	n:90000
Cons ci ratio: 1.132672e-01	ci left: 1.238892e-02	ci right 1.388715e-02	k: 1181	n:90000
KS ci ratio: 4.044159e-03	ci left: 9.107248e-01	ci right 9.144263e-01	k: 82133	n:90000
ERCC2   90000 perm   24 sec   (3776 perm/sec)   p_kst 9.125889e-01   p_cons 1.312222e-02   p_joint 1.851333e-01

Joint ci ratio: 2.562387e-02	ci left: 1.872143e-01	ci right 1.920837e-01	k: 18964	n:100000
Cons ci ratio: 1.066485e-01	ci left: 1.261860e-02	ci right 1.404983e-02	k: 1332	n:100000
KS ci ratio: 3.882573e-03	ci left: 9.088853e-01	ci right 9.124308e-01	k: 91067	n:100000
ERCC2   100000 perm   27 sec   (3750 perm/sec)   p_kst 9.106700e-01   p_cons 1.332000e-02   p_joint 1.896400e-01

Joint ci ratio: 2.444985e-02	ci left: 1.870972e-01	ci right 1.917374e-01	k: 20835	n:110000
Cons ci ratio: 1.018016e-01	ci left: 1.262248e-02	ci right 1.398518e-02	k: 1462	n:110000
KS ci ratio: 3.689598e-03	ci left: 9.095128e-01	ci right 9.128837e-01	k: 100233	n:110000
ERCC2   110000 perm   30 sec   (3720 perm/sec)   p_kst 9.112091e-01   p_cons 1.329091e-02   p_joint 1.894091e-01

Joint ci ratio: 2.351827e-02	ci left: 1.857762e-01	ci right 1.902056e-01	k: 22558	n:120000
Cons ci ratio: 9.743670e-02	ci left: 1.265946e-02	ci right 1.396421e-02	k: 1596	n:120000
KS ci ratio: 3.530163e-03	ci left: 9.096941e-01	ci right 9.129194e-01	k: 109358	n:120000
ERCC2   120000 perm   33 sec   (3684 perm/sec)   p_kst 9.113167e-01   p_cons 1.330000e-02   p_joint 1.879833e-01

Outputting figure to mutsig2_images.part000000000058/ERCC2.4_2432_120000_0.91132_0.0133_0.18798.png
                gene_name: ERCC2
               theta_stop: 0.097 
                    nperm: 120000 
                     p_ks: 0.91 
        ci_ks_bounds_left: 0.91 
       ci_ks_bounds_right: 0.91 
                   p_cons: 0.013 
      ci_cons_bounds_left: 0.013 
     ci_cons_bounds_right: 0.014 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.19 

Current progress: 20 percent done.
ERG
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: 1.113846e-01	ci left: 1.040292e-01	ci right 1.163989e-01	k: 1101	n:10000
KS ci ratio: 1.008704e-01	ci left: 1.245431e-01	ci right 1.378726e-01	k: 1311	n:10000
ERG   10000 perm   2 sec   (6423 perm/sec)   p_kst 1.311000e-01   p_cons 1.101000e-01   p_joint 7.079000e-01

Joint ci ratio: 2.398046e-02	ci left: 5.650075e-01	ci right 5.787716e-01	k: 11438	n:20000
Cons ci ratio: 7.932974e-02	ci left: 1.044674e-01	ci right 1.131467e-01	k: 2175	n:20000
KS ci ratio: 7.135872e-02	ci left: 1.264021e-01	ci right 1.358055e-01	k: 2621	n:20000
ERG   20000 perm   4 sec   (5658 perm/sec)   p_kst 1.310500e-01   p_cons 1.087500e-01   p_joint 5.719000e-01

Outputting figure to mutsig2_images.part000000000058/ERG.2_1523_20000_0.13105_0.10875_0.5719.png
                gene_name: ERG
               theta_stop: 0.079 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.57 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.58 

Current progress: 40 percent done.
ESPL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.499682e-01	ci left: 2.099569e-02	ci right 2.708592e-02	k: 239	n:10000
Cons ci ratio: 1.585526e-01	ci left: 5.301669e-02	ci right 6.224312e-02	k: 575	n:10000
KS ci ratio: 3.650251e-01	ci left: 9.321618e-03	ci right 1.357016e-02	k: 113	n:10000
ESPL1   10000 perm   2 sec   (4826 perm/sec)   p_kst 1.130000e-02   p_cons 5.750000e-02   p_joint 2.390000e-02

Joint ci ratio: 7.682562e-01	ci left: 8.090923e-04	ci right 1.844697e-03	k: 25	n:20000
Cons ci ratio: 1.072598e-01	ci left: 5.923278e-02	ci right 6.599506e-02	k: 1251	n:20000
KS ci ratio: 2.525733e-01	ci left: 1.039659e-02	ci right 1.344778e-02	k: 237	n:20000
ESPL1   20000 perm   5 sec   (4385 perm/sec)   p_kst 1.185000e-02   p_cons 6.255000e-02   p_joint 1.250000e-03

Joint ci ratio: 6.925834e-01	ci left: 7.022045e-04	ci right 1.466416e-03	k: 31	n:30000
Cons ci ratio: 9.129107e-02	ci left: 5.525076e-02	ci right 6.056859e-02	k: 1736	n:30000
KS ci ratio: 2.053554e-01	ci left: 1.076700e-02	ci right 1.326218e-02	k: 359	n:30000
ESPL1   30000 perm   7 sec   (4213 perm/sec)   p_kst 1.196667e-02   p_cons 5.786667e-02   p_joint 1.033333e-03

Joint ci ratio: 4.681136e-01	ci left: 1.342393e-03	ci right 2.182598e-03	k: 69	n:40000
Cons ci ratio: 7.616998e-02	ci left: 5.972974e-02	ci right 6.448408e-02	k: 2483	n:40000
KS ci ratio: 1.791708e-01	ci left: 1.076482e-02	ci right 1.290693e-02	k: 472	n:40000
ESPL1   40000 perm   10 sec   (4099 perm/sec)   p_kst 1.180000e-02   p_cons 6.207500e-02   p_joint 1.725000e-03

Joint ci ratio: 4.061028e-01	ci left: 1.483550e-03	ci right 2.256126e-03	k: 92	n:50000
Cons ci ratio: 6.787264e-02	ci left: 6.041340e-02	ci right 6.467756e-02	k: 3126	n:50000
KS ci ratio: 1.592030e-01	ci left: 1.102558e-02	ci right 1.295170e-02	k: 598	n:50000
ESPL1   50000 perm   12 sec   (4003 perm/sec)   p_kst 1.196000e-02   p_cons 6.252000e-02   p_joint 1.840000e-03

Joint ci ratio: 3.636078e-01	ci left: 1.582656e-03	ci right 2.300226e-03	k: 115	n:60000
Cons ci ratio: 6.219275e-02	ci left: 6.016539e-02	ci right 6.404376e-02	k: 3725	n:60000
KS ci ratio: 1.447017e-01	ci left: 1.120836e-02	ci right 1.297264e-02	k: 724	n:60000
ESPL1   60000 perm   15 sec   (3919 perm/sec)   p_kst 1.206667e-02   p_cons 6.208333e-02   p_joint 1.916667e-03

Joint ci ratio: 4.019076e-01	ci left: 1.085297e-03	ci right 1.643070e-03	k: 94	n:70000
Cons ci ratio: 5.774952e-02	ci left: 5.997090e-02	ci right 6.355125e-02	k: 4322	n:70000
KS ci ratio: 1.341956e-01	ci left: 1.123414e-02	ci right 1.286383e-02	k: 842	n:70000
ESPL1   70000 perm   18 sec   (3844 perm/sec)   p_kst 1.202857e-02   p_cons 6.174286e-02   p_joint 1.342857e-03

Joint ci ratio: 3.841353e-01	ci left: 1.051017e-03	ci right 1.561254e-03	k: 103	n:80000
Cons ci ratio: 5.412243e-02	ci left: 5.986957e-02	ci right 6.321231e-02	k: 4922	n:80000
KS ci ratio: 1.250975e-01	ci left: 1.136597e-02	ci right 1.289471e-02	k: 969	n:80000
ESPL1   80000 perm   21 sec   (3777 perm/sec)   p_kst 1.211250e-02   p_cons 6.152500e-02   p_joint 1.287500e-03

Joint ci ratio: 3.685290e-01	ci left: 1.024779e-03	ci right 1.497201e-03	k: 112	n:90000
Cons ci ratio: 5.117685e-02	ci left: 5.963164e-02	ci right 6.277450e-02	k: 5507	n:90000
KS ci ratio: 1.190102e-01	ci left: 1.120177e-02	ci right 1.262994e-02	k: 1071	n:90000
ESPL1   90000 perm   24 sec   (3714 perm/sec)   p_kst 1.190000e-02   p_cons 6.118889e-02   p_joint 1.244444e-03

Joint ci ratio: 3.346770e-01	ci left: 1.141164e-03	ci right 1.608528e-03	k: 136	n:100000
Cons ci ratio: 4.857178e-02	ci left: 5.966280e-02	ci right 6.264272e-02	k: 6114	n:100000
KS ci ratio: 1.131973e-01	ci left: 1.117878e-02	ci right 1.252975e-02	k: 1184	n:100000
ESPL1   100000 perm   27 sec   (3655 perm/sec)   p_kst 1.184000e-02   p_cons 6.114000e-02   p_joint 1.360000e-03

Joint ci ratio: 8.777380e-02	ci left: 1.702681e-02	ci right 1.859876e-02	k: 1958	n:110000
Cons ci ratio: 4.625831e-02	ci left: 5.986248e-02	ci right 6.270616e-02	k: 6740	n:110000
KS ci ratio: 1.078667e-01	ci left: 1.122330e-02	ci right 1.251172e-02	k: 1304	n:110000
ESPL1   110000 perm   31 sec   (3597 perm/sec)   p_kst 1.185455e-02   p_cons 6.127273e-02   p_joint 1.780000e-02

Joint ci ratio: 8.811488e-02	ci left: 1.550957e-02	ci right 1.694728e-02	k: 1946	n:120000
Cons ci ratio: 4.432693e-02	ci left: 5.982552e-02	ci right 6.254573e-02	k: 7341	n:120000
KS ci ratio: 1.030053e-01	ci left: 1.131037e-02	ci right 1.254672e-02	k: 1430	n:120000
ESPL1   120000 perm   34 sec   (3542 perm/sec)   p_kst 1.191667e-02   p_cons 6.117500e-02   p_joint 1.621667e-02

Joint ci ratio: 1.037147e-01	ci left: 1.030518e-02	ci right 1.143987e-02	k: 1412	n:130000
Cons ci ratio: 4.272496e-02	ci left: 5.951458e-02	ci right 6.212044e-02	k: 7905	n:130000
KS ci ratio: 9.949338e-02	ci left: 1.121256e-02	ci right 1.239398e-02	k: 1533	n:130000
ESPL1   130000 perm   37 sec   (3489 perm/sec)   p_kst 1.179231e-02   p_cons 6.080769e-02   p_joint 1.086154e-02

Joint ci ratio: 7.836954e-02	ci left: 1.686861e-02	ci right 1.825148e-02	k: 2457	n:140000
Cons ci ratio: 4.111725e-02	ci left: 5.970942e-02	ci right 6.222309e-02	k: 8534	n:140000
KS ci ratio: 9.602140e-02	ci left: 1.119907e-02	ci right 1.233557e-02	k: 1646	n:140000
ESPL1   140000 perm   41 sec   (3437 perm/sec)   p_kst 1.175714e-02   p_cons 6.095714e-02   p_joint 1.755000e-02

Outputting figure to mutsig2_images.part000000000058/ESPL1.2_6483_140000_0.011757_0.060957_0.01755.png
                gene_name: ESPL1
               theta_stop: 0.096 
                    nperm: 140000 
                     p_ks: 0.012 
        ci_ks_bounds_left: 0.011 
       ci_ks_bounds_right: 0.012 
                   p_cons: 0.061 
      ci_cons_bounds_left: 0.060 
     ci_cons_bounds_right: 0.062 
                  p_joint: 0.018 
     ci_joint_bounds_left: 0.017 
    ci_joint_bounds_right: 0.018 

Current progress: 60 percent done.
EVC2
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: 1.437565e-02	ci left: 8.750041e-01	ci right 8.877728e-01	k: 8815	n:10000
KS ci ratio: 1.608669e-02	ci left: 8.488632e-01	ci right 8.627288e-01	k: 8559	n:10000
EVC2   10000 perm   2 sec   (5441 perm/sec)   p_kst 8.559000e-01   p_cons 8.815000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000058/EVC2.2_4015_10000_0.8559_0.8815_1.png
                gene_name: EVC2
               theta_stop: 0.016 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.86 
                   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: 80 percent done.
EVL
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.079018e-02	ci left: 6.087955e-01	ci right 6.279355e-01	k: 6184	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: 4.152849e-02	ci left: 4.612762e-01	ci right 4.809407e-01	k: 4711	n:10000
EVL   10000 perm   1 sec   (6791 perm/sec)   p_kst 4.711000e-01   p_cons 3.105000e-01   p_joint 6.184000e-01

Outputting figure to mutsig2_images.part000000000058/EVL.2_1313_10000_0.4711_0.3105_0.6184.png
                gene_name: EVL
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.62 
     ci_joint_bounds_left: 0.61 
    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.165.3896/
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/181708/iteration1/scatter.0000000058
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 58 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119819: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000059> was used as the working directory.
Started at Wed Oct 10 10:42:49 2012
Results reported at Wed Oct 10 10:44:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000059.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000059.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 59  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    125.83 sec.
    Max Memory :      1118 MB
    Max Swap   :      3752 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.165.3896/
-whichjob
59
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 59: processing genes 5248 - 5338
Calculating significance of each gene.
Using projection method.
5248	EXO1	3.486970e-01
5249	EXOC1	1
5250	EXOC2	1
5251	EXOC3	1.172435e-01
5252	EXOC3L	1
5253	EXOC3L2	1
5254	EXOC4	1
5255	EXOC5	1
5256	EXOC6	2.208427e-01
5257	EXOC6B	2.850539e-01
5258	EXOC7	1
5259	EXOC8	1
5260	EXOG	1.084723e-01
5261	EXOSC1	1
5262	EXOSC10	1.305860e-01
5263	EXOSC2	1
5264	EXOSC3	1
5265	EXOSC4	1
5266	EXOSC5	1.179669e-01
5267	EXOSC7	1
5268	EXOSC8	1
5269	EXOSC9	1
5270	EXPH5	1
5271	EXT1	1.639728e-02
5272	EXT2	1
5273	EXTL1	8.116351e-02
5274	EXTL2	1.291703e-01
5275	EXTL3	4.084090e-01
5276	EYA1	1
5277	EYA2	1
5278	EYA3	1
5279	EYA4	1
5280	EZH1	2.352103e-02
5281	EZH2	1
5282	EZR	1
5283	F10	1
5284	F11	1
5285	F11R	1
5286	F12	7.143470e-02
5287	F13A1	1
5288	F13B	1
5289	F2	1
5290	F2R	1
5291	F2RL1	1.433620e-01
5292	F2RL2	1
5293	F2RL3	1
5294	F3	1
5295	F5	5.519994e-01
5296	F7	1
5297	F8	3.046639e-01
5298	F9	1.022244e-01
5299	FA2H	1
5300	FAAH	1
5301	FAAH2	1
5302	FABP1	1
5303	FABP12	1
5304	FABP2	1
5305	FABP3	1
5306	FABP4	1
5307	FABP5	1
5308	FABP6	1
5309	FABP7	1
5310	FABP9	1
5311	FADD	1.071876e-01
5312	FADS1	1.711071e-01
5313	FADS2	1
5314	FADS3	1
5315	FADS6	1
5316	FAF1	1
5317	FAF2	1
5318	FAH	1
5319	FAHD1	1
5320	FAHD2A	1
5321	FAHD2B	1
5322	FAIM	1
5323	FAIM2	1
5324	FAIM3	1
5325	FAM100A	1
5326	FAM100B	1
5327	FAM101A	1
5328	FAM101B	5.128786e-02
5329	FAM102A	1
5330	FAM102B	1.880773e-01
5331	FAM103A1	1
5332	FAM104A	1
5333	FAM104B	1
5334	FAM105A	7.876303e-02
5335	FAM105B	1
5336	FAM107A	1
5337	FAM107B	1.240505e-01
5338	FAM108A1	1
Done

Running MutSig 2:
Scatter job 59: processing genes 5248 - 5338
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
EXT1
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: 4.143695e-02	ci left: 4.623746e-01	ci right 4.820416e-01	k: 4722	n:10000
KS ci ratio: 8.952882e-03	ci left: 9.460656e-01	ci right 9.546696e-01	k: 9505	n:10000
EXT1   10000 perm   2 sec   (5582 perm/sec)   p_kst 9.505000e-01   p_cons 4.722000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000059/EXT1.2_2285_10000_0.9505_0.4722_1.png
                gene_name: EXT1
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.95 
                   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: 33 percent done.
EZH1
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: 9.289701e-03	ci left: 9.423233e-01	ci right 9.512142e-01	k: 9469	n:10000
KS ci ratio: 4.698613e-02	ci left: 4.006365e-01	ci right 4.200158e-01	k: 4103	n:10000
EZH1   10000 perm   2 sec   (6046 perm/sec)   p_kst 4.103000e-01   p_cons 9.469000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000059/EZH1.2_2320_10000_0.4103_0.9469_1.png
                gene_name: EZH1
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.95 
      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: 67 percent done.
F8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.911583e-02	ci left: 4.911511e-01	ci right 5.108483e-01	k: 5010	n:10000
Cons ci ratio: 6.149978e-02	ci left: 2.799299e-01	ci right 2.977933e-01	k: 2888	n:10000
KS ci ratio: 3.775496e-02	ci left: 5.088528e-01	ci right 5.285363e-01	k: 5187	n:10000
F8   10000 perm   2 sec   (4284 perm/sec)   p_kst 5.187000e-01   p_cons 2.888000e-01   p_joint 5.010000e-01

Outputting figure to mutsig2_images.part000000000059/F8.2_7188_10000_0.5187_0.2888_0.501.png
                gene_name: F8
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.28 
     ci_cons_bounds_right: 0.30 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    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.165.3896/
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/181708/iteration1/scatter.0000000059
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 59 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119823: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000060> was used as the working directory.
Started at Wed Oct 10 10:42:49 2012
Results reported at Wed Oct 10 10:44:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000060.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000060.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 60  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    111.34 sec.
    Max Memory :      1048 MB
    Max Swap   :      3823 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.165.3896/
-whichjob
60
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 60: processing genes 5339 - 5428
Calculating significance of each gene.
Using projection method.
5339	FAM108B1	8.992437e-02
5340	FAM108C1	1
5341	FAM109A	1
5342	FAM109B	1
5343	FAM110A	1
5344	FAM110B	1
5345	FAM110C	1
5346	FAM111A	1
5347	FAM111B	1
5348	FAM113A	1
5349	FAM113B	1
5350	FAM114A1	1
5351	FAM114A2	1.603113e-01
5352	FAM115A	1
5353	FAM115C	1
5354	FAM116A	1
5355	FAM116B	1
5356	FAM117A	1
5357	FAM117B	1
5358	FAM118A	1
5359	FAM118B	1
5360	FAM119A	1
5361	FAM119B	1
5362	FAM120A	1.660235e-01
5363	FAM120AOS	1
5364	FAM120B	1
5365	FAM120C	3.005768e-01
5366	FAM122A	1
5367	FAM122B	1
5368	FAM122C	1
5369	FAM123A	6.460307e-02
5370	FAM123B	1.465917e-01
5371	FAM123C	1
5372	FAM124A	1
5373	FAM124B	1
5374	FAM125A	1
5375	FAM125B	8.472299e-02
5376	FAM126A	9.012276e-02
5377	FAM126B	6.749308e-02
5378	FAM127A	1
5379	FAM127B	4.957098e-02
5380	FAM127C	1
5381	FAM128A	1
5382	FAM128B	1
5383	FAM129A	1
5384	FAM129B	1
5385	FAM129C	1
5386	FAM131A	1
5387	FAM131B	1
5388	FAM131C	1
5389	FAM132A	1
5390	FAM133A	1
5391	FAM133B	1
5392	FAM134A	1
5393	FAM134B	1
5394	FAM134C	1
5395	FAM135A	1
5396	FAM135B	2.894103e-01
5397	FAM136A	1
5398	FAM136B	4.462655e-03
5399	FAM13A	1
5400	FAM13B	1
5401	FAM13C	1.429749e-01
5402	FAM149A	1
5403	FAM150A	1
5404	FAM150B	1
5405	FAM151A	1
5406	FAM151B	1
5407	FAM153A	1
5408	FAM153B	1
5409	FAM153C	1
5410	FAM154A	1
5411	FAM154B	1
5412	FAM155A	2.213437e-01
5413	FAM155B	1
5414	FAM158A	1
5415	FAM159A	1
5416	FAM160A2	1
5417	FAM160B1	1
5418	FAM160B2	5.113084e-02
5419	FAM161A	1
5420	FAM161B	1
5421	FAM162A	1
5422	FAM162B	1
5423	FAM163A	1
5424	FAM164A	1
5425	FAM164C	1
5426	FAM165B	1
5427	FAM166A	1.138267e-01
5428	FAM166B	1
Done

Running MutSig 2:
Scatter job 60: processing genes 5339 - 5428
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FAM166A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.947820e-02	ci left: 7.940522e-01	ci right 8.097715e-01	k: 8020	n:10000
Cons ci ratio: 4.165368e-02	ci left: 4.597784e-01	ci right 4.794394e-01	k: 4696	n:10000
KS ci ratio: 4.905673e-02	ci left: 3.800254e-01	ci right 3.992390e-01	k: 3896	n:10000
FAM166A   10000 perm   2 sec   (6041 perm/sec)   p_kst 3.896000e-01   p_cons 4.696000e-01   p_joint 8.020000e-01

Outputting figure to mutsig2_images.part000000000060/FAM166A.2_982_10000_0.3896_0.4696_0.802.png
                gene_name: FAM166A
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.48 
                  p_joint: 0.80 
     ci_joint_bounds_left: 0.79 
    ci_joint_bounds_right: 0.81 

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.165.3896/
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/181708/iteration1/scatter.0000000060
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 60 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119833: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000061> was used as the working directory.
Started at Wed Oct 10 10:42:49 2012
Results reported at Wed Oct 10 10:44:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000061.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000061.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 61  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    147.26 sec.
    Max Memory :      1385 MB
    Max Swap   :      3934 MB

    Max Processes  :         7
    Max Threads    :        62

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/
-whichjob
61
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 61: processing genes 5429 - 5519
Calculating significance of each gene.
Using projection method.
5429	FAM167A	1
5430	FAM167B	1
5431	FAM168A	1
5432	FAM168B	1
5433	FAM169A	5.468431e-02
5434	FAM169B	2.293746e-02
5435	FAM170A	1
5436	FAM171A1	1
5437	FAM171B	1.975550e-01
5438	FAM172A	1
5439	FAM173A	1
5440	FAM173B	1
5441	FAM174A	7.747503e-02
5442	FAM174B	1
5443	FAM175A	1
5444	FAM175B	8.259120e-02
5445	FAM176A	1
5446	FAM176B	1
5447	FAM177A1	6.081498e-02
5448	FAM177B	1
5449	FAM178A	9.109835e-02
5450	FAM179A	1
5451	FAM179B	4.484339e-01
5452	FAM180A	1
5453	FAM181A	4.773456e-02
5454	FAM181B	1
5455	FAM183A	1
5456	FAM184A	1
5457	FAM186B	1.163115e-01
5458	FAM187B	1
5459	FAM188A	1
5460	FAM188B	3.527928e-01
5461	FAM189A2	1
5462	FAM189B	1
5463	FAM18A	1
5464	FAM18B	1
5465	FAM18B2	1
5466	FAM190A	1
5467	FAM190B	1
5468	FAM192A	1
5469	FAM193A	1.514217e-02
5470	FAM193B	1
5471	FAM194A	1
5472	FAM195A	1
5473	FAM196A	1
5474	FAM198B	1.409192e-01
5475	FAM199X	1
5476	FAM19A1	1
5477	FAM19A2	1
5478	FAM19A3	1
5479	FAM19A4	1
5480	FAM19A5	1
5481	FAM20A	1
5482	FAM20B	1
5483	FAM21A	7.602160e-02
5484	FAM21B	1
5485	FAM21C	4.189030e-02
5486	FAM22F	1
5487	FAM22G	1
5488	FAM24A	1
5489	FAM24B	1
5490	FAM26D	1
5491	FAM26E	1
5492	FAM26F	1
5493	FAM32A	1
5494	FAM35A	1
5495	FAM36A	2.537705e-03
5496	FAM3A	1
5497	FAM3B	1
5498	FAM3C	1
5499	FAM3D	1
5500	FAM40A	1
5501	FAM40B	1.479693e-01
5502	FAM43A	1
5503	FAM43B	1
5504	FAM45A	3.646928e-02
5505	FAM46A	1.729250e-01
5506	FAM46B	1
5507	FAM46C	1
5508	FAM46D	1
5509	FAM47A	2.879638e-02
5510	FAM47B	1
5511	FAM47C	1.192448e-01
5512	FAM48A	9.936363e-02
5513	FAM48B1	1.694593e-01
5514	FAM48B2	1
5515	FAM49A	1
5516	FAM49B	1
5517	FAM50A	1
5518	FAM50B	1
5519	FAM53A	1
Done

Running MutSig 2:
Scatter job 61: processing genes 5429 - 5519
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FAM193A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.068000e-02	ci left: 4.715636e-01	ci right 4.912473e-01	k: 4814	n:10000
Cons ci ratio: 2.159954e-02	ci left: 7.586885e-01	ci right 7.753556e-01	k: 7671	n:10000
KS ci ratio: 8.363681e-02	ci left: 1.725141e-01	ci right 1.876728e-01	k: 1800	n:10000
FAM193A   10000 perm   2 sec   (4560 perm/sec)   p_kst 1.800000e-01   p_cons 7.671000e-01   p_joint 4.814000e-01

Outputting figure to mutsig2_images.part000000000061/FAM193A.3_3743_10000_0.18_0.7671_0.4814.png
                gene_name: FAM193A
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.78 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 17 percent done.
FAM171B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.387201e-02	ci left: 2.647803e-01	ci right 2.823518e-01	k: 2735	n:10000
Cons ci ratio: 6.043923e-02	ci left: 2.870634e-01	ci right 3.050555e-01	k: 2960	n:10000
KS ci ratio: 1.341162e-01	ci left: 7.339876e-02	ci right 8.404819e-02	k: 786	n:10000
FAM171B   10000 perm   3 sec   (3445 perm/sec)   p_kst 7.860000e-02   p_cons 2.960000e-01   p_joint 2.735000e-01

Joint ci ratio: 4.923067e-02	ci left: 2.347386e-01	ci right 2.466369e-01	k: 4813	n:20000
Cons ci ratio: 4.291725e-02	ci left: 2.879893e-01	ci right 3.006705e-01	k: 5886	n:20000
KS ci ratio: 9.496748e-02	ci left: 7.476008e-02	ci right 8.226301e-02	k: 1569	n:20000
FAM171B   20000 perm   6 sec   (3235 perm/sec)   p_kst 7.845000e-02   p_cons 2.943000e-01   p_joint 2.406500e-01

Outputting figure to mutsig2_images.part000000000061/FAM171B.2_2513_20000_0.07845_0.2943_0.24065.png
                gene_name: FAM171B
               theta_stop: 0.095 
                    nperm: 20000 
                     p_ks: 0.078 
        ci_ks_bounds_left: 0.075 
       ci_ks_bounds_right: 0.082 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.29 
     ci_cons_bounds_right: 0.30 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.25 

Current progress: 33 percent done.
FAM178A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.211988e-02	ci left: 3.517769e-01	ci right 3.707040e-01	k: 3612	n:10000
Cons ci ratio: 5.086757e-02	ci left: 3.630124e-01	ci right 3.820619e-01	k: 3725	n:10000
KS ci ratio: 3.651132e-02	ci left: 5.255657e-01	ci right 5.452137e-01	k: 5354	n:10000
FAM178A   10000 perm   2 sec   (4861 perm/sec)   p_kst 5.354000e-01   p_cons 3.725000e-01   p_joint 3.612000e-01

Outputting figure to mutsig2_images.part000000000061/FAM178A.2_3677_10000_0.5354_0.3725_0.3612.png
                gene_name: FAM178A
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 50 percent done.
FAM179B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.998313e-02	ci left: 1.522755e-01	ci right 1.667234e-01	k: 1594	n:10000
Cons ci ratio: 1.113278e-01	ci left: 1.041267e-01	ci right 1.165013e-01	k: 1102	n:10000
KS ci ratio: 1.578567e-02	ci left: 8.535544e-01	ci right 8.672349e-01	k: 8605	n:10000
FAM179B   10000 perm   2 sec   (4391 perm/sec)   p_kst 8.605000e-01   p_cons 1.102000e-01   p_joint 1.594000e-01

Joint ci ratio: 6.902878e-02	ci left: 1.340362e-01	ci right 1.436691e-01	k: 2776	n:20000
Cons ci ratio: 8.242343e-02	ci left: 9.739693e-02	ci right 1.058193e-01	k: 2031	n:20000
KS ci ratio: 1.127724e-02	ci left: 8.530855e-01	ci right 8.628102e-01	k: 17160	n:20000
FAM179B   20000 perm   5 sec   (3957 perm/sec)   p_kst 8.580000e-01   p_cons 1.015500e-01   p_joint 1.388000e-01

Outputting figure to mutsig2_images.part000000000061/FAM179B.2_5239_20000_0.858_0.10155_0.1388.png
                gene_name: FAM179B
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.10 
      ci_cons_bounds_left: 0.097 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.14 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 67 percent done.
FAM21C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.079150e-02	ci left: 3.637086e-01	ci right 3.827653e-01	k: 3732	n:10000
Cons ci ratio: 4.261065e-02	ci left: 4.484977e-01	ci right 4.681266e-01	k: 4583	n:10000
KS ci ratio: 6.775073e-02	ci left: 2.422288e-01	ci right 2.593166e-01	k: 2507	n:10000
FAM21C   10000 perm   2 sec   (4595 perm/sec)   p_kst 2.507000e-01   p_cons 4.583000e-01   p_joint 3.732000e-01

Outputting figure to mutsig2_images.part000000000061/FAM21C.2_4083_10000_0.2507_0.4583_0.3732.png
                gene_name: FAM21C
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.46 
      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: 83 percent done.
FAM47A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.199832e-03	ci left: 9.800565e-01	ci right 9.852569e-01	k: 9828	n:10000
Cons ci ratio: 2.607094e-02	ci left: 6.841568e-01	ci right 7.023305e-01	k: 6933	n:10000
KS ci ratio: 4.398338e-02	ci left: 4.328329e-01	ci right 4.524006e-01	k: 4426	n:10000
FAM47A   10000 perm   2 sec   (6130 perm/sec)   p_kst 4.426000e-01   p_cons 6.933000e-01   p_joint 9.828000e-01

Outputting figure to mutsig2_images.part000000000061/FAM47A.2_2380_10000_0.4426_0.6933_0.9828.png
                gene_name: FAM47A
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.69 
      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: 0.99 

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.165.3896/
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/181708/iteration1/scatter.0000000061
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 61 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119840: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000062> was used as the working directory.
Started at Wed Oct 10 10:42:49 2012
Results reported at Wed Oct 10 10:44:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000062.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000062.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 62  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    135.34 sec.
    Max Memory :      1064 MB
    Max Swap   :      3811 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.165.3896/
-whichjob
62
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 62: processing genes 5520 - 5609
Calculating significance of each gene.
Using projection method.
5520	FAM53B	1
5521	FAM53C	1
5522	FAM54A	1
5523	FAM54B	1
5524	FAM55A	1
5525	FAM55B	1
5526	FAM55C	1
5527	FAM55D	1.619963e-01
5528	FAM57A	1.740451e-03
5529	FAM57B	1
5530	FAM58A	1
5531	FAM58B	1
5532	FAM59A	1.548574e-01
5533	FAM5B	2.472034e-01
5534	FAM5C	7.814226e-03
5535	FAM60A	1
5536	FAM63A	5.431461e-03
5537	FAM63B	1.988246e-01
5538	FAM64A	1
5539	FAM65A	1.631884e-01
5540	FAM65B	1
5541	FAM65C	1
5542	FAM69A	1
5543	FAM69B	1
5544	FAM69C	1
5545	FAM70A	1
5546	FAM70B	1
5547	FAM71A	1.942951e-01
5548	FAM71B	1
5549	FAM71C	5.711564e-02
5550	FAM71D	1
5551	FAM71E1	1
5552	FAM71F1	1
5553	FAM71F2	1
5554	FAM72A	1
5555	FAM72B	1
5556	FAM72D	1
5557	FAM73A	2.473476e-01
5558	FAM73B	1
5559	FAM75A6	1.316288e-01
5560	FAM75C1	1
5561	FAM76A	1
5562	FAM76B	1
5563	FAM78A	1
5564	FAM78B	1
5565	FAM81A	1
5566	FAM81B	2.066574e-01
5567	FAM82A1	1
5568	FAM82A2	1
5569	FAM82B	1
5570	FAM83A	1
5571	FAM83B	1
5572	FAM83C	2.083132e-01
5573	FAM83D	1
5574	FAM83E	1.398699e-02
5575	FAM83F	1
5576	FAM83G	1
5577	FAM83H	3.489972e-01
5578	FAM84A	1
5579	FAM84B	2.152969e-02
5580	FAM86A	1
5581	FAM86B1	1
5582	FAM86B2	1
5583	FAM86C	1
5584	FAM89A	1
5585	FAM89B	5.146505e-02
5586	FAM8A1	1
5587	FAM90A1	1
5588	FAM91A1	1
5589	FAM92A1	1
5590	FAM92B	1
5591	FAM96A	6.047824e-02
5592	FAM96B	1
5593	FAM98A	1
5594	FAM98B	1
5595	FAM98C	1
5596	FAM9A	1
5597	FAM9B	1
5598	FAM9C	1
5599	FANCA	1.181627e-01
5600	FANCB	1
5601	FANCC	1
5602	FANCD2	1.396201e-01
5603	FANCE	1
5604	FANCF	1
5605	FANCG	1
5606	FANCI	4.843300e-01
5607	FANCL	1
5608	FANCM	6.686436e-01
5609	FANK1	1
Done

Running MutSig 2:
Scatter job 62: processing genes 5520 - 5609
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FANCD2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.509389e-02	ci left: 3.267412e-01	ci right 3.453544e-01	k: 3360	n:10000
Cons ci ratio: 2.470529e-02	ci left: 7.067471e-01	ci right 7.245272e-01	k: 7157	n:10000
KS ci ratio: 1.057501e-01	ci left: 1.143760e-01	ci right 1.272458e-01	k: 1207	n:10000
FANCD2   10000 perm   2 sec   (4406 perm/sec)   p_kst 1.207000e-01   p_cons 7.157000e-01   p_joint 3.360000e-01

Joint ci ratio: 5.163549e-02	ci left: 2.178906e-01	ci right 2.294899e-01	k: 4473	n:20000
Cons ci ratio: 1.750186e-02	ci left: 7.086376e-01	ci right 7.211999e-01	k: 14299	n:20000
KS ci ratio: 7.394489e-02	ci left: 1.186258e-01	ci right 1.277841e-01	k: 2463	n:20000
FANCD2   20000 perm   7 sec   (2972 perm/sec)   p_kst 1.231500e-01   p_cons 7.149500e-01   p_joint 2.236500e-01

Outputting figure to mutsig2_images.part000000000062/FANCD2.3_4663_20000_0.12315_0.71495_0.22365.png
                gene_name: FANCD2
               theta_stop: 0.074 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.23 

Current progress: 17 percent done.
FAM57A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.306490e-02	ci left: 2.152677e-01	ci right 2.316936e-01	k: 2234	n:10000
Cons ci ratio: 6.154471e-02	ci left: 2.796327e-01	ci right 2.974906e-01	k: 2885	n:10000
KS ci ratio: 7.017888e-02	ci left: 2.293843e-01	ci right 2.461688e-01	k: 2377	n:10000
FAM57A   10000 perm   2 sec   (6056 perm/sec)   p_kst 2.377000e-01   p_cons 2.885000e-01   p_joint 2.234000e-01

Outputting figure to mutsig2_images.part000000000062/FAM57A.2_794_10000_0.2377_0.2885_0.2234.png
                gene_name: FAM57A
               theta_stop: 0.073 
                    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: 0.28 
     ci_cons_bounds_right: 0.30 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.23 

Current progress: 33 percent done.
FAM5C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.921421e-02	ci left: 7.984155e-01	ci right 8.140057e-01	k: 8063	n:10000
Cons ci ratio: 3.997784e-02	ci left: 4.802562e-01	ci right 4.999496e-01	k: 4901	n:10000
KS ci ratio: 2.319292e-02	ci left: 7.319911e-01	ci right 7.492685e-01	k: 7407	n:10000
FAM5C   10000 perm   2 sec   (5688 perm/sec)   p_kst 7.407000e-01   p_cons 4.901000e-01   p_joint 8.063000e-01

Outputting figure to mutsig2_images.part000000000062/FAM5C.2_2329_10000_0.7407_0.4901_0.8063.png
                gene_name: FAM5C
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.75 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.81 
     ci_joint_bounds_left: 0.80 
    ci_joint_bounds_right: 0.81 

Current progress: 50 percent done.
FAM63A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.577464e-02	ci left: 4.132907e-01	ci right 4.327542e-01	k: 4230	n:10000
Cons ci ratio: 1.161806e-01	ci left: 9.623212e-02	ci right 1.082007e-01	k: 1021	n:10000
KS ci ratio: 4.615168e-02	ci left: 4.093044e-01	ci right 4.287428e-01	k: 4190	n:10000
FAM63A   10000 perm   2 sec   (4844 perm/sec)   p_kst 4.190000e-01   p_cons 1.021000e-01   p_joint 4.230000e-01

Joint ci ratio: 8.409147e-03	ci left: 9.118148e-01	ci right 9.195639e-01	k: 18315	n:20000
Cons ci ratio: 8.159898e-02	ci left: 9.921306e-02	ci right 1.077026e-01	k: 2068	n:20000
KS ci ratio: 3.265392e-02	ci left: 4.118998e-01	ci right 4.256238e-01	k: 8375	n:20000
FAM63A   20000 perm   4 sec   (4791 perm/sec)   p_kst 4.187500e-01   p_cons 1.034000e-01   p_joint 9.157500e-01

Outputting figure to mutsig2_images.part000000000062/FAM63A.2_1594_20000_0.41875_0.1034_0.91575.png
                gene_name: FAM63A
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.10 
      ci_cons_bounds_left: 0.099 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.92 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 67 percent done.
FAM83E
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.517326e-02	ci left: 6.989787e-01	ci right 7.169000e-01	k: 7080	n:10000
Cons ci ratio: 3.606605e-02	ci left: 5.316731e-01	ci right 5.513027e-01	k: 5415	n:10000
KS ci ratio: 3.928043e-02	ci left: 4.890517e-01	ci right 5.087489e-01	k: 4989	n:10000
FAM83E   10000 perm   2 sec   (5600 perm/sec)   p_kst 4.989000e-01   p_cons 5.415000e-01   p_joint 7.080000e-01

Outputting figure to mutsig2_images.part000000000062/FAM83E.2_1457_10000_0.4989_0.5415_0.708.png
                gene_name: FAM83E
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.55 
                  p_joint: 0.71 
     ci_joint_bounds_left: 0.70 
    ci_joint_bounds_right: 0.72 

Current progress: 83 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: 2.374251e-02	ci left: 7.227983e-01	ci right 7.402667e-01	k: 7316	n:10000
KS ci ratio: 1.182134e-02	ci left: 9.111117e-01	ci right 9.220441e-01	k: 9167	n:10000
FANCA   10000 perm   2 sec   (5135 perm/sec)   p_kst 9.167000e-01   p_cons 7.316000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000062/FANCA.2_4545_10000_0.9167_0.7316_1.png
                gene_name: FANCA
               theta_stop: 0.024 
                    nperm: 10000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.91 
       ci_ks_bounds_right: 0.92 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.74 
                  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.165.3896/
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/181708/iteration1/scatter.0000000062
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 62 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119847: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000063> was used as the working directory.
Started at Wed Oct 10 10:42:59 2012
Results reported at Wed Oct 10 10:54:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000063.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000063.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 63  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    745.36 sec.
    Max Memory :      1406 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.165.3896/
-whichjob
63
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 63: processing genes 5610 - 5700
Calculating significance of each gene.
Using projection method.
5610	FAP	1
5611	FAR1	1
5612	FAR2	1
5613	FARP1	3.103888e-01
5614	FARP2	1
5615	FARS2	1
5616	FARSA	1
5617	FARSB	1
5618	FAS	1
5619	FASLG	1
5620	FASN	4.171453e-01
5621	FASTK	1
5622	FASTKD1	1
5623	FASTKD2	1
5624	FASTKD3	1.210837e-01
5625	FASTKD5	2.135065e-01
5626	FAT1	1.558329e-01
5627	FAT2	1
5628	FAT3	5.258610e-01
5629	FAT4	4.464318e-01
5630	FATE1	1
5631	FAU	1
5632	FBF1	1.019741e-01
5633	FBL	1
5634	FBLIM1	1
5635	FBLN1	1
5636	FBLN2	1
5637	FBLN5	1
5638	FBLN7	1
5639	FBN1	5.459620e-01
5640	FBN2	1
5641	FBN3	6.184419e-01
5642	FBP1	1
5643	FBP2	1
5644	FBRS	1
5645	FBXL12	1
5646	FBXL13	1
5647	FBXL14	1
5648	FBXL15	1
5649	FBXL16	1
5650	FBXL17	1
5651	FBXL18	1
5652	FBXL19	1.185395e-02
5653	FBXL2	1.467348e-01
5654	FBXL20	1.183914e-01
5655	FBXL21	9.441377e-02
5656	FBXL22	1
5657	FBXL3	1
5658	FBXL4	1
5659	FBXL5	1
5660	FBXL6	1
5661	FBXL7	2.237182e-01
5662	FBXL8	1
5663	FBXO10	1
5664	FBXO11	1
5665	FBXO15	1
5666	FBXO16	4.995200e-02
5667	FBXO17	1
5668	FBXO18	1
5669	FBXO2	1
5670	FBXO21	1.612693e-01
5671	FBXO22	4.042829e-02
5672	FBXO24	1
5673	FBXO25	1
5674	FBXO27	1
5675	FBXO28	1
5676	FBXO3	1
5677	FBXO30	1
5678	FBXO31	1
5679	FBXO32	1
5680	FBXO33	1.437837e-01
5681	FBXO34	1
5682	FBXO36	1
5683	FBXO38	4.534477e-01
5684	FBXO39	1
5685	FBXO4	8.476576e-03
5686	FBXO40	1.126385e-02
5687	FBXO41	1
5688	FBXO42	3.918473e-02
5689	FBXO43	1
5690	FBXO44	1
5691	FBXO45	1
5692	FBXO46	1
5693	FBXO47	1
5694	FBXO48	6.988192e-02
5695	FBXO5	1
5696	FBXO6	1
5697	FBXO7	1
5698	FBXO8	7.801010e-02
5699	FBXO9	1
5700	FBXW10	1
Done

Running MutSig 2:
Scatter job 63: processing genes 5610 - 5700
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FAT4
Processing conservation and coverage...
66% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.360087e-02	ci left: 5.666442e-01	ci right 5.861113e-01	k: 5764	n:10000
Cons ci ratio: 2.977477e-02	ci left: 6.245712e-01	ci right 6.435506e-01	k: 6341	n:10000
KS ci ratio: 4.478554e-02	ci left: 4.239572e-01	ci right 4.434814e-01	k: 4337	n:10000
FAT4   10000 perm   4 sec   (2706 perm/sec)   p_kst 4.337000e-01   p_cons 6.341000e-01   p_joint 5.764000e-01

Outputting figure to mutsig2_images.part000000000063/FAT4.5_15014_10000_0.4337_0.6341_0.5764.png
                gene_name: FAT4
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.64 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 12 percent done.
FAT1
Processing conservation and coverage...
72% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.493376e-02	ci left: 1.680897e-01	ci right 1.830998e-01	k: 1755	n:10000
Cons ci ratio: 5.424083e-02	ci left: 3.336927e-01	ci right 3.523989e-01	k: 3430	n:10000
KS ci ratio: 1.397872e-01	ci left: 6.778282e-02	ci right 7.806763e-02	k: 728	n:10000
FAT1   10000 perm   3 sec   (3157 perm/sec)   p_kst 7.280000e-02   p_cons 3.430000e-01   p_joint 1.755000e-01

Joint ci ratio: 6.068790e-02	ci left: 1.673361e-01	ci right 1.778592e-01	k: 3451	n:20000
Cons ci ratio: 3.840512e-02	ci left: 3.358718e-01	ci right 3.490741e-01	k: 6849	n:20000
KS ci ratio: 9.826617e-02	ci left: 7.006718e-02	ci right 7.735734e-02	k: 1473	n:20000
FAT1   20000 perm   7 sec   (2916 perm/sec)   p_kst 7.365000e-02   p_cons 3.424500e-01   p_joint 1.725500e-01

Outputting figure to mutsig2_images.part000000000063/FAT1.3_13871_20000_0.07365_0.34245_0.17255.png
                gene_name: FAT1
               theta_stop: 0.098 
                    nperm: 20000 
                     p_ks: 0.074 
        ci_ks_bounds_left: 0.070 
       ci_ks_bounds_right: 0.077 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.35 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 25 percent done.
FBXO42
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: 2.454149e-02	ci left: 7.094718e-01	ci right 7.272009e-01	k: 7184	n:10000
KS ci ratio: 2.451724e-02	ci left: 7.098755e-01	ci right 7.275970e-01	k: 7188	n:10000
FBXO42   10000 perm   2 sec   (5833 perm/sec)   p_kst 7.188000e-01   p_cons 7.184000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000063/FBXO42.3_2190_10000_0.7188_0.7184_1.png
                gene_name: FBXO42
               theta_stop: 0.025 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.72 
      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: 38 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: 3.323762e-02	ci left: 5.719593e-01	ci right 5.913931e-01	k: 5817	n:10000
KS ci ratio: 3.311486e-02	ci left: 5.737646e-01	ci right 5.931867e-01	k: 5835	n:10000
FAT3   10000 perm   3 sec   (3299 perm/sec)   p_kst 5.835000e-01   p_cons 5.817000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000063/FAT3.2_13774_10000_0.5835_0.5817_1.png
                gene_name: FAT3
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.58 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.59 
                   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.
FBXL19
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.333732e-02	ci left: 8.901588e-01	ci right 9.022093e-01	k: 8963	n:10000
Cons ci ratio: 1.953336e-02	ci left: 7.931392e-01	ci right 8.088851e-01	k: 8011	n:10000
KS ci ratio: 2.421431e-02	ci left: 7.149223e-01	ci right 7.325471e-01	k: 7238	n:10000
FBXL19   10000 perm   2 sec   (5081 perm/sec)   p_kst 7.238000e-01   p_cons 8.011000e-01   p_joint 8.963000e-01

Outputting figure to mutsig2_images.part000000000063/FBXL19.2_2129_10000_0.7238_0.8011_0.8963.png
                gene_name: FBXL19
               theta_stop: 0.024 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.81 
                  p_joint: 0.90 
     ci_joint_bounds_left: 0.89 
    ci_joint_bounds_right: 0.90 

Current progress: 62 percent done.
FBXO21
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: 3.259309e-02	ci left: 5.814892e-01	ci right 6.008577e-01	k: 5912	n:10000
KS ci ratio: 7.677370e-01	ci left: 1.618501e-03	ci right 3.688296e-03	k: 25	n:10000
FBXO21   10000 perm   2 sec   (6112 perm/sec)   p_kst 2.500000e-03   p_cons 5.912000e-01   p_joint 2.500000e-03

Joint ci ratio: 6.270744e-01	ci left: 1.344893e-03	ci right 2.606975e-03	k: 38	n:20000
Cons ci ratio: 2.257202e-02	ci left: 5.944247e-01	ci right 6.080458e-01	k: 12025	n:20000
KS ci ratio: 6.270744e-01	ci left: 1.344893e-03	ci right 2.606975e-03	k: 38	n:20000
FBXO21   20000 perm   4 sec   (5458 perm/sec)   p_kst 1.900000e-03   p_cons 6.012500e-01   p_joint 1.900000e-03

Joint ci ratio: 5.431258e-01	ci left: 1.266016e-03	ci right 2.234588e-03	k: 51	n:30000
Cons ci ratio: 1.843095e-02	ci left: 5.956663e-01	ci right 6.067807e-01	k: 18037	n:30000
KS ci ratio: 5.431258e-01	ci left: 1.266016e-03	ci right 2.234588e-03	k: 51	n:30000
FBXO21   30000 perm   6 sec   (5199 perm/sec)   p_kst 1.700000e-03   p_cons 6.012333e-01   p_joint 1.700000e-03

Joint ci ratio: 4.552634e-01	ci left: 1.430773e-03	ci right 2.294124e-03	k: 73	n:40000
Cons ci ratio: 1.660746e-02	ci left: 5.772232e-01	ci right 5.869148e-01	k: 23283	n:40000
KS ci ratio: 4.552634e-01	ci left: 1.430773e-03	ci right 2.294124e-03	k: 73	n:40000
FBXO21   40000 perm   8 sec   (5026 perm/sec)   p_kst 1.825000e-03   p_cons 5.820750e-01   p_joint 1.825000e-03

Joint ci ratio: 4.248179e-01	ci left: 1.340248e-03	ci right 2.079538e-03	k: 84	n:50000
Cons ci ratio: 1.483823e-02	ci left: 5.782629e-01	ci right 5.869275e-01	k: 29130	n:50000
KS ci ratio: 4.248179e-01	ci left: 1.340248e-03	ci right 2.079538e-03	k: 84	n:50000
FBXO21   50000 perm   10 sec   (4882 perm/sec)   p_kst 1.680000e-03   p_cons 5.826000e-01   p_joint 1.680000e-03

Joint ci ratio: 4.325921e-01	ci left: 1.072235e-03	ci right 1.677652e-03	k: 81	n:60000
Cons ci ratio: 1.350278e-02	ci left: 5.801773e-01	ci right 5.880812e-01	k: 35048	n:60000
KS ci ratio: 3.916699e-01	ci left: 1.341235e-03	ci right 2.008455e-03	k: 99	n:60000
FBXO21   60000 perm   13 sec   (4769 perm/sec)   p_kst 1.650000e-03   p_cons 5.841333e-01   p_joint 1.350000e-03

Joint ci ratio: 4.062121e-01	ci left: 1.059627e-03	ci right 1.611615e-03	k: 92	n:70000
Cons ci ratio: 1.249285e-02	ci left: 5.807958e-01	ci right 5.881115e-01	k: 40912	n:70000
KS ci ratio: 3.668399e-01	ci left: 1.330579e-03	ci right 1.940500e-03	k: 113	n:70000
FBXO21   70000 perm   15 sec   (4666 perm/sec)   p_kst 1.614286e-03   p_cons 5.844571e-01   p_joint 1.314286e-03

Joint ci ratio: 3.787048e-01	ci left: 1.084925e-03	ci right 1.602327e-03	k: 106	n:80000
Cons ci ratio: 1.123564e-02	ci left: 6.000127e-01	ci right 6.068048e-01	k: 48273	n:80000
KS ci ratio: 3.409085e-01	ci left: 1.369286e-03	ci right 1.942828e-03	k: 131	n:80000
FBXO21   80000 perm   18 sec   (4570 perm/sec)   p_kst 1.637500e-03   p_cons 6.034125e-01   p_joint 1.325000e-03

Joint ci ratio: 3.286977e-01	ci left: 1.318910e-03	ci right 1.847384e-03	k: 141	n:90000
Cons ci ratio: 1.056411e-02	ci left: 6.015192e-01	ci right 6.079185e-01	k: 54425	n:90000
KS ci ratio: 3.286977e-01	ci left: 1.318910e-03	ci right 1.847384e-03	k: 141	n:90000
FBXO21   90000 perm   20 sec   (4485 perm/sec)   p_kst 1.566667e-03   p_cons 6.047222e-01   p_joint 1.566667e-03

Joint ci ratio: 3.146163e-01	ci left: 1.306526e-03	ci right 1.803105e-03	k: 154	n:100000
Cons ci ratio: 1.002268e-02	ci left: 6.016517e-01	ci right 6.077222e-01	k: 60469	n:100000
KS ci ratio: 3.146163e-01	ci left: 1.306526e-03	ci right 1.803105e-03	k: 154	n:100000
FBXO21   100000 perm   23 sec   (4404 perm/sec)   p_kst 1.540000e-03   p_cons 6.046900e-01   p_joint 1.540000e-03

Joint ci ratio: 3.049412e-01	ci left: 1.271592e-03	ci right 1.737146e-03	k: 164	n:110000
Cons ci ratio: 9.567696e-03	ci left: 6.012209e-01	ci right 6.070099e-01	k: 66453	n:110000
KS ci ratio: 3.049412e-01	ci left: 1.271592e-03	ci right 1.737146e-03	k: 164	n:110000
FBXO21   110000 perm   25 sec   (4325 perm/sec)   p_kst 1.490909e-03   p_cons 6.041182e-01   p_joint 1.490909e-03

Joint ci ratio: 3.685874e-01	ci left: 7.685639e-04	ci right 1.122936e-03	k: 112	n:120000
Cons ci ratio: 9.162003e-03	ci left: 6.012596e-01	ci right 6.068020e-01	k: 72484	n:120000
KS ci ratio: 2.927747e-01	ci left: 1.273549e-03	ci right 1.717769e-03	k: 178	n:120000
FBXO21   120000 perm   28 sec   (4222 perm/sec)   p_kst 1.483333e-03   p_cons 6.040333e-01   p_joint 9.333333e-04

Joint ci ratio: 2.812284e-01	ci left: 1.282667e-03	ci right 1.709297e-03	k: 193	n:130000
Cons ci ratio: 8.789463e-03	ci left: 6.020823e-01	ci right 6.074053e-01	k: 78617	n:130000
KS ci ratio: 2.812284e-01	ci left: 1.282667e-03	ci right 1.709297e-03	k: 193	n:130000
FBXO21   130000 perm   31 sec   (4152 perm/sec)   p_kst 1.484615e-03   p_cons 6.047462e-01   p_joint 1.484615e-03

Joint ci ratio: 2.722564e-01	ci left: 1.277462e-03	ci right 1.686489e-03	k: 206	n:140000
Cons ci ratio: 8.470181e-03	ci left: 6.021547e-01	ci right 6.072838e-01	k: 84661	n:140000
KS ci ratio: 2.722564e-01	ci left: 1.277462e-03	ci right 1.686489e-03	k: 206	n:140000
FBXO21   140000 perm   34 sec   (4086 perm/sec)   p_kst 1.471429e-03   p_cons 6.047214e-01   p_joint 1.471429e-03

Joint ci ratio: 2.605571e-01	ci left: 1.310512e-03	ci right 1.709155e-03	k: 225	n:150000
Cons ci ratio: 8.180377e-03	ci left: 6.023940e-01	ci right 6.073486e-01	k: 90731	n:150000
KS ci ratio: 2.605571e-01	ci left: 1.310512e-03	ci right 1.709155e-03	k: 225	n:150000
FBXO21   150000 perm   37 sec   (4022 perm/sec)   p_kst 1.500000e-03   p_cons 6.048733e-01   p_joint 1.500000e-03

Joint ci ratio: 2.502470e-01	ci left: 1.339759e-03	ci right 1.728662e-03	k: 244	n:160000
Cons ci ratio: 7.920488e-03	ci left: 6.024808e-01	ci right 6.072779e-01	k: 96781	n:160000
KS ci ratio: 2.502470e-01	ci left: 1.339759e-03	ci right 1.728662e-03	k: 244	n:160000
FBXO21   160000 perm   40 sec   (3955 perm/sec)   p_kst 1.525000e-03   p_cons 6.048813e-01   p_joint 1.525000e-03

Joint ci ratio: 2.452950e-01	ci left: 1.316119e-03	ci right 1.689448e-03	k: 254	n:170000
Cons ci ratio: 7.685501e-03	ci left: 6.024595e-01	ci right 6.071134e-01	k: 102814	n:170000
KS ci ratio: 2.452950e-01	ci left: 1.316119e-03	ci right 1.689448e-03	k: 254	n:170000
FBXO21   170000 perm   44 sec   (3894 perm/sec)   p_kst 1.494118e-03   p_cons 6.047882e-01   p_joint 1.494118e-03

Joint ci ratio: 2.366349e-01	ci left: 1.342188e-03	ci right 1.707502e-03	k: 273	n:180000
Cons ci ratio: 7.461147e-03	ci left: 6.030264e-01	ci right 6.075480e-01	k: 108952	n:180000
KS ci ratio: 2.366349e-01	ci left: 1.342188e-03	ci right 1.707502e-03	k: 273	n:180000
FBXO21   180000 perm   47 sec   (3837 perm/sec)   p_kst 1.516667e-03   p_cons 6.052889e-01   p_joint 1.516667e-03

Joint ci ratio: 2.284415e-01	ci left: 1.370681e-03	ci right 1.729013e-03	k: 293	n:190000
Cons ci ratio: 7.268061e-03	ci left: 6.026976e-01	ci right 6.070992e-01	k: 114931	n:190000
KS ci ratio: 2.284415e-01	ci left: 1.370681e-03	ci right 1.729013e-03	k: 293	n:190000
FBXO21   190000 perm   50 sec   (3781 perm/sec)   p_kst 1.542105e-03   p_cons 6.049000e-01   p_joint 1.542105e-03

Joint ci ratio: 2.199940e-01	ci left: 1.410694e-03	ci right 1.764005e-03	k: 316	n:200000
Cons ci ratio: 7.086255e-03	ci left: 6.026033e-01	ci right 6.068936e-01	k: 120950	n:200000
KS ci ratio: 2.199940e-01	ci left: 1.410694e-03	ci right 1.764005e-03	k: 316	n:200000
FBXO21   200000 perm   54 sec   (3727 perm/sec)   p_kst 1.580000e-03   p_cons 6.047500e-01   p_joint 1.580000e-03

Joint ci ratio: 2.159467e-01	ci left: 1.397540e-03	ci right 1.740264e-03	k: 328	n:210000
Cons ci ratio: 6.918337e-03	ci left: 6.024573e-01	ci right 6.066445e-01	k: 126956	n:210000
KS ci ratio: 2.159467e-01	ci left: 1.397540e-03	ci right 1.740264e-03	k: 328	n:210000
FBXO21   210000 perm   57 sec   (3675 perm/sec)   p_kst 1.561905e-03   p_cons 6.045524e-01   p_joint 1.561905e-03

Joint ci ratio: 2.111865e-01	ci left: 1.398551e-03	ci right 1.732984e-03	k: 343	n:220000
Cons ci ratio: 6.757831e-03	ci left: 6.026079e-01	ci right 6.066985e-01	k: 133024	n:220000
KS ci ratio: 2.111865e-01	ci left: 1.398551e-03	ci right 1.732984e-03	k: 343	n:220000
FBXO21   220000 perm   61 sec   (3596 perm/sec)   p_kst 1.559091e-03   p_cons 6.046545e-01   p_joint 1.559091e-03

Joint ci ratio: 2.084799e-01	ci left: 1.374817e-03	ci right 1.698823e-03	k: 352	n:230000
Cons ci ratio: 6.609083e-03	ci left: 6.026680e-01	ci right 6.066685e-01	k: 139074	n:230000
KS ci ratio: 2.084799e-01	ci left: 1.374817e-03	ci right 1.698823e-03	k: 352	n:230000
FBXO21   230000 perm   65 sec   (3548 perm/sec)   p_kst 1.530435e-03   p_cons 6.046696e-01   p_joint 1.530435e-03

Joint ci ratio: 2.039097e-01	ci left: 1.380758e-03	ci right 1.698142e-03	k: 368	n:240000
Cons ci ratio: 6.468785e-03	ci left: 6.027948e-01	ci right 6.067110e-01	k: 145141	n:240000
KS ci ratio: 2.039097e-01	ci left: 1.380758e-03	ci right 1.698142e-03	k: 368	n:240000
FBXO21   240000 perm   69 sec   (3501 perm/sec)   p_kst 1.533333e-03   p_cons 6.047542e-01   p_joint 1.533333e-03

Joint ci ratio: 2.001488e-01	ci left: 1.378695e-03	ci right 1.689046e-03	k: 382	n:250000
Cons ci ratio: 6.338278e-03	ci left: 6.028203e-01	ci right 6.066573e-01	k: 151185	n:250000
KS ci ratio: 2.001488e-01	ci left: 1.378695e-03	ci right 1.689046e-03	k: 382	n:250000
FBXO21   250000 perm   72 sec   (3455 perm/sec)   p_kst 1.528000e-03   p_cons 6.047400e-01   p_joint 1.528000e-03

Joint ci ratio: 1.941547e-01	ci left: 1.413423e-03	ci right 1.720937e-03	k: 406	n:260000
Cons ci ratio: 6.213564e-03	ci left: 6.029831e-01	ci right 6.067453e-01	k: 157265	n:260000
KS ci ratio: 1.941547e-01	ci left: 1.413423e-03	ci right 1.720937e-03	k: 406	n:260000
FBXO21   260000 perm   76 sec   (3410 perm/sec)   p_kst 1.561538e-03   p_cons 6.048654e-01   p_joint 1.561538e-03

Joint ci ratio: 1.891086e-01	ci left: 1.438648e-03	ci right 1.742582e-03	k: 428	n:270000
Cons ci ratio: 6.096122e-03	ci left: 6.031197e-01	ci right 6.068113e-01	k: 163341	n:270000
KS ci ratio: 1.891086e-01	ci left: 1.438648e-03	ci right 1.742582e-03	k: 428	n:270000
FBXO21   270000 perm   80 sec   (3367 perm/sec)   p_kst 1.585185e-03   p_cons 6.049667e-01   p_joint 1.585185e-03

Joint ci ratio: 1.867314e-01	ci left: 1.424705e-03	ci right 1.721480e-03	k: 439	n:280000
Cons ci ratio: 5.983799e-03	ci left: 6.033509e-01	ci right 6.069755e-01	k: 169446	n:280000
KS ci ratio: 1.867314e-01	ci left: 1.424705e-03	ci right 1.721480e-03	k: 439	n:280000
FBXO21   280000 perm   84 sec   (3327 perm/sec)   p_kst 1.567857e-03   p_cons 6.051643e-01   p_joint 1.567857e-03

Joint ci ratio: 1.844417e-01	ci left: 1.411745e-03	ci right 1.701811e-03	k: 450	n:290000
Cons ci ratio: 5.880559e-03	ci left: 6.033147e-01	ci right 6.068763e-01	k: 175478	n:290000
KS ci ratio: 1.844417e-01	ci left: 1.411745e-03	ci right 1.701811e-03	k: 450	n:290000
FBXO21   290000 perm   88 sec   (3287 perm/sec)   p_kst 1.551724e-03   p_cons 6.050966e-01   p_joint 1.551724e-03

Joint ci ratio: 1.810604e-01	ci left: 1.418762e-03	ci right 1.704339e-03	k: 467	n:300000
Cons ci ratio: 5.781678e-03	ci left: 6.033481e-01	ci right 6.068499e-01	k: 181530	n:300000
KS ci ratio: 1.810604e-01	ci left: 1.418762e-03	ci right 1.704339e-03	k: 467	n:300000
FBXO21   300000 perm   92 sec   (3246 perm/sec)   p_kst 1.556667e-03   p_cons 6.051000e-01   p_joint 1.556667e-03

Joint ci ratio: 1.791581e-01	ci left: 1.403798e-03	ci right 1.683073e-03	k: 477	n:310000
Cons ci ratio: 5.686279e-03	ci left: 6.034929e-01	ci right 6.069374e-01	k: 187617	n:310000
KS ci ratio: 1.791581e-01	ci left: 1.403798e-03	ci right 1.683073e-03	k: 477	n:310000
FBXO21   310000 perm   97 sec   (3207 perm/sec)   p_kst 1.538710e-03   p_cons 6.052161e-01   p_joint 1.538710e-03

Joint ci ratio: 1.771328e-01	ci left: 1.392771e-03	ci right 1.666384e-03	k: 488	n:320000
Cons ci ratio: 5.595781e-03	ci left: 6.036008e-01	ci right 6.069910e-01	k: 193695	n:320000
KS ci ratio: 1.771328e-01	ci left: 1.392771e-03	ci right 1.666384e-03	k: 488	n:320000
FBXO21   320000 perm   101 sec   (3168 perm/sec)   p_kst 1.525000e-03   p_cons 6.052969e-01   p_joint 1.525000e-03

Joint ci ratio: 1.734461e-01	ci left: 1.411411e-03	ci right 1.682311e-03	k: 509	n:330000
Cons ci ratio: 5.509295e-03	ci left: 6.037178e-01	ci right 6.070561e-01	k: 199778	n:330000
KS ci ratio: 1.734461e-01	ci left: 1.411411e-03	ci right 1.682311e-03	k: 509	n:330000
FBXO21   330000 perm   105 sec   (3130 perm/sec)   p_kst 1.542424e-03   p_cons 6.053879e-01   p_joint 1.542424e-03

Joint ci ratio: 1.706252e-01	ci left: 1.417747e-03	ci right 1.684982e-03	k: 526	n:340000
Cons ci ratio: 5.428537e-03	ci left: 6.036664e-01	ci right 6.069553e-01	k: 205806	n:340000
KS ci ratio: 1.706252e-01	ci left: 1.417747e-03	ci right 1.684982e-03	k: 526	n:340000
FBXO21   340000 perm   110 sec   (3095 perm/sec)   p_kst 1.547059e-03   p_cons 6.053118e-01   p_joint 1.547059e-03

Joint ci ratio: 1.680925e-01	ci left: 1.421016e-03	ci right 1.684489e-03	k: 542	n:350000
Cons ci ratio: 5.352060e-03	ci left: 6.035440e-01	ci right 6.067857e-01	k: 211808	n:350000
KS ci ratio: 1.680925e-01	ci left: 1.421016e-03	ci right 1.684489e-03	k: 542	n:350000
FBXO21   350000 perm   115 sec   (3055 perm/sec)   p_kst 1.548571e-03   p_cons 6.051657e-01   p_joint 1.548571e-03

Joint ci ratio: 1.650788e-01	ci left: 1.434784e-03	ci right 1.695567e-03	k: 562	n:360000
Cons ci ratio: 5.277162e-03	ci left: 6.035705e-01	ci right 6.067667e-01	k: 217861	n:360000
KS ci ratio: 1.650788e-01	ci left: 1.434784e-03	ci right 1.695567e-03	k: 562	n:360000
FBXO21   360000 perm   119 sec   (3014 perm/sec)   p_kst 1.561111e-03   p_cons 6.051694e-01   p_joint 1.561111e-03

Joint ci ratio: 1.634905e-01	ci left: 1.424513e-03	ci right 1.680692e-03	k: 573	n:370000
Cons ci ratio: 5.206206e-03	ci left: 6.035146e-01	ci right 6.066675e-01	k: 223884	n:370000
KS ci ratio: 1.634905e-01	ci left: 1.424513e-03	ci right 1.680692e-03	k: 573	n:370000
FBXO21   370000 perm   124 sec   (2973 perm/sec)   p_kst 1.548649e-03   p_cons 6.050919e-01   p_joint 1.548649e-03

Joint ci ratio: 1.618086e-01	ci left: 1.417319e-03	ci right 1.669327e-03	k: 585	n:380000
Cons ci ratio: 5.137754e-03	ci left: 6.034884e-01	ci right 6.065995e-01	k: 229917	n:380000
KS ci ratio: 1.618086e-01	ci left: 1.417319e-03	ci right 1.669327e-03	k: 585	n:380000
FBXO21   380000 perm   129 sec   (2940 perm/sec)   p_kst 1.539474e-03   p_cons 6.050447e-01   p_joint 1.539474e-03

Joint ci ratio: 1.599100e-01	ci left: 1.415430e-03	ci right 1.663866e-03	k: 599	n:390000
Cons ci ratio: 5.070898e-03	ci left: 6.035612e-01	ci right 6.066321e-01	k: 235988	n:390000
KS ci ratio: 1.599100e-01	ci left: 1.415430e-03	ci right 1.663866e-03	k: 599	n:390000
FBXO21   390000 perm   134 sec   (2910 perm/sec)   p_kst 1.535897e-03   p_cons 6.050974e-01   p_joint 1.535897e-03

Joint ci ratio: 1.579479e-01	ci left: 1.416053e-03	ci right 1.661259e-03	k: 614	n:400000
Cons ci ratio: 5.007111e-03	ci left: 6.035806e-01	ci right 6.066129e-01	k: 242039	n:400000
KS ci ratio: 1.579479e-01	ci left: 1.416053e-03	ci right 1.661259e-03	k: 614	n:400000
FBXO21   400000 perm   139 sec   (2882 perm/sec)   p_kst 1.535000e-03   p_cons 6.050975e-01   p_joint 1.535000e-03

Joint ci ratio: 1.549517e-01	ci left: 1.437761e-03	ci right 1.681565e-03	k: 638	n:410000
Cons ci ratio: 4.944813e-03	ci left: 6.036823e-01	ci right 6.066772e-01	k: 248124	n:410000
KS ci ratio: 1.549517e-01	ci left: 1.437761e-03	ci right 1.681565e-03	k: 638	n:410000
FBXO21   410000 perm   144 sec   (2853 perm/sec)   p_kst 1.556098e-03   p_cons 6.051805e-01   p_joint 1.556098e-03

Joint ci ratio: 1.533997e-01	ci left: 1.433287e-03	ci right 1.673674e-03	k: 651	n:420000
Cons ci ratio: 4.884516e-03	ci left: 6.038056e-01	ci right 6.067644e-01	k: 254220	n:420000
KS ci ratio: 1.533997e-01	ci left: 1.433287e-03	ci right 1.673674e-03	k: 651	n:420000
FBXO21   420000 perm   149 sec   (2824 perm/sec)   p_kst 1.550000e-03   p_cons 6.052857e-01   p_joint 1.550000e-03

Joint ci ratio: 1.510989e-01	ci left: 1.444695e-03	ci right 1.683033e-03	k: 671	n:430000
Cons ci ratio: 4.827594e-03	ci left: 6.038023e-01	ci right 6.067265e-01	k: 260264	n:430000
KS ci ratio: 1.510989e-01	ci left: 1.444695e-03	ci right 1.683033e-03	k: 671	n:430000
FBXO21   430000 perm   154 sec   (2795 perm/sec)   p_kst 1.560465e-03   p_cons 6.052651e-01   p_joint 1.560465e-03

Joint ci ratio: 1.490065e-01	ci left: 1.453422e-03	ci right 1.689583e-03	k: 690	n:440000
Cons ci ratio: 4.774023e-03	ci left: 6.036584e-01	ci right 6.065494e-01	k: 266246	n:440000
KS ci ratio: 1.490065e-01	ci left: 1.453422e-03	ci right 1.689583e-03	k: 690	n:440000
FBXO21   440000 perm   159 sec   (2767 perm/sec)   p_kst 1.568182e-03   p_cons 6.051045e-01   p_joint 1.568182e-03

Joint ci ratio: 1.465857e-01	ci left: 1.470345e-03	ci right 1.705036e-03	k: 713	n:450000
Cons ci ratio: 4.720484e-03	ci left: 6.036944e-01	ci right 6.065531e-01	k: 272306	n:450000
KS ci ratio: 1.465857e-01	ci left: 1.470345e-03	ci right 1.705036e-03	k: 713	n:450000
FBXO21   450000 perm   164 sec   (2739 perm/sec)   p_kst 1.584444e-03   p_cons 6.051244e-01   p_joint 1.584444e-03

Joint ci ratio: 1.451697e-01	ci left: 1.467705e-03	ci right 1.699515e-03	k: 727	n:460000
Cons ci ratio: 4.668197e-03	ci left: 6.037813e-01	ci right 6.066086e-01	k: 278390	n:460000
KS ci ratio: 1.451697e-01	ci left: 1.467705e-03	ci right 1.699515e-03	k: 727	n:460000
FBXO21   460000 perm   170 sec   (2713 perm/sec)   p_kst 1.580435e-03   p_cons 6.051957e-01   p_joint 1.580435e-03

Joint ci ratio: 1.438911e-01	ci left: 1.463137e-03	ci right 1.692014e-03	k: 740	n:470000
Cons ci ratio: 4.617117e-03	ci left: 6.039158e-01	ci right 6.067127e-01	k: 284498	n:470000
KS ci ratio: 1.438911e-01	ci left: 1.463137e-03	ci right 1.692014e-03	k: 740	n:470000
FBXO21   470000 perm   175 sec   (2684 perm/sec)   p_kst 1.574468e-03   p_cons 6.053149e-01   p_joint 1.574468e-03

Joint ci ratio: 1.421743e-01	ci left: 1.468813e-03	ci right 1.695605e-03	k: 758	n:480000
Cons ci ratio: 4.568832e-03	ci left: 6.039239e-01	ci right 6.066915e-01	k: 290548	n:480000
KS ci ratio: 1.421743e-01	ci left: 1.468813e-03	ci right 1.695605e-03	k: 758	n:480000
FBXO21   480000 perm   181 sec   (2658 perm/sec)   p_kst 1.579167e-03   p_cons 6.053083e-01   p_joint 1.579167e-03

Joint ci ratio: 1.407900e-01	ci left: 1.468366e-03	ci right 1.692696e-03	k: 773	n:490000
Cons ci ratio: 4.522880e-03	ci left: 6.038420e-01	ci right 6.065813e-01	k: 296554	n:490000
KS ci ratio: 1.407900e-01	ci left: 1.468366e-03	ci right 1.692696e-03	k: 773	n:490000
FBXO21   490000 perm   186 sec   (2632 perm/sec)   p_kst 1.577551e-03   p_cons 6.052122e-01   p_joint 1.577551e-03

Joint ci ratio: 1.398008e-01	ci left: 1.460226e-03	ci right 1.681614e-03	k: 784	n:500000
Cons ci ratio: 4.479393e-03	ci left: 6.036454e-01	ci right 6.063574e-01	k: 302501	n:500000
KS ci ratio: 1.398008e-01	ci left: 1.460226e-03	ci right 1.681614e-03	k: 784	n:500000
FBXO21   500000 perm   192 sec   (2606 perm/sec)   p_kst 1.568000e-03   p_cons 6.050020e-01   p_joint 1.568000e-03

Joint ci ratio: 1.381386e-01	ci left: 1.467554e-03	ci right 1.687190e-03	k: 803	n:510000
Cons ci ratio: 4.435061e-03	ci left: 6.036803e-01	ci right 6.063655e-01	k: 308562	n:510000
KS ci ratio: 1.381386e-01	ci left: 1.467554e-03	ci right 1.687190e-03	k: 803	n:510000
FBXO21   510000 perm   198 sec   (2581 perm/sec)   p_kst 1.574510e-03   p_cons 6.050235e-01   p_joint 1.574510e-03

Joint ci ratio: 1.367842e-01	ci left: 1.469043e-03	ci right 1.686571e-03	k: 819	n:520000
Cons ci ratio: 4.392319e-03	ci left: 6.036813e-01	ci right 6.063406e-01	k: 314606	n:520000
KS ci ratio: 1.367842e-01	ci left: 1.469043e-03	ci right 1.686571e-03	k: 819	n:520000
FBXO21   520000 perm   203 sec   (2557 perm/sec)   p_kst 1.575000e-03   p_cons 6.050115e-01   p_joint 1.575000e-03

Joint ci ratio: 1.361228e-01	ci left: 1.455903e-03	ci right 1.670359e-03	k: 827	n:530000
Cons ci ratio: 4.350601e-03	ci left: 6.037032e-01	ci right 6.063372e-01	k: 320661	n:530000
KS ci ratio: 1.361228e-01	ci left: 1.455903e-03	ci right 1.670359e-03	k: 827	n:530000
FBXO21   530000 perm   209 sec   (2530 perm/sec)   p_kst 1.560377e-03   p_cons 6.050208e-01   p_joint 1.560377e-03

Joint ci ratio: 1.347464e-01	ci left: 1.459357e-03	ci right 1.671974e-03	k: 844	n:540000
Cons ci ratio: 4.310267e-03	ci left: 6.037002e-01	ci right 6.063098e-01	k: 326703	n:540000
KS ci ratio: 1.347464e-01	ci left: 1.459357e-03	ci right 1.671974e-03	k: 844	n:540000
FBXO21   540000 perm   215 sec   (2508 perm/sec)   p_kst 1.562963e-03   p_cons 6.050056e-01   p_joint 1.562963e-03

Joint ci ratio: 1.332562e-01	ci left: 1.466211e-03	ci right 1.677277e-03	k: 863	n:550000
Cons ci ratio: 4.270530e-03	ci left: 6.037539e-01	ci right 6.063395e-01	k: 332776	n:550000
KS ci ratio: 1.332562e-01	ci left: 1.466211e-03	ci right 1.677277e-03	k: 863	n:550000
FBXO21   550000 perm   221 sec   (2486 perm/sec)   p_kst 1.569091e-03   p_cons 6.050473e-01   p_joint 1.569091e-03

Joint ci ratio: 1.323408e-01	ci left: 1.460745e-03	ci right 1.669466e-03	k: 875	n:560000
Cons ci ratio: 4.231272e-03	ci left: 6.038737e-01	ci right 6.064360e-01	k: 338887	n:560000
KS ci ratio: 1.323408e-01	ci left: 1.460745e-03	ci right 1.669466e-03	k: 875	n:560000
FBXO21   560000 perm   227 sec   (2465 perm/sec)   p_kst 1.562500e-03   p_cons 6.051554e-01   p_joint 1.562500e-03

Joint ci ratio: 1.310014e-01	ci left: 1.465657e-03	ci right 1.672795e-03	k: 893	n:570000
Cons ci ratio: 4.194000e-03	ci left: 6.038840e-01	ci right 6.064237e-01	k: 344938	n:570000
KS ci ratio: 1.310014e-01	ci left: 1.465657e-03	ci right 1.672795e-03	k: 893	n:570000
FBXO21   570000 perm   233 sec   (2443 perm/sec)   p_kst 1.566667e-03   p_cons 6.051544e-01   p_joint 1.566667e-03

Joint ci ratio: 1.302755e-01	ci left: 1.457065e-03	ci right 1.661759e-03	k: 903	n:580000
Cons ci ratio: 4.158536e-03	ci left: 6.037975e-01	ci right 6.063153e-01	k: 350933	n:580000
KS ci ratio: 1.302755e-01	ci left: 1.457065e-03	ci right 1.661759e-03	k: 903	n:580000
FBXO21   580000 perm   240 sec   (2422 perm/sec)   p_kst 1.556897e-03   p_cons 6.050569e-01   p_joint 1.556897e-03

Joint ci ratio: 1.287180e-01	ci left: 1.468449e-03	ci right 1.672088e-03	k: 925	n:590000
Cons ci ratio: 4.123444e-03	ci left: 6.037733e-01	ci right 6.062697e-01	k: 356963	n:590000
KS ci ratio: 1.287180e-01	ci left: 1.468449e-03	ci right 1.672088e-03	k: 925	n:590000
FBXO21   590000 perm   246 sec   (2401 perm/sec)   p_kst 1.567797e-03   p_cons 6.050220e-01   p_joint 1.567797e-03

Joint ci ratio: 1.280977e-01	ci left: 1.458493e-03	ci right 1.659702e-03	k: 934	n:600000
Cons ci ratio: 4.088898e-03	ci left: 6.037884e-01	ci right 6.062639e-01	k: 363016	n:600000
KS ci ratio: 1.280977e-01	ci left: 1.458493e-03	ci right 1.659702e-03	k: 934	n:600000
FBXO21   600000 perm   252 sec   (2380 perm/sec)   p_kst 1.556667e-03   p_cons 6.050267e-01   p_joint 1.556667e-03

Joint ci ratio: 1.269486e-01	ci left: 1.461563e-03	ci right 1.661251e-03	k: 951	n:610000
Cons ci ratio: 4.054706e-03	ci left: 6.038621e-01	ci right 6.063172e-01	k: 369105	n:610000
KS ci ratio: 1.269486e-01	ci left: 1.461563e-03	ci right 1.661251e-03	k: 951	n:610000
FBXO21   610000 perm   258 sec   (2361 perm/sec)   p_kst 1.559016e-03   p_cons 6.050902e-01   p_joint 1.559016e-03

Joint ci ratio: 1.259603e-01	ci left: 1.461418e-03	ci right 1.659416e-03	k: 966	n:620000
Cons ci ratio: 4.021451e-03	ci left: 6.039223e-01	ci right 6.063574e-01	k: 375187	n:620000
KS ci ratio: 1.259603e-01	ci left: 1.461418e-03	ci right 1.659416e-03	k: 966	n:620000
FBXO21   620000 perm   265 sec   (2341 perm/sec)   p_kst 1.558065e-03   p_cons 6.051403e-01   p_joint 1.558065e-03

Joint ci ratio: 1.251863e-01	ci left: 1.456670e-03	ci right 1.652722e-03	k: 978	n:630000
Cons ci ratio: 3.988525e-03	ci left: 6.040378e-01	ci right 6.064533e-01	k: 381305	n:630000
KS ci ratio: 1.251863e-01	ci left: 1.456670e-03	ci right 1.652722e-03	k: 978	n:630000
FBXO21   630000 perm   271 sec   (2321 perm/sec)   p_kst 1.552381e-03   p_cons 6.052460e-01   p_joint 1.552381e-03

Joint ci ratio: 1.240508e-01	ci left: 1.461158e-03	ci right 1.655899e-03	k: 996	n:640000
Cons ci ratio: 3.957960e-03	ci left: 6.039605e-01	ci right 6.063573e-01	k: 387302	n:640000
KS ci ratio: 1.240508e-01	ci left: 1.461158e-03	ci right 1.655899e-03	k: 996	n:640000
FBXO21   640000 perm   278 sec   (2302 perm/sec)   p_kst 1.556250e-03   p_cons 6.051594e-01   p_joint 1.556250e-03

Joint ci ratio: 1.231891e-01	ci left: 1.459551e-03	ci right 1.652628e-03	k: 1010	n:650000
Cons ci ratio: 3.926784e-03	ci left: 6.040443e-01	ci right 6.064224e-01	k: 393402	n:650000
KS ci ratio: 1.231891e-01	ci left: 1.459551e-03	ci right 1.652628e-03	k: 1010	n:650000
FBXO21   650000 perm   285 sec   (2282 perm/sec)   p_kst 1.553846e-03   p_cons 6.052338e-01   p_joint 1.553846e-03

Joint ci ratio: 1.223450e-01	ci left: 1.457997e-03	ci right 1.649451e-03	k: 1024	n:660000
Cons ci ratio: 3.897285e-03	ci left: 6.040089e-01	ci right 6.063690e-01	k: 399425	n:660000
KS ci ratio: 1.223450e-01	ci left: 1.457997e-03	ci right 1.649451e-03	k: 1024	n:660000
FBXO21   660000 perm   292 sec   (2262 perm/sec)   p_kst 1.551515e-03   p_cons 6.051894e-01   p_joint 1.551515e-03

Joint ci ratio: 1.211682e-01	ci left: 1.465178e-03	ci right 1.655592e-03	k: 1044	n:670000
Cons ci ratio: 3.868283e-03	ci left: 6.039940e-01	ci right 6.063364e-01	k: 405461	n:670000
KS ci ratio: 1.211682e-01	ci left: 1.465178e-03	ci right 1.655592e-03	k: 1044	n:670000
FBXO21   670000 perm   299 sec   (2245 perm/sec)   p_kst 1.558209e-03   p_cons 6.051657e-01   p_joint 1.558209e-03

Joint ci ratio: 1.204788e-01	ci left: 1.460744e-03	ci right 1.649425e-03	k: 1056	n:680000
Cons ci ratio: 3.840511e-03	ci left: 6.039061e-01	ci right 6.062313e-01	k: 411447	n:680000
KS ci ratio: 1.204788e-01	ci left: 1.460744e-03	ci right 1.649425e-03	k: 1056	n:680000
FBXO21   680000 perm   305 sec   (2227 perm/sec)   p_kst 1.552941e-03   p_cons 6.050691e-01   p_joint 1.552941e-03

Joint ci ratio: 1.198571e-01	ci left: 1.455037e-03	ci right 1.641942e-03	k: 1067	n:690000
Cons ci ratio: 3.812148e-03	ci left: 6.039686e-01	ci right 6.062769e-01	k: 417535	n:690000
KS ci ratio: 1.198571e-01	ci left: 1.455037e-03	ci right 1.641942e-03	k: 1067	n:690000
FBXO21   690000 perm   312 sec   (2209 perm/sec)   p_kst 1.546377e-03   p_cons 6.051232e-01   p_joint 1.546377e-03

Joint ci ratio: 1.192450e-01	ci left: 1.449495e-03	ci right 1.634670e-03	k: 1078	n:700000
Cons ci ratio: 3.784292e-03	ci left: 6.040438e-01	ci right 6.063354e-01	k: 423633	n:700000
KS ci ratio: 1.192450e-01	ci left: 1.449495e-03	ci right 1.634670e-03	k: 1078	n:700000
FBXO21   700000 perm   319 sec   (2192 perm/sec)   p_kst 1.540000e-03   p_cons 6.051900e-01   p_joint 1.540000e-03

Joint ci ratio: 1.187513e-01	ci left: 1.441378e-03	ci right 1.624700e-03	k: 1087	n:710000
Cons ci ratio: 3.756682e-03	ci left: 6.041619e-01	ci right 6.064372e-01	k: 429763	n:710000
KS ci ratio: 1.187513e-01	ci left: 1.441378e-03	ci right 1.624700e-03	k: 1087	n:710000
FBXO21   710000 perm   326 sec   (2175 perm/sec)   p_kst 1.530986e-03   p_cons 6.053000e-01   p_joint 1.530986e-03

Joint ci ratio: 1.176743e-01	ci left: 1.448315e-03	ci right 1.630733e-03	k: 1107	n:720000
Cons ci ratio: 3.730774e-03	ci left: 6.041351e-01	ci right 6.063946e-01	k: 435791	n:720000
KS ci ratio: 1.176743e-01	ci left: 1.448315e-03	ci right 1.630733e-03	k: 1107	n:720000
FBXO21   720000 perm   334 sec   (2157 perm/sec)   p_kst 1.537500e-03   p_cons 6.052653e-01   p_joint 1.537500e-03

Joint ci ratio: 1.168858e-01	ci left: 1.448420e-03	ci right 1.629545e-03	k: 1122	n:730000
Cons ci ratio: 3.706829e-03	ci left: 6.039241e-01	ci right 6.061682e-01	k: 441684	n:730000
KS ci ratio: 1.168858e-01	ci left: 1.448420e-03	ci right 1.629545e-03	k: 1122	n:730000
FBXO21   730000 perm   341 sec   (2141 perm/sec)   p_kst 1.536986e-03   p_cons 6.050466e-01   p_joint 1.536986e-03

Joint ci ratio: 1.161640e-01	ci left: 1.447215e-03	ci right 1.626994e-03	k: 1136	n:740000
Cons ci ratio: 3.681401e-03	ci left: 6.039703e-01	ci right 6.061992e-01	k: 447763	n:740000
KS ci ratio: 1.161640e-01	ci left: 1.447215e-03	ci right 1.626994e-03	k: 1136	n:740000
FBXO21   740000 perm   348 sec   (2125 perm/sec)   p_kst 1.535135e-03   p_cons 6.050851e-01   p_joint 1.535135e-03

Joint ci ratio: 1.155058e-01	ci left: 1.444749e-03	ci right 1.623136e-03	k: 1149	n:750000
Cons ci ratio: 3.657274e-03	ci left: 6.039126e-01	ci right 6.061266e-01	k: 453765	n:750000
KS ci ratio: 1.155058e-01	ci left: 1.444749e-03	ci right 1.623136e-03	k: 1149	n:750000
FBXO21   750000 perm   356 sec   (2108 perm/sec)   p_kst 1.532000e-03   p_cons 6.050200e-01   p_joint 1.532000e-03

Joint ci ratio: 1.146121e-01	ci left: 1.448742e-03	ci right 1.626144e-03	k: 1167	n:760000
Cons ci ratio: 3.633025e-03	ci left: 6.039341e-01	ci right 6.061335e-01	k: 459826	n:760000
KS ci ratio: 1.146121e-01	ci left: 1.448742e-03	ci right 1.626144e-03	k: 1167	n:760000
FBXO21   760000 perm   364 sec   (2089 perm/sec)   p_kst 1.535526e-03   p_cons 6.050342e-01   p_joint 1.535526e-03

Joint ci ratio: 1.137388e-01	ci left: 1.452637e-03	ci right 1.629069e-03	k: 1185	n:770000
Cons ci ratio: 3.610734e-03	ci left: 6.037589e-01	ci right 6.059442e-01	k: 465736	n:770000
KS ci ratio: 1.137388e-01	ci left: 1.452637e-03	ci right 1.629069e-03	k: 1185	n:770000
FBXO21   770000 perm   372 sec   (2070 perm/sec)   p_kst 1.538961e-03   p_cons 6.048519e-01   p_joint 1.538961e-03

Joint ci ratio: 1.133102e-01	ci left: 1.445224e-03	ci right 1.620050e-03	k: 1194	n:780000
Cons ci ratio: 3.587788e-03	ci left: 6.037294e-01	ci right 6.059006e-01	k: 471756	n:780000
KS ci ratio: 1.133102e-01	ci left: 1.445224e-03	ci right 1.620050e-03	k: 1194	n:780000
FBXO21   780000 perm   380 sec   (2054 perm/sec)   p_kst 1.530769e-03   p_cons 6.048154e-01   p_joint 1.530769e-03

Joint ci ratio: 1.123271e-01	ci left: 1.452762e-03	ci right 1.626875e-03	k: 1215	n:790000
Cons ci ratio: 3.565718e-03	ci left: 6.036411e-01	ci right 6.057986e-01	k: 477729	n:790000
KS ci ratio: 1.123271e-01	ci left: 1.452762e-03	ci right 1.626875e-03	k: 1215	n:790000
FBXO21   790000 perm   387 sec   (2039 perm/sec)   p_kst 1.537975e-03   p_cons 6.047203e-01   p_joint 1.537975e-03

Joint ci ratio: 1.113692e-01	ci left: 1.460119e-03	ci right 1.633523e-03	k: 1236	n:800000
Cons ci ratio: 3.542910e-03	ci left: 6.037089e-01	ci right 6.058528e-01	k: 483825	n:800000
KS ci ratio: 1.113692e-01	ci left: 1.460119e-03	ci right 1.633523e-03	k: 1236	n:800000
FBXO21   800000 perm   395 sec   (2025 perm/sec)   p_kst 1.545000e-03   p_cons 6.047813e-01   p_joint 1.545000e-03

Joint ci ratio: 1.107000e-01	ci left: 1.460097e-03	ci right 1.632388e-03	k: 1251	n:810000
Cons ci ratio: 3.520580e-03	ci left: 6.037689e-01	ci right 6.058995e-01	k: 489916	n:810000
KS ci ratio: 1.107000e-01	ci left: 1.460097e-03	ci right 1.632388e-03	k: 1251	n:810000
FBXO21   810000 perm   403 sec   (2010 perm/sec)   p_kst 1.544444e-03   p_cons 6.048346e-01   p_joint 1.544444e-03

Joint ci ratio: 1.101735e-01	ci left: 1.456520e-03	ci right 1.627520e-03	k: 1263	n:820000
Cons ci ratio: 3.498398e-03	ci left: 6.038641e-01	ci right 6.059815e-01	k: 496037	n:820000
KS ci ratio: 1.101735e-01	ci left: 1.456520e-03	ci right 1.627520e-03	k: 1263	n:820000
FBXO21   820000 perm   411 sec   (1996 perm/sec)   p_kst 1.540244e-03   p_cons 6.049232e-01   p_joint 1.540244e-03

Joint ci ratio: 1.096545e-01	ci left: 1.453032e-03	ci right 1.622766e-03	k: 1275	n:830000
Cons ci ratio: 3.477788e-03	ci left: 6.037979e-01	ci right 6.059026e-01	k: 502026	n:830000
KS ci ratio: 1.096545e-01	ci left: 1.453032e-03	ci right 1.622766e-03	k: 1275	n:830000
FBXO21   830000 perm   419 sec   (1982 perm/sec)   p_kst 1.536145e-03   p_cons 6.048506e-01   p_joint 1.536145e-03

Joint ci ratio: 1.091003e-01	ci left: 1.450787e-03	ci right 1.619347e-03	k: 1288	n:840000
Cons ci ratio: 3.457218e-03	ci left: 6.037774e-01	ci right 6.058695e-01	k: 508052	n:840000
KS ci ratio: 1.091003e-01	ci left: 1.450787e-03	ci right 1.619347e-03	k: 1288	n:840000
FBXO21   840000 perm   427 sec   (1968 perm/sec)   p_kst 1.533333e-03   p_cons 6.048238e-01   p_joint 1.533333e-03

Joint ci ratio: 1.085127e-01	ci left: 1.449741e-03	ci right 1.617215e-03	k: 1302	n:850000
Cons ci ratio: 3.436232e-03	ci left: 6.038657e-01	ci right 6.059454e-01	k: 514170	n:850000
KS ci ratio: 1.085127e-01	ci left: 1.449741e-03	ci right 1.617215e-03	k: 1302	n:850000
FBXO21   850000 perm   435 sec   (1954 perm/sec)   p_kst 1.531765e-03   p_cons 6.049059e-01   p_joint 1.531765e-03

Joint ci ratio: 1.079755e-01	ci left: 1.447591e-03	ci right 1.613935e-03	k: 1315	n:860000
Cons ci ratio: 3.415913e-03	ci left: 6.039112e-01	ci right 6.059788e-01	k: 520253	n:860000
KS ci ratio: 1.079755e-01	ci left: 1.447591e-03	ci right 1.613935e-03	k: 1315	n:860000
FBXO21   860000 perm   443 sec   (1940 perm/sec)   p_kst 1.529070e-03   p_cons 6.049453e-01   p_joint 1.529070e-03

Joint ci ratio: 1.076086e-01	ci left: 1.441017e-03	ci right 1.606008e-03	k: 1324	n:870000
Cons ci ratio: 3.396596e-03	ci left: 6.038649e-01	ci right 6.059206e-01	k: 526257	n:870000
KS ci ratio: 1.076086e-01	ci left: 1.441017e-03	ci right 1.606008e-03	k: 1324	n:870000
FBXO21   870000 perm   452 sec   (1925 perm/sec)   p_kst 1.521839e-03   p_cons 6.048931e-01   p_joint 1.521839e-03

Joint ci ratio: 1.071248e-01	ci left: 1.437912e-03	ci right 1.601761e-03	k: 1336	n:880000
Cons ci ratio: 3.377234e-03	ci left: 6.038720e-01	ci right 6.059160e-01	k: 532307	n:880000
KS ci ratio: 1.071248e-01	ci left: 1.437912e-03	ci right 1.601761e-03	k: 1336	n:880000
FBXO21   880000 perm   460 sec   (1911 perm/sec)   p_kst 1.518182e-03   p_cons 6.048943e-01   p_joint 1.518182e-03

Joint ci ratio: 1.065289e-01	ci left: 1.438159e-03	ci right 1.601068e-03	k: 1351	n:890000
Cons ci ratio: 3.358017e-03	ci left: 6.039048e-01	ci right 6.059372e-01	k: 538380	n:890000
KS ci ratio: 1.065289e-01	ci left: 1.438159e-03	ci right 1.601068e-03	k: 1351	n:890000
FBXO21   890000 perm   469 sec   (1898 perm/sec)   p_kst 1.517978e-03   p_cons 6.049213e-01   p_joint 1.517978e-03

Joint ci ratio: 1.057493e-01	ci left: 1.443812e-03	ci right 1.606090e-03	k: 1371	n:900000
Cons ci ratio: 3.339520e-03	ci left: 6.038802e-01	ci right 6.059013e-01	k: 544402	n:900000
KS ci ratio: 1.057493e-01	ci left: 1.443812e-03	ci right 1.606090e-03	k: 1371	n:900000
FBXO21   900000 perm   478 sec   (1885 perm/sec)   p_kst 1.523333e-03   p_cons 6.048911e-01   p_joint 1.523333e-03

Joint ci ratio: 1.050244e-01	ci left: 1.448275e-03	ci right 1.609869e-03	k: 1390	n:910000
Cons ci ratio: 3.320883e-03	ci left: 6.039200e-01	ci right 6.059299e-01	k: 550482	n:910000
KS ci ratio: 1.050244e-01	ci left: 1.448275e-03	ci right 1.609869e-03	k: 1390	n:910000
FBXO21   910000 perm   486 sec   (1871 perm/sec)   p_kst 1.527473e-03   p_cons 6.049253e-01   p_joint 1.527473e-03

Joint ci ratio: 1.044255e-01	ci left: 1.449469e-03	ci right 1.610217e-03	k: 1406	n:920000
Cons ci ratio: 3.303126e-03	ci left: 6.038762e-01	ci right 6.058753e-01	k: 556486	n:920000
KS ci ratio: 1.044255e-01	ci left: 1.449469e-03	ci right 1.610217e-03	k: 1406	n:920000
FBXO21   920000 perm   495 sec   (1858 perm/sec)   p_kst 1.528261e-03   p_cons 6.048761e-01   p_joint 1.528261e-03

Joint ci ratio: 1.039099e-01	ci left: 1.448545e-03	ci right 1.608349e-03	k: 1420	n:930000
Cons ci ratio: 3.285554e-03	ci left: 6.038475e-01	ci right 6.058357e-01	k: 562503	n:930000
KS ci ratio: 1.039099e-01	ci left: 1.448545e-03	ci right 1.608349e-03	k: 1420	n:930000
FBXO21   930000 perm   504 sec   (1845 perm/sec)   p_kst 1.526882e-03   p_cons 6.048419e-01   p_joint 1.526882e-03

Joint ci ratio: 1.033297e-01	ci left: 1.449715e-03	ci right 1.608701e-03	k: 1436	n:940000
Cons ci ratio: 3.267976e-03	ci left: 6.038608e-01	ci right 6.058385e-01	k: 568559	n:940000
KS ci ratio: 1.033297e-01	ci left: 1.449715e-03	ci right 1.608701e-03	k: 1436	n:940000
FBXO21   940000 perm   513 sec   (1832 perm/sec)   p_kst 1.527660e-03   p_cons 6.048500e-01   p_joint 1.527660e-03

Joint ci ratio: 1.027946e-01	ci left: 1.449837e-03	ci right 1.607964e-03	k: 1451	n:950000
Cons ci ratio: 3.251120e-03	ci left: 6.038087e-01	ci right 6.057759e-01	k: 574553	n:950000
KS ci ratio: 1.027946e-01	ci left: 1.449837e-03	ci right 1.607964e-03	k: 1451	n:950000
FBXO21   950000 perm   522 sec   (1820 perm/sec)   p_kst 1.527368e-03   p_cons 6.047926e-01   p_joint 1.527368e-03

Joint ci ratio: 1.022329e-01	ci left: 1.450974e-03	ci right 1.608308e-03	k: 1467	n:960000
Cons ci ratio: 3.234650e-03	ci left: 6.037389e-01	ci right 6.056959e-01	k: 580529	n:960000
KS ci ratio: 1.022329e-01	ci left: 1.450974e-03	ci right 1.608308e-03	k: 1467	n:960000
FBXO21   960000 perm   531 sec   (1807 perm/sec)   p_kst 1.528125e-03   p_cons 6.047177e-01   p_joint 1.528125e-03

Joint ci ratio: 1.016802e-01	ci left: 1.452090e-03	ci right 1.608643e-03	k: 1483	n:970000
Cons ci ratio: 3.217532e-03	ci left: 6.038036e-01	ci right 6.057504e-01	k: 586634	n:970000
KS ci ratio: 1.016802e-01	ci left: 1.452090e-03	ci right 1.608643e-03	k: 1483	n:970000
FBXO21   970000 perm   541 sec   (1794 perm/sec)   p_kst 1.528866e-03   p_cons 6.047773e-01   p_joint 1.528866e-03

Joint ci ratio: 1.009009e-01	ci left: 1.460148e-03	ci right 1.616291e-03	k: 1506	n:980000
Cons ci ratio: 3.201100e-03	ci left: 6.038047e-01	ci right 6.057416e-01	k: 592678	n:980000
KS ci ratio: 1.009009e-01	ci left: 1.460148e-03	ci right 1.616291e-03	k: 1506	n:980000
FBXO21   980000 perm   550 sec   (1781 perm/sec)   p_kst 1.536735e-03   p_cons 6.047735e-01   p_joint 1.536735e-03

Joint ci ratio: 1.001065e-01	ci left: 1.469032e-03	ci right 1.624816e-03	k: 1530	n:990000
Cons ci ratio: 3.184870e-03	ci left: 6.038129e-01	ci right 6.057400e-01	k: 598729	n:990000
KS ci ratio: 1.001065e-01	ci left: 1.469032e-03	ci right 1.624816e-03	k: 1530	n:990000
FBXO21   990000 perm   560 sec   (1769 perm/sec)   p_kst 1.545455e-03   p_cons 6.047768e-01   p_joint 1.545455e-03

Joint ci ratio: 9.965196e-02	ci left: 1.467992e-03	ci right 1.622918e-03	k: 1544	n:1000000
Cons ci ratio: 3.169129e-03	ci left: 6.037840e-01	ci right 6.057014e-01	k: 604743	n:1000000
KS ci ratio: 9.965196e-02	ci left: 1.467992e-03	ci right 1.622918e-03	k: 1544	n:1000000
FBXO21   1000000 perm   569 sec   (1757 perm/sec)   p_kst 1.544000e-03   p_cons 6.047430e-01   p_joint 1.544000e-03

Outputting figure to mutsig2_images.part000000000063/FBXO21.2_1935_1000000_0.001544_0.60474_0.001544.png
                gene_name: FBXO21
               theta_stop: 0.100 
                    nperm: 1000000 
                     p_ks: 0.0015 
        ci_ks_bounds_left: 0.0015 
       ci_ks_bounds_right: 0.0016 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.60 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.0015 
     ci_joint_bounds_left: 0.0015 
    ci_joint_bounds_right: 0.0016 

Current progress: 75 percent done.
FBXO4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.207474e-02	ci left: 3.521745e-01	ci right 3.711061e-01	k: 3616	n:10000
Cons ci ratio: 8.093572e-02	ci left: 1.822537e-01	ci right 1.977273e-01	k: 1899	n:10000
KS ci ratio: 3.780791e-02	ci left: 5.081525e-01	ci right 5.278370e-01	k: 5180	n:10000
FBXO4   10000 perm   2 sec   (6544 perm/sec)   p_kst 5.180000e-01   p_cons 1.899000e-01   p_joint 3.616000e-01

Outputting figure to mutsig2_images.part000000000063/FBXO4.2_1218_10000_0.518_0.1899_0.3616.png
                gene_name: FBXO4
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 88 percent done.
FBXO40
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: 9.545154e-03	ci left: 9.394165e-01	ci right 9.485227e-01	k: 9441	n:10000
KS ci ratio: 2.017470e-02	ci left: 7.824912e-01	ci right 7.985392e-01	k: 7906	n:10000
FBXO40   10000 perm   2 sec   (6071 perm/sec)   p_kst 7.906000e-01   p_cons 9.441000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000063/FBXO40.2_2142_10000_0.7906_0.9441_1.png
                gene_name: FBXO40
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.80 
                   p_cons: 0.94 
      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.165.3896/
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/181708/iteration1/scatter.0000000063
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 63 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119855: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000064> was used as the working directory.
Started at Wed Oct 10 10:42:59 2012
Results reported at Wed Oct 10 10:49:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000064.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000064.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 64  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    462.58 sec.
    Max Memory :      1179 MB
    Max Swap   :      3865 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.165.3896/
-whichjob
64
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 64: processing genes 5701 - 5790
Calculating significance of each gene.
Using projection method.
5701	FBXW11	1.698299e-01
5702	FBXW12	1.277681e-01
5703	FBXW2	1
5704	FBXW4	1
5705	FBXW5	1.817558e-02
5706	FBXW7	1.081328e-05
5707	FBXW8	1
5708	FBXW9	2.007001e-01
5709	FCAMR	1
5710	FCAR	1
5711	FCER1A	1
5712	FCER1G	1
5713	FCER2	1
5714	FCF1	1
5715	FCGBP	7.352509e-01
5716	FCGR1A	1
5717	FCGR1B	1
5718	FCGR2A	1
5719	FCGR2B	1
5720	FCGR2C	1
5721	FCGR3A	1
5722	FCGR3B	5.624868e-02
5723	FCGRT	1
5724	FCHO1	1
5725	FCHO2	1
5726	FCHSD1	2.075878e-01
5727	FCHSD2	1
5728	FCN1	1
5729	FCN2	1
5730	FCN3	8.556949e-02
5731	FCRL1	1
5732	FCRL2	1
5733	FCRL3	1
5734	FCRL4	1
5735	FCRL5	4.335962e-01
5736	FCRL6	1
5737	FCRLA	1
5738	FCRLB	1
5739	FDFT1	1
5740	FDPS	1
5741	FDX1	1
5742	FDX1L	1
5743	FDXACB1	1
5744	FDXR	1
5745	FECH	1
5746	FEM1A	8.656442e-02
5747	FEM1B	1
5748	FEM1C	1
5749	FEN1	1
5750	FER	3.644616e-01
5751	FER1L5	5.724426e-02
5752	FER1L6	6.591750e-01
5753	FERD3L	1.001384e-02
5754	FERMT1	1
5755	FERMT2	1
5756	FERMT3	1
5757	FES	1
5758	FETUB	1
5759	FEV	1
5760	FEZ1	1
5761	FEZ2	4.448910e-03
5762	FEZF1	1
5763	FEZF2	1
5764	FFAR1	1
5765	FFAR2	1
5766	FFAR3	1
5767	FGA	5.011884e-03
5768	FGB	1
5769	FGD1	7.775920e-03
5770	FGD2	1
5771	FGD3	1
5772	FGD4	3.466819e-01
5773	FGD5	4.101905e-01
5774	FGD6	4.632675e-01
5775	FGF1	1
5776	FGF10	1
5777	FGF11	1
5778	FGF12	1
5779	FGF13	1
5780	FGF14	1
5781	FGF16	1
5782	FGF17	1
5783	FGF18	1
5784	FGF19	1
5785	FGF2	1
5786	FGF20	1
5787	FGF21	1
5788	FGF22	1
5789	FGF23	1
5790	FGF3	2.277555e-02
Done

Running MutSig 2:
Scatter job 64: processing genes 5701 - 5790
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FBXW7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.003467e-01	ci left: 4.581663e-03	ci right 7.716529e-03	k: 60	n:10000
Cons ci ratio: 1.597330e-01	ci left: 5.224686e-02	ci right 6.141345e-02	k: 567	n:10000
KS ci ratio: 8.163954e-01	ci left: 1.379226e-03	ci right 3.328943e-03	k: 22	n:10000
FBXW7   10000 perm   2 sec   (4070 perm/sec)   p_kst 2.200000e-03   p_cons 5.670000e-02   p_joint 6.000000e-03

Joint ci ratio: 4.373811e-01	ci left: 3.128462e-03	ci right 4.920482e-03	k: 79	n:20000
Cons ci ratio: 1.121678e-01	ci left: 5.431319e-02	ci right 6.081619e-02	k: 1150	n:20000
KS ci ratio: 5.230852e-01	ci left: 2.072328e-03	ci right 3.578018e-03	k: 55	n:20000
FBXW7   20000 perm   9 sec   (2184 perm/sec)   p_kst 2.750000e-03   p_cons 5.750000e-02   p_joint 3.950000e-03

Joint ci ratio: 4.933466e-01	ci left: 1.584857e-03	ci right 2.648601e-03	k: 62	n:30000
Cons ci ratio: 9.222460e-02	ci left: 5.417457e-02	ci right 5.944500e-02	k: 1703	n:30000
KS ci ratio: 4.296732e-01	ci left: 2.174473e-03	ci right 3.391668e-03	k: 82	n:30000
FBXW7   30000 perm   12 sec   (2470 perm/sec)   p_kst 2.733333e-03   p_cons 5.676667e-02   p_joint 2.066667e-03

Joint ci ratio: 2.800285e-01	ci left: 4.192829e-03	ci right 5.580551e-03	k: 194	n:40000
Cons ci ratio: 7.949883e-02	ci left: 5.501754e-02	ci right 5.959699e-02	k: 2291	n:40000
KS ci ratio: 3.838828e-01	ci left: 2.102270e-03	ci right 3.122080e-03	k: 103	n:40000
FBXW7   40000 perm   15 sec   (2637 perm/sec)   p_kst 2.575000e-03   p_cons 5.727500e-02   p_joint 4.850000e-03

Joint ci ratio: 2.759364e-01	ci left: 3.465711e-03	ci right 4.593073e-03	k: 200	n:50000
Cons ci ratio: 7.129103e-02	ci left: 5.498361e-02	ci right 5.906801e-02	k: 2850	n:50000
KS ci ratio: 3.544634e-01	ci left: 2.008446e-03	ci right 2.890909e-03	k: 121	n:50000
FBXW7   50000 perm   18 sec   (2752 perm/sec)   p_kst 2.420000e-03   p_cons 5.700000e-02   p_joint 4.000000e-03

Joint ci ratio: 2.231513e-01	ci left: 4.545749e-03	ci right 5.702915e-03	k: 306	n:60000
Cons ci ratio: 6.556056e-02	ci left: 5.438676e-02	ci right 5.808964e-02	k: 3373	n:60000
KS ci ratio: 3.240239e-01	ci left: 2.039699e-03	ci right 2.842973e-03	k: 145	n:60000
FBXW7   60000 perm   21 sec   (2853 perm/sec)   p_kst 2.416667e-03   p_cons 5.621667e-02   p_joint 5.100000e-03

Joint ci ratio: 1.529198e-01	ci left: 8.588442e-03	ci right 1.002410e-02	k: 650	n:70000
Cons ci ratio: 6.092179e-02	ci left: 5.413907e-02	ci right 5.755501e-02	k: 3908	n:70000
KS ci ratio: 2.870442e-01	ci left: 2.276131e-03	ci right 3.051725e-03	k: 185	n:70000
FBXW7   70000 perm   24 sec   (2892 perm/sec)   p_kst 2.642857e-03   p_cons 5.582857e-02   p_joint 9.285714e-03

Joint ci ratio: 1.689077e-01	ci left: 6.122445e-03	ci right 7.263771e-03	k: 534	n:80000
Cons ci ratio: 5.720740e-02	ci left: 5.384936e-02	ci right 5.703297e-02	k: 4434	n:80000
KS ci ratio: 2.676054e-01	ci left: 2.317310e-03	ci right 3.044503e-03	k: 213	n:80000
FBXW7   80000 perm   27 sec   (2929 perm/sec)   p_kst 2.662500e-03   p_cons 5.542500e-02   p_joint 6.675000e-03

Joint ci ratio: 1.584382e-01	ci left: 6.220111e-03	ci right 7.300937e-03	k: 607	n:90000
Cons ci ratio: 5.394928e-02	ci left: 5.391426e-02	ci right 5.691448e-02	k: 4986	n:90000
KS ci ratio: 2.532254e-01	ci left: 2.319489e-03	ci right 3.002085e-03	k: 238	n:90000
FBXW7   90000 perm   31 sec   (2943 perm/sec)   p_kst 2.644444e-03   p_cons 5.540000e-02   p_joint 6.744444e-03

Joint ci ratio: 1.560574e-01	ci left: 5.780519e-03	ci right 6.768447e-03	k: 626	n:100000
Cons ci ratio: 5.111790e-02	ci left: 5.411850e-02	ci right 5.696735e-02	k: 5553	n:100000
KS ci ratio: 2.373603e-01	ci left: 2.397286e-03	ci right 3.052087e-03	k: 271	n:100000
FBXW7   100000 perm   34 sec   (2959 perm/sec)   p_kst 2.710000e-03   p_cons 5.553000e-02   p_joint 6.260000e-03

Joint ci ratio: 1.495276e-01	ci left: 5.744641e-03	ci right 6.681680e-03	k: 682	n:110000
Cons ci ratio: 4.869431e-02	ci left: 5.427999e-02	ci right 5.699804e-02	k: 6119	n:110000
KS ci ratio: 2.283123e-01	ci left: 2.367684e-03	ci right 2.986274e-03	k: 293	n:110000
FBXW7   110000 perm   37 sec   (2964 perm/sec)   p_kst 2.663636e-03   p_cons 5.562727e-02   p_joint 6.200000e-03

Joint ci ratio: 1.540540e-01	ci left: 4.953105e-03	ci right 5.787740e-03	k: 643	n:120000
Cons ci ratio: 4.658568e-02	ci left: 5.441723e-02	ci right 5.702096e-02	k: 6685	n:120000
KS ci ratio: 2.168127e-01	ci left: 2.422193e-03	ci right 3.018909e-03	k: 325	n:120000
FBXW7   120000 perm   41 sec   (2961 perm/sec)   p_kst 2.708333e-03   p_cons 5.570833e-02   p_joint 5.358333e-03

Joint ci ratio: 1.380785e-01	ci left: 5.735928e-03	ci right 6.594017e-03	k: 800	n:130000
Cons ci ratio: 4.472594e-02	ci left: 5.454311e-02	ci right 5.704599e-02	k: 7252	n:130000
KS ci ratio: 2.068922e-01	ci left: 2.468977e-03	ci right 3.045867e-03	k: 357	n:130000
FBXW7   130000 perm   44 sec   (2954 perm/sec)   p_kst 2.746154e-03   p_cons 5.578462e-02   p_joint 6.153846e-03

Joint ci ratio: 1.322571e-01	ci left: 5.823135e-03	ci right 6.654657e-03	k: 872	n:140000
Cons ci ratio: 4.306085e-02	ci left: 5.468105e-02	ci right 5.709452e-02	k: 7823	n:140000
KS ci ratio: 1.979652e-01	ci left: 2.516398e-03	ci right 3.075939e-03	k: 390	n:140000
FBXW7   140000 perm   48 sec   (2943 perm/sec)   p_kst 2.785714e-03   p_cons 5.587857e-02   p_joint 6.228571e-03

Joint ci ratio: 1.366849e-01	ci left: 5.080457e-03	ci right 5.832187e-03	k: 817	n:150000
Cons ci ratio: 4.160562e-02	ci left: 5.470969e-02	ci right 5.704085e-02	k: 8380	n:150000
KS ci ratio: 1.921582e-01	ci left: 2.500823e-03	ci right 3.038683e-03	k: 414	n:150000
FBXW7   150000 perm   51 sec   (2928 perm/sec)   p_kst 2.760000e-03   p_cons 5.586667e-02   p_joint 5.446667e-03

Joint ci ratio: 1.349777e-01	ci left: 4.889685e-03	ci right 5.603423e-03	k: 838	n:160000
Cons ci ratio: 4.021955e-02	ci left: 5.491548e-02	ci right 5.717564e-02	k: 8966	n:160000
KS ci ratio: 1.864087e-01	ci left: 2.499323e-03	ci right 3.018956e-03	k: 440	n:160000
FBXW7   160000 perm   55 sec   (2911 perm/sec)   p_kst 2.750000e-03   p_cons 5.603750e-02   p_joint 5.237500e-03

Joint ci ratio: 1.313510e-01	ci left: 4.869314e-03	ci right 5.559490e-03	k: 885	n:170000
Cons ci ratio: 3.900447e-02	ci left: 5.498745e-02	ci right 5.718066e-02	k: 9533	n:170000
KS ci ratio: 1.817324e-01	ci left: 2.481362e-03	ci right 2.982894e-03	k: 463	n:170000
FBXW7   170000 perm   59 sec   (2887 perm/sec)   p_kst 2.723529e-03   p_cons 5.607647e-02   p_joint 5.205882e-03

Joint ci ratio: 1.326551e-01	ci left: 4.507415e-03	ci right 5.153137e-03	k: 868	n:180000
Cons ci ratio: 3.800099e-02	ci left: 5.475502e-02	ci right 5.688154e-02	k: 10046	n:180000
KS ci ratio: 1.772089e-01	ci left: 2.470851e-03	ci right 2.956496e-03	k: 487	n:180000
FBXW7   180000 perm   63 sec   (2866 perm/sec)   p_kst 2.705556e-03   p_cons 5.581111e-02   p_joint 4.822222e-03

Joint ci ratio: 1.366800e-01	ci left: 4.015818e-03	ci right 4.609988e-03	k: 818	n:190000
Cons ci ratio: 3.699700e-02	ci left: 5.475640e-02	ci right 5.682560e-02	k: 10599	n:190000
KS ci ratio: 1.708459e-01	ci left: 2.527069e-03	ci right 3.004092e-03	k: 524	n:190000
FBXW7   190000 perm   67 sec   (2843 perm/sec)   p_kst 2.757895e-03   p_cons 5.578421e-02   p_joint 4.305263e-03

Joint ci ratio: 1.343273e-01	ci left: 3.955103e-03	ci right 4.529412e-03	k: 847	n:200000
Cons ci ratio: 3.609603e-02	ci left: 5.467900e-02	ci right 5.669390e-02	k: 11136	n:200000
KS ci ratio: 1.658639e-01	ci left: 2.553978e-03	ci right 3.020619e-03	k: 556	n:200000
FBXW7   200000 perm   71 sec   (2811 perm/sec)   p_kst 2.780000e-03   p_cons 5.568000e-02   p_joint 4.235000e-03

Joint ci ratio: 1.313421e-01	ci left: 3.946307e-03	ci right 4.505610e-03	k: 886	n:210000
Cons ci ratio: 3.516066e-02	ci left: 5.489759e-02	ci right 5.686707e-02	k: 11734	n:210000
KS ci ratio: 1.610198e-01	ci left: 2.587647e-03	ci right 3.045296e-03	k: 590	n:210000
FBXW7   210000 perm   75 sec   (2788 perm/sec)   p_kst 2.809524e-03   p_cons 5.587619e-02   p_joint 4.219048e-03

Joint ci ratio: 1.287571e-01	ci left: 3.925239e-03	ci right 4.469770e-03	k: 922	n:220000
Cons ci ratio: 3.436827e-02	ci left: 5.487149e-02	ci right 5.679478e-02	k: 12282	n:220000
KS ci ratio: 1.574635e-01	ci left: 2.587864e-03	ci right 3.034487e-03	k: 617	n:220000
FBXW7   220000 perm   80 sec   (2764 perm/sec)   p_kst 2.804545e-03   p_cons 5.582727e-02   p_joint 4.190909e-03

Joint ci ratio: 1.287689e-01	ci left: 3.754555e-03	ci right 4.275458e-03	k: 922	n:230000
Cons ci ratio: 3.366606e-02	ci left: 5.472733e-02	ci right 5.660562e-02	k: 12802	n:230000
KS ci ratio: 1.544937e-01	ci left: 2.575621e-03	ci right 3.010972e-03	k: 641	n:230000
FBXW7   230000 perm   84 sec   (2728 perm/sec)   p_kst 2.786957e-03   p_cons 5.566087e-02   p_joint 4.008696e-03

Joint ci ratio: 1.271985e-01	ci left: 3.690872e-03	ci right 4.196223e-03	k: 945	n:240000
Cons ci ratio: 3.300913e-02	ci left: 5.458317e-02	ci right 5.641925e-02	k: 13319	n:240000
KS ci ratio: 1.516857e-01	ci left: 2.564472e-03	ci right 2.989344e-03	k: 665	n:240000
FBXW7   240000 perm   89 sec   (2705 perm/sec)   p_kst 2.770833e-03   p_cons 5.549583e-02   p_joint 3.937500e-03

Joint ci ratio: 1.245916e-01	ci left: 3.698200e-03	ci right 4.193410e-03	k: 985	n:250000
Cons ci ratio: 3.235086e-02	ci left: 5.457392e-02	ci right 5.637240e-02	k: 13867	n:250000
KS ci ratio: 1.488094e-01	ci left: 2.561983e-03	ci right 2.977678e-03	k: 691	n:250000
FBXW7   250000 perm   93 sec   (2682 perm/sec)   p_kst 2.764000e-03   p_cons 5.546800e-02   p_joint 3.940000e-03

Joint ci ratio: 1.239716e-01	ci left: 3.593215e-03	ci right 4.071796e-03	k: 995	n:260000
Cons ci ratio: 3.170253e-02	ci left: 5.465734e-02	ci right 5.642182e-02	k: 14439	n:260000
KS ci ratio: 1.463977e-01	ci left: 2.548639e-03	ci right 2.954880e-03	k: 714	n:260000
FBXW7   260000 perm   98 sec   (2658 perm/sec)   p_kst 2.746154e-03   p_cons 5.553462e-02   p_joint 3.826923e-03

Joint ci ratio: 1.576325e-01	ci left: 2.105030e-03	ci right 2.468748e-03	k: 616	n:270000
Cons ci ratio: 3.109057e-02	ci left: 5.473859e-02	ci right 5.647097e-02	k: 15012	n:270000
KS ci ratio: 1.439042e-01	ci left: 2.543474e-03	ci right 2.941393e-03	k: 739	n:270000
FBXW7   270000 perm   102 sec   (2635 perm/sec)   p_kst 2.737037e-03   p_cons 5.560000e-02   p_joint 2.281481e-03

Joint ci ratio: 1.609403e-01	ci left: 1.944110e-03	ci right 2.287754e-03	k: 591	n:280000
Cons ci ratio: 3.052726e-02	ci left: 5.476470e-02	ci right 5.646595e-02	k: 15571	n:280000
KS ci ratio: 1.413487e-01	ci left: 2.545623e-03	ci right 2.936211e-03	k: 766	n:280000
FBXW7   280000 perm   108 sec   (2600 perm/sec)   p_kst 2.735714e-03   p_cons 5.561071e-02   p_joint 2.110714e-03

Joint ci ratio: 1.634554e-01	ci left: 1.817512e-03	ci right 2.144292e-03	k: 573	n:290000
Cons ci ratio: 3.000631e-02	ci left: 5.474476e-02	ci right 5.641586e-02	k: 16117	n:290000
KS ci ratio: 1.387497e-01	ci left: 2.554340e-03	ci right 2.938463e-03	k: 795	n:290000
FBXW7   290000 perm   113 sec   (2568 perm/sec)   p_kst 2.741379e-03   p_cons 5.557586e-02   p_joint 1.975862e-03

Joint ci ratio: 1.593416e-01	ci left: 1.852893e-03	ci right 2.176848e-03	k: 603	n:300000
Cons ci ratio: 2.951396e-02	ci left: 5.471645e-02	ci right 5.635882e-02	k: 16660	n:300000
KS ci ratio: 1.353868e-01	ci left: 2.597961e-03	ci right 2.978412e-03	k: 835	n:300000
FBXW7   300000 perm   118 sec   (2532 perm/sec)   p_kst 2.783333e-03   p_cons 5.553333e-02   p_joint 2.010000e-03

Joint ci ratio: 1.565162e-01	ci left: 1.861286e-03	ci right 2.180396e-03	k: 625	n:310000
Cons ci ratio: 2.900938e-02	ci left: 5.481832e-02	ci right 5.643516e-02	k: 17243	n:310000
KS ci ratio: 1.329437e-01	ci left: 2.610800e-03	ci right 2.985687e-03	k: 866	n:310000
FBXW7   310000 perm   124 sec   (2507 perm/sec)   p_kst 2.793548e-03   p_cons 5.562258e-02   p_joint 2.016129e-03

Joint ci ratio: 1.534803e-01	ci left: 1.878217e-03	ci right 2.193410e-03	k: 650	n:320000
Cons ci ratio: 2.855698e-02	ci left: 5.481473e-02	ci right 5.640583e-02	k: 17794	n:320000
KS ci ratio: 1.304100e-01	ci left: 2.631965e-03	ci right 3.002130e-03	k: 900	n:320000
FBXW7   320000 perm   129 sec   (2485 perm/sec)   p_kst 2.812500e-03   p_cons 5.560625e-02   p_joint 2.031250e-03

Joint ci ratio: 1.467494e-01	ci left: 1.999219e-03	ci right 2.318715e-03	k: 711	n:330000
Cons ci ratio: 2.810646e-02	ci left: 5.488077e-02	ci right 5.644825e-02	k: 18368	n:330000
KS ci ratio: 1.284297e-01	ci left: 2.634310e-03	ci right 2.998750e-03	k: 928	n:330000
FBXW7   330000 perm   135 sec   (2445 perm/sec)   p_kst 2.812121e-03   p_cons 5.566061e-02   p_joint 2.154545e-03

Joint ci ratio: 1.495150e-01	ci left: 1.866772e-03	ci right 2.171227e-03	k: 685	n:340000
Cons ci ratio: 2.767505e-02	ci left: 5.494896e-02	ci right 5.649391e-02	k: 18944	n:340000
KS ci ratio: 1.270707e-01	ci left: 2.613772e-03	ci right 2.971256e-03	k: 948	n:340000
FBXW7   340000 perm   141 sec   (2415 perm/sec)   p_kst 2.788235e-03   p_cons 5.571765e-02   p_joint 2.014706e-03

Joint ci ratio: 1.495193e-01	ci left: 1.813432e-03	ci right 2.109197e-03	k: 685	n:350000
Cons ci ratio: 2.728291e-02	ci left: 5.493678e-02	ci right 5.645916e-02	k: 19493	n:350000
KS ci ratio: 1.254298e-01	ci left: 2.608265e-03	ci right 2.960047e-03	k: 973	n:350000
FBXW7   350000 perm   146 sec   (2393 perm/sec)   p_kst 2.780000e-03   p_cons 5.569429e-02   p_joint 1.957143e-03

Joint ci ratio: 1.485503e-01	ci left: 1.787125e-03	ci right 2.076542e-03	k: 694	n:360000
Cons ci ratio: 2.689419e-02	ci left: 5.497510e-02	ci right 5.647650e-02	k: 20060	n:360000
KS ci ratio: 1.239131e-01	ci left: 2.600400e-03	ci right 2.946569e-03	k: 997	n:360000
FBXW7   360000 perm   153 sec   (2360 perm/sec)   p_kst 2.769444e-03   p_cons 5.572222e-02   p_joint 1.927778e-03

Joint ci ratio: 1.197205e-01	ci left: 2.716175e-03	ci right 3.064656e-03	k: 1068	n:370000
Cons ci ratio: 2.652776e-02	ci left: 5.498733e-02	ci right 5.646829e-02	k: 20618	n:370000
KS ci ratio: 1.225103e-01	ci left: 2.590364e-03	ci right 2.931011e-03	k: 1020	n:370000
FBXW7   370000 perm   158 sec   (2341 perm/sec)   p_kst 2.756757e-03   p_cons 5.572432e-02   p_joint 2.886486e-03

Joint ci ratio: 1.180211e-01	ci left: 2.723850e-03	ci right 3.068010e-03	k: 1099	n:380000
Cons ci ratio: 2.616217e-02	ci left: 5.505396e-02	ci right 5.651598e-02	k: 21197	n:380000
KS ci ratio: 1.208641e-01	ci left: 2.593638e-03	ci right 2.929805e-03	k: 1048	n:380000
FBXW7   380000 perm   164 sec   (2321 perm/sec)   p_kst 2.757895e-03   p_cons 5.578158e-02   p_joint 2.892105e-03

Joint ci ratio: 1.415886e-01	ci left: 1.822632e-03	ci right 2.102799e-03	k: 764	n:390000
Cons ci ratio: 2.583203e-02	ci left: 5.503321e-02	ci right 5.647596e-02	k: 21743	n:390000
KS ci ratio: 1.185672e-01	ci left: 2.629118e-03	ci right 2.962953e-03	k: 1089	n:390000
FBXW7   390000 perm   169 sec   (2301 perm/sec)   p_kst 2.792308e-03   p_cons 5.575128e-02   p_joint 1.958974e-03

Joint ci ratio: 1.396842e-01	ci left: 1.827719e-03	ci right 2.104575e-03	k: 785	n:400000
Cons ci ratio: 2.549893e-02	ci left: 5.507574e-02	ci right 5.650071e-02	k: 22314	n:400000
KS ci ratio: 1.172309e-01	ci left: 2.624046e-03	ci right 2.953222e-03	k: 1114	n:400000
FBXW7   400000 perm   175 sec   (2281 perm/sec)   p_kst 2.785000e-03   p_cons 5.578500e-02   p_joint 1.962500e-03

Joint ci ratio: 1.391564e-01	ci left: 1.797262e-03	ci right 2.068391e-03	k: 791	n:410000
Cons ci ratio: 2.519123e-02	ci left: 5.506296e-02	ci right 5.647016e-02	k: 22863	n:410000
KS ci ratio: 1.159897e-01	ci left: 2.616874e-03	ci right 2.941436e-03	k: 1138	n:410000
FBXW7   410000 perm   182 sec   (2258 perm/sec)   p_kst 2.775610e-03   p_cons 5.576341e-02   p_joint 1.929268e-03

Joint ci ratio: 1.404989e-01	ci left: 1.720001e-03	ci right 1.982186e-03	k: 776	n:420000
Cons ci ratio: 2.487865e-02	ci left: 5.511716e-02	ci right 5.650802e-02	k: 23440	n:420000
KS ci ratio: 1.145898e-01	ci left: 2.619312e-03	ci right 2.939990e-03	k: 1166	n:420000
FBXW7   420000 perm   188 sec   (2239 perm/sec)   p_kst 2.776190e-03   p_cons 5.580952e-02   p_joint 1.847619e-03

Joint ci ratio: 1.389869e-01	ci left: 1.718153e-03	ci right 1.977005e-03	k: 793	n:430000
Cons ci ratio: 2.457309e-02	ci left: 5.518745e-02	ci right 5.656273e-02	k: 24025	n:430000
KS ci ratio: 1.130971e-01	ci left: 2.628438e-03	ci right 2.945762e-03	k: 1197	n:430000
FBXW7   430000 perm   194 sec   (2219 perm/sec)   p_kst 2.783721e-03   p_cons 5.587209e-02   p_joint 1.844186e-03

Joint ci ratio: 1.371842e-01	ci left: 1.725183e-03	ci right 1.981448e-03	k: 814	n:440000
Cons ci ratio: 2.429578e-02	ci left: 5.518006e-02	ci right 5.653943e-02	k: 24577	n:440000
KS ci ratio: 1.117524e-01	ci left: 2.632757e-03	ci right 2.946575e-03	k: 1226	n:440000
FBXW7   440000 perm   200 sec   (2200 perm/sec)   p_kst 2.786364e-03   p_cons 5.585682e-02   p_joint 1.850000e-03

Joint ci ratio: 1.292471e-01	ci left: 1.908124e-03	ci right 2.173908e-03	k: 917	n:450000
Cons ci ratio: 2.400792e-02	ci left: 5.525927e-02	ci right 5.660423e-02	k: 25168	n:450000
KS ci ratio: 1.101910e-01	ci left: 2.649872e-03	ci right 2.961029e-03	k: 1261	n:450000
FBXW7   450000 perm   206 sec   (2180 perm/sec)   p_kst 2.802222e-03   p_cons 5.592889e-02   p_joint 2.037778e-03

Joint ci ratio: 1.335457e-01	ci left: 1.744690e-03	ci right 1.996433e-03	k: 859	n:460000
Cons ci ratio: 2.373933e-02	ci left: 5.529405e-02	ci right 5.662460e-02	k: 25740	n:460000
KS ci ratio: 1.087353e-01	ci left: 2.664156e-03	ci right 2.972594e-03	k: 1295	n:460000
FBXW7   460000 perm   213 sec   (2161 perm/sec)   p_kst 2.815217e-03   p_cons 5.595652e-02   p_joint 1.867391e-03

Joint ci ratio: 1.323209e-01	ci left: 1.740479e-03	ci right 1.989130e-03	k: 875	n:470000
Cons ci ratio: 2.349043e-02	ci left: 5.527876e-02	ci right 5.659481e-02	k: 26289	n:470000
KS ci ratio: 1.079068e-01	ci left: 2.648871e-03	ci right 2.953054e-03	k: 1315	n:470000
FBXW7   470000 perm   219 sec   (2143 perm/sec)   p_kst 2.797872e-03   p_cons 5.593404e-02   p_joint 1.861702e-03

Joint ci ratio: 9.003862e-02	ci left: 3.756182e-03	ci right 4.112347e-03	k: 1887	n:480000
Cons ci ratio: 2.325334e-02	ci left: 5.524553e-02	ci right 5.654734e-02	k: 26829	n:480000
KS ci ratio: 1.070568e-01	ci left: 2.636259e-03	ci right 2.936459e-03	k: 1336	n:480000
FBXW7   480000 perm   226 sec   (2122 perm/sec)   p_kst 2.783333e-03   p_cons 5.589375e-02   p_joint 3.931250e-03

Joint ci ratio: 9.915403e-02	ci left: 3.021893e-03	ci right 3.339129e-03	k: 1557	n:490000
Cons ci ratio: 2.299526e-02	ci left: 5.534160e-02	ci right 5.663100e-02	k: 27432	n:490000
KS ci ratio: 1.061482e-01	ci left: 2.628145e-03	ci right 2.924722e-03	k: 1359	n:490000
FBXW7   490000 perm   234 sec   (2095 perm/sec)   p_kst 2.773469e-03   p_cons 5.598367e-02   p_joint 3.177551e-03

Joint ci ratio: 9.836862e-02	ci left: 3.010219e-03	ci right 3.323582e-03	k: 1582	n:500000
Cons ci ratio: 2.277400e-02	ci left: 5.530261e-02	ci right 5.657854e-02	k: 27969	n:500000
KS ci ratio: 1.053770e-01	ci left: 2.614523e-03	ci right 2.907286e-03	k: 1379	n:500000
FBXW7   500000 perm   241 sec   (2078 perm/sec)   p_kst 2.758000e-03   p_cons 5.593800e-02   p_joint 3.164000e-03

Joint ci ratio: 9.763205e-02	ci left: 2.997100e-03	ci right 3.306626e-03	k: 1606	n:510000
Cons ci ratio: 2.256277e-02	ci left: 5.524765e-02	ci right 5.651034e-02	k: 28497	n:510000
KS ci ratio: 1.046599e-01	ci left: 2.599533e-03	ci right 2.888515e-03	k: 1398	n:510000
FBXW7   510000 perm   247 sec   (2061 perm/sec)   p_kst 2.741176e-03   p_cons 5.587647e-02   p_joint 3.149020e-03

Joint ci ratio: 9.670382e-02	ci left: 2.997630e-03	ci right 3.304101e-03	k: 1637	n:520000
Cons ci ratio: 2.234061e-02	ci left: 5.527329e-02	ci right 5.652397e-02	k: 29066	n:520000
KS ci ratio: 1.037009e-01	ci left: 2.598239e-03	ci right 2.884269e-03	k: 1424	n:520000
FBXW7   520000 perm   255 sec   (2040 perm/sec)   p_kst 2.738462e-03   p_cons 5.589615e-02   p_joint 3.148077e-03

Joint ci ratio: 9.594584e-02	ci left: 2.988945e-03	ci right 3.291998e-03	k: 1663	n:530000
Cons ci ratio: 2.213398e-02	ci left: 5.525485e-02	ci right 5.649341e-02	k: 29612	n:530000
KS ci ratio: 1.028388e-01	ci left: 2.593329e-03	ci right 2.876302e-03	k: 1448	n:530000
FBXW7   530000 perm   262 sec   (2024 perm/sec)   p_kst 2.732075e-03   p_cons 5.587170e-02   p_joint 3.137736e-03

Joint ci ratio: 9.520542e-02	ci left: 2.980591e-03	ci right 3.280335e-03	k: 1689	n:540000
Cons ci ratio: 2.193761e-02	ci left: 5.521504e-02	ci right 5.644158e-02	k: 30146	n:540000
KS ci ratio: 1.020674e-01	ci left: 2.585000e-03	ci right 2.864822e-03	k: 1470	n:540000
FBXW7   540000 perm   269 sec   (2008 perm/sec)   p_kst 2.722222e-03   p_cons 5.582593e-02   p_joint 3.127778e-03

Joint ci ratio: 9.434409e-02	ci left: 2.981426e-03	ci right 3.278392e-03	k: 1720	n:550000
Cons ci ratio: 2.173999e-02	ci left: 5.520748e-02	ci right 5.642266e-02	k: 30697	n:550000
KS ci ratio: 1.010758e-01	ci left: 2.589388e-03	ci right 2.866800e-03	k: 1499	n:550000
FBXW7   550000 perm   277 sec   (1988 perm/sec)   p_kst 2.725455e-03   p_cons 5.581273e-02   p_joint 3.127273e-03

Joint ci ratio: 9.331890e-02	ci left: 2.994452e-03	ci right 3.289297e-03	k: 1758	n:560000
Cons ci ratio: 2.153157e-02	ci left: 5.527840e-02	ci right 5.648334e-02	k: 31292	n:560000
KS ci ratio: 9.998143e-02	ci left: 2.600597e-03	ci right 2.876016e-03	k: 1532	n:560000
FBXW7   560000 perm   284 sec   (1972 perm/sec)   p_kst 2.735714e-03   p_cons 5.587857e-02   p_joint 3.139286e-03

Outputting figure to mutsig2_images.part000000000064/FBXW7.6_2584_560000_0.0027357_0.055879_0.0031393.png
                gene_name: FBXW7
               theta_stop: 0.100 
                    nperm: 560000 
                     p_ks: 0.0027 
        ci_ks_bounds_left: 0.0026 
       ci_ks_bounds_right: 0.0029 
                   p_cons: 0.056 
      ci_cons_bounds_left: 0.055 
     ci_cons_bounds_right: 0.056 
                  p_joint: 0.0031 
     ci_joint_bounds_left: 0.0030 
    ci_joint_bounds_right: 0.0033 

Current progress: 20 percent done.
FGA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.090642e-02	ci left: 2.838926e-01	ci right 3.018282e-01	k: 2928	n:10000
Cons ci ratio: 4.122148e-02	ci left: 4.649712e-01	ci right 4.846435e-01	k: 4748	n:10000
KS ci ratio: 9.671176e-02	ci left: 1.342342e-01	ci right 1.479756e-01	k: 1410	n:10000
FGA   10000 perm   2 sec   (5385 perm/sec)   p_kst 1.410000e-01   p_cons 4.748000e-01   p_joint 2.928000e-01

Outputting figure to mutsig2_images.part000000000064/FGA.4_2669_10000_0.141_0.4748_0.2928.png
                gene_name: FGA
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.48 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.30 

Current progress: 40 percent done.
FER1L5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.610624e-02	ci left: 8.485573e-01	ci right 8.624349e-01	k: 8556	n:10000
Cons ci ratio: 3.361463e-02	ci left: 5.664436e-01	ci right 5.859120e-01	k: 5762	n:10000
KS ci ratio: 5.613456e-02	ci left: 3.185017e-01	ci right 3.369988e-01	k: 3277	n:10000
FER1L5   10000 perm   3 sec   (3995 perm/sec)   p_kst 3.277000e-01   p_cons 5.762000e-01   p_joint 8.556000e-01

Outputting figure to mutsig2_images.part000000000064/FER1L5.2_6490_10000_0.3277_0.5762_0.8556.png
                gene_name: FER1L5
               theta_stop: 0.056 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.86 

Current progress: 60 percent done.
FEZ2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.454625e-01	ci left: 6.275582e-02	ci right 7.269780e-02	k: 676	n:10000
Cons ci ratio: 4.362865e-02	ci left: 4.368230e-01	ci right 4.564081e-01	k: 4466	n:10000
KS ci ratio: 1.966875e-01	ci left: 3.443296e-02	ci right 4.203907e-02	k: 381	n:10000
FEZ2   10000 perm   2 sec   (6583 perm/sec)   p_kst 3.810000e-02   p_cons 4.466000e-01   p_joint 6.760000e-02

Joint ci ratio: 7.986614e-02	ci left: 1.031904e-01	ci right 1.118241e-01	k: 2149	n:20000
Cons ci ratio: 3.042265e-02	ci left: 4.466326e-01	ci right 4.604809e-01	k: 9071	n:20000
KS ci ratio: 1.397493e-01	ci left: 3.519929e-02	ci right 4.053615e-02	k: 756	n:20000
FEZ2   20000 perm   4 sec   (5696 perm/sec)   p_kst 3.780000e-02   p_cons 4.535500e-01   p_joint 1.074500e-01

Joint ci ratio: 4.162931e-02	ci left: 2.233616e-01	ci right 2.328911e-01	k: 6843	n:30000
Cons ci ratio: 2.486325e-02	ci left: 4.474551e-01	ci right 4.587540e-01	k: 13593	n:30000
KS ci ratio: 1.131511e-01	ci left: 3.628610e-02	ci right 4.067052e-02	k: 1153	n:30000
FEZ2   30000 perm   6 sec   (5379 perm/sec)   p_kst 3.843333e-02   p_cons 4.531000e-01   p_joint 2.281000e-01

Joint ci ratio: 3.442078e-02	ci left: 2.406174e-01	ci right 2.490697e-01	k: 9793	n:40000
Cons ci ratio: 2.154555e-02	ci left: 4.479130e-01	ci right 4.576938e-01	k: 18112	n:40000
KS ci ratio: 9.668172e-02	ci left: 3.756333e-02	ci right 4.140389e-02	k: 1578	n:40000
FEZ2   40000 perm   8 sec   (5172 perm/sec)   p_kst 3.945000e-02   p_cons 4.528000e-01   p_joint 2.448250e-01

Outputting figure to mutsig2_images.part000000000064/FEZ2.2_1179_40000_0.03945_0.4528_0.24482.png
                gene_name: FEZ2
               theta_stop: 0.097 
                    nperm: 40000 
                     p_ks: 0.039 
        ci_ks_bounds_left: 0.038 
       ci_ks_bounds_right: 0.041 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.25 

Current progress: 80 percent done.
FGD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.023059e-02	ci left: 9.313350e-01	ci right 9.410090e-01	k: 9363	n:10000
Cons ci ratio: 1.267511e-02	ci left: 8.994953e-01	ci right 9.110674e-01	k: 9054	n:10000
KS ci ratio: 4.599094e-02	ci left: 4.109985e-01	ci right 4.304477e-01	k: 4207	n:10000
FGD1   10000 perm   2 sec   (5456 perm/sec)   p_kst 4.207000e-01   p_cons 9.054000e-01   p_joint 9.363000e-01

Outputting figure to mutsig2_images.part000000000064/FGD1.2_2958_10000_0.4207_0.9054_0.9363.png
                gene_name: FGD1
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.91 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.91 
                  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.165.3896/
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/181708/iteration1/scatter.0000000064
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 64 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1420>
Subject: Job 1119862: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, 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/181708/iteration1/scatter.0000000065> was used as the working directory.
Started at Wed Oct 10 10:42:59 2012
Results reported at Wed Oct 10 10:45:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000065.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000065.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 65  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    172.86 sec.
    Max Memory :      1460 MB
    Max Swap   :      3878 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.165.3896/
-whichjob
65
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 65: processing genes 5791 - 5881
Calculating significance of each gene.
Using projection method.
5791	FGF4	1
5792	FGF5	1
5793	FGF6	1
5794	FGF7	1
5795	FGF8	3.192175e-03
5796	FGF9	1
5797	FGFBP1	1
5798	FGFBP2	1
5799	FGFBP3	1
5800	FGFR1	1
5801	FGFR1OP	1
5802	FGFR1OP2	1
5803	FGFR2	1
5804	FGFR3	2.110540e-02
5805	FGFR4	1.742917e-01
5806	FGFRL1	3.237794e-02
5807	FGG	4.135789e-02
5808	FGGY	1
5809	FGL1	1
5810	FGL2	1
5811	FGR	1
5812	FH	1
5813	FHDC1	1
5814	FHIT	1
5815	FHL1	1
5816	FHL2	1
5817	FHL3	1
5818	FHL5	7.479263e-02
5819	FHOD1	1.172849e-01
5820	FHOD3	1
5821	FIBCD1	1
5822	FIBIN	1
5823	FIBP	1.523610e-01
5824	FICD	1
5825	FIG4	1
5826	FIGF	1
5827	FIGLA	1
5828	FIGN	1.177473e-02
5829	FIGNL1	1
5830	FILIP1	1
5831	FILIP1L	1
5832	FIP1L1	1
5833	FIS1	1
5834	FITM1	1
5835	FITM2	1
5836	FIZ1	1
5837	FJX1	2.922541e-02
5838	FKBP10	1
5839	FKBP11	1
5840	FKBP14	1
5841	FKBP15	2.291707e-01
5842	FKBP1A	1
5843	FKBP1B	1
5844	FKBP2	1
5845	FKBP3	1
5846	FKBP4	1
5847	FKBP5	1.189194e-02
5848	FKBP6	1
5849	FKBP7	3.369219e-02
5850	FKBP8	1
5851	FKBP9	1
5852	FKBPL	1
5853	FKRP	1
5854	FKSG83	1
5855	FKTN	1
5856	FLAD1	1
5857	FLCN	1.638305e-01
5858	FLG	1.663866e-02
5859	FLG2	3.597608e-02
5860	FLI1	1
5861	FLII	1
5862	FLJ10357	1
5863	FLJ35220	1
5864	FLJ37543	1
5865	FLJ43860	1
5866	FLJ44635	1
5867	FLJ46321	3.697526e-01
5868	FLNA	5.329315e-01
5869	FLNB	6.944088e-01
5870	FLNC	4.670645e-01
5871	FLOT1	1
5872	FLOT2	1
5873	FLRT1	1.585757e-01
5874	FLRT2	1.038991e-01
5875	FLRT3	1
5876	FLT1	1
5877	FLT3	1
5878	FLT3LG	1
5879	FLT4	1
5880	FLVCR1	3.495078e-02
5881	FLVCR2	1
Done

Running MutSig 2:
Scatter job 65: processing genes 5791 - 5881
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: 1.412003e-02	ci left: 8.787895e-01	ci right 8.913852e-01	k: 8852	n:10000
Cons ci ratio: 4.582155e-02	ci left: 4.127924e-01	ci right 4.322528e-01	k: 4225	n:10000
KS ci ratio: 1.917731e-02	ci left: 7.990245e-01	ci right 8.145964e-01	k: 8069	n:10000
FLG   10000 perm   5 sec   (1918 perm/sec)   p_kst 8.069000e-01   p_cons 4.225000e-01   p_joint 8.852000e-01

Outputting figure to mutsig2_images.part000000000065/FLG.8_12194_10000_0.8069_0.4225_0.8852.png
                gene_name: FLG
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.81 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.89 
     ci_joint_bounds_left: 0.88 
    ci_joint_bounds_right: 0.89 

Current progress: 14 percent done.
FLG2
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: 3.120912e-02	ci left: 6.023677e-01	ci right 6.215670e-01	k: 6120	n:10000
KS ci ratio: 3.810422e-02	ci left: 5.042512e-01	ci right 5.239406e-01	k: 5141	n:10000
FLG2   10000 perm   4 sec   (2808 perm/sec)   p_kst 5.141000e-01   p_cons 6.120000e-01   p_joint 6.787000e-01

Outputting figure to mutsig2_images.part000000000065/FLG2.5_7184_10000_0.5141_0.612_0.6787.png
                gene_name: FLG2
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.52 
                   p_cons: 0.61 
      ci_cons_bounds_left: 0.60 
     ci_cons_bounds_right: 0.62 
                  p_joint: 0.68 
     ci_joint_bounds_left: 0.67 
    ci_joint_bounds_right: 0.69 

Current progress: 29 percent done.
FGF8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.315671e-02	ci left: 7.325974e-01	ci right 7.498618e-01	k: 7413	n:10000
Cons ci ratio: 4.808088e-02	ci left: 3.895819e-01	ci right 4.088768e-01	k: 3992	n:10000
KS ci ratio: 2.016804e-01	ci left: 3.271977e-02	ci right 4.015343e-02	k: 363	n:10000
FGF8   10000 perm   1 sec   (6891 perm/sec)   p_kst 3.630000e-02   p_cons 3.992000e-01   p_joint 7.413000e-01

Joint ci ratio: 3.909733e-02	ci left: 3.279108e-01	ci right 3.410374e-01	k: 6689	n:20000
Cons ci ratio: 3.414731e-02	ci left: 3.903590e-01	ci right 4.039709e-01	k: 7943	n:20000
KS ci ratio: 1.380522e-01	ci left: 3.606913e-02	ci right 4.146602e-02	k: 774	n:20000
FGF8   20000 perm   3 sec   (5748 perm/sec)   p_kst 3.870000e-02   p_cons 3.971500e-01   p_joint 3.344500e-01

Joint ci ratio: 3.191328e-02	ci left: 3.292602e-01	ci right 3.399719e-01	k: 10038	n:30000
Cons ci ratio: 2.777078e-02	ci left: 3.935185e-01	ci right 4.046343e-01	k: 11972	n:30000
KS ci ratio: 1.140274e-01	ci left: 3.573495e-02	ci right 4.008846e-02	k: 1136	n:30000
FGF8   30000 perm   6 sec   (5450 perm/sec)   p_kst 3.786667e-02   p_cons 3.990667e-01   p_joint 3.346000e-01

Joint ci ratio: 2.749455e-02	ci left: 3.322925e-01	ci right 3.415812e-01	k: 13477	n:40000
Cons ci ratio: 2.394395e-02	ci left: 3.963915e-01	ci right 4.060228e-01	k: 16048	n:40000
KS ci ratio: 9.854849e-02	ci left: 3.617182e-02	ci right 3.994562e-02	k: 1521	n:40000
FGF8   40000 perm   8 sec   (5239 perm/sec)   p_kst 3.802500e-02   p_cons 4.012000e-01   p_joint 3.369250e-01

Outputting figure to mutsig2_images.part000000000065/FGF8.2_759_40000_0.038025_0.4012_0.33692.png
                gene_name: FGF8
               theta_stop: 0.099 
                    nperm: 40000 
                     p_ks: 0.038 
        ci_ks_bounds_left: 0.036 
       ci_ks_bounds_right: 0.040 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.41 
                  p_joint: 0.34 
     ci_joint_bounds_left: 0.33 
    ci_joint_bounds_right: 0.34 

Current progress: 43 percent done.
FGFR3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.009549e-02	ci left: 7.838091e-01	ci right 7.998206e-01	k: 7919	n:10000
Cons ci ratio: 3.008344e-02	ci left: 6.197470e-01	ci right 6.387777e-01	k: 6293	n:10000
KS ci ratio: 5.186117e-02	ci left: 3.540633e-01	ci right 3.730162e-01	k: 3635	n:10000
FGFR3   10000 perm   2 sec   (4628 perm/sec)   p_kst 3.635000e-01   p_cons 6.293000e-01   p_joint 7.919000e-01

Outputting figure to mutsig2_images.part000000000065/FGFR3.2_2644_10000_0.3635_0.6293_0.7919.png
                gene_name: FGFR3
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.64 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.80 

Current progress: 57 percent done.
FHOD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.115922e-02	ci left: 9.197660e-01	ci right 9.301849e-01	k: 9251	n:10000
Cons ci ratio: 3.138680e-02	ci left: 5.996565e-01	ci right 6.188798e-01	k: 6093	n:10000
KS ci ratio: 1.714820e-02	ci left: 8.320551e-01	ci right 8.465466e-01	k: 8394	n:10000
FHOD1   10000 perm   2 sec   (5049 perm/sec)   p_kst 8.394000e-01   p_cons 6.093000e-01   p_joint 9.251000e-01

Outputting figure to mutsig2_images.part000000000065/FHOD1.2_3583_10000_0.8394_0.6093_0.9251.png
                gene_name: FHOD1
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.61 
      ci_cons_bounds_left: 0.60 
     ci_cons_bounds_right: 0.62 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

Current progress: 71 percent done.
FIGN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.152048e-03	ci left: 9.867570e-01	ci right 9.909509e-01	k: 9890	n:10000
Cons ci ratio: 3.873442e-02	ci left: 4.960503e-01	ci right 5.157462e-01	k: 5059	n:10000
KS ci ratio: 2.235422e-02	ci left: 7.460424e-01	ci right 7.630091e-01	k: 7546	n:10000
FIGN   10000 perm   2 sec   (6027 perm/sec)   p_kst 7.546000e-01   p_cons 5.059000e-01   p_joint 9.890000e-01

Outputting figure to mutsig2_images.part000000000065/FIGN.2_2288_10000_0.7546_0.5059_0.989.png
                gene_name: FIGN
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.50 
     ci_cons_bounds_right: 0.52 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 86 percent done.
FKBP5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.142503e-02	ci left: 2.804252e-01	ci right 2.982977e-01	k: 2893	n:10000
Cons ci ratio: 5.618554e-02	ci left: 3.181047e-01	ci right 3.365960e-01	k: 3273	n:10000
KS ci ratio: 5.263190e-02	ci left: 3.473041e-01	ci right 3.661794e-01	k: 3567	n:10000
FKBP5   10000 perm   2 sec   (6222 perm/sec)   p_kst 3.567000e-01   p_cons 3.273000e-01   p_joint 2.893000e-01

Outputting figure to mutsig2_images.part000000000065/FKBP5.2_1472_10000_0.3567_0.3273_0.2893.png
                gene_name: FKBP5
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.34 
                  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.165.3896/
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/181708/iteration1/scatter.0000000065
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 65 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1531>
Subject: Job 1119866: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1531>, 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/181708/iteration1/scatter.0000000066> was used as the working directory.
Started at Wed Oct 10 10:42:59 2012
Results reported at Wed Oct 10 10:45:19 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000066.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000066.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 66  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    140.13 sec.
    Max Memory :      1324 MB
    Max Swap   :      3870 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.165.3896/
-whichjob
66
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 66: processing genes 5882 - 5971
Calculating significance of each gene.
Using projection method.
5882	FLYWCH1	1
5883	FLYWCH2	1
5884	FMN1	4.008429e-01
5885	FMN2	3.616660e-01
5886	FMNL1	1
5887	FMNL2	1
5888	FMNL3	1
5889	FMO1	1
5890	FMO2	1.257503e-01
5891	FMO3	8.906780e-03
5892	FMO4	1.766890e-01
5893	FMO5	1
5894	FMOD	1
5895	FMR1	1
5896	FMR1NB	1
5897	FN1	1
5898	FN3K	1.230654e-01
5899	FN3KRP	1
5900	FNBP1	1
5901	FNBP1L	7.494948e-02
5902	FNBP4	4.029795e-01
5903	FNDC1	1
5904	FNDC3A	2.664346e-01
5905	FNDC3B	4.531676e-01
5906	FNDC4	1
5907	FNDC5	1
5908	FNDC7	2.286346e-01
5909	FNDC8	1
5910	FNIP1	4.009222e-01
5911	FNIP2	1
5912	FNTA	6.741870e-02
5913	FNTB	1
5914	FOLH1	2.725454e-02
5915	FOLH1B	1.123234e-01
5916	FOLR1	1
5917	FOLR2	1
5918	FOLR3	1
5919	FOLR4	1
5920	FOS	8.988678e-02
5921	FOSB	1
5922	FOSL1	1
5923	FOSL2	1.706218e-01
5924	FOXA1	1
5925	FOXA2	1.562825e-01
5926	FOXA3	1
5927	FOXB1	1
5928	FOXB2	1
5929	FOXC1	1
5930	FOXC2	1
5931	FOXD2	1
5932	FOXD3	1
5933	FOXD4	1
5934	FOXD4L1	1
5935	FOXD4L3	1
5936	FOXD4L5	1
5937	FOXE1	1
5938	FOXE3	1
5939	FOXF1	7.471304e-02
5940	FOXF2	1
5941	FOXG1	1.148203e-01
5942	FOXH1	1
5943	FOXI1	1
5944	FOXJ1	1
5945	FOXJ2	1
5946	FOXJ3	1
5947	FOXK1	1
5948	FOXK2	1
5949	FOXL1	1
5950	FOXL2	1
5951	FOXM1	6.567759e-03
5952	FOXN1	1.775070e-01
5953	FOXN2	1.803083e-01
5954	FOXN3	1.270046e-01
5955	FOXN4	1
5956	FOXO1	1
5957	FOXO3	1
5958	FOXO4	1
5959	FOXP1	2.731478e-01
5960	FOXP2	2.129368e-02
5961	FOXP3	1
5962	FOXP4	1
5963	FOXQ1	4.526008e-02
5964	FOXR1	1
5965	FOXR2	4.694785e-02
5966	FOXRED1	1
5967	FOXRED2	2.018963e-01
5968	FOXS1	1.302477e-01
5969	FPGS	1
5970	FPGT	8.148250e-02
5971	FPR1	1
Done

Running MutSig 2:
Scatter job 66: processing genes 5882 - 5971
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
FOXM1
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: 5.851007e-02	ci left: 3.006442e-01	ci right 3.188667e-01	k: 3097	n:10000
KS ci ratio: 2.475992e-02	ci left: 7.058389e-01	ci right 7.236358e-01	k: 7148	n:10000
FOXM1   10000 perm   2 sec   (4775 perm/sec)   p_kst 7.148000e-01   p_cons 3.097000e-01   p_joint 5.824000e-01

Outputting figure to mutsig2_images.part000000000066/FOXM1.3_2442_10000_0.7148_0.3097_0.5824.png
                gene_name: FOXM1
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 20 percent done.
FMO3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.070122e-02	ci left: 2.852798e-01	ci right 3.032402e-01	k: 2942	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: 4.030713e-02	ci left: 4.761593e-01	ci right 4.958489e-01	k: 4860	n:10000
FMO3   10000 perm   2 sec   (5160 perm/sec)   p_kst 4.860000e-01   p_cons 3.335000e-01   p_joint 2.942000e-01

Outputting figure to mutsig2_images.part000000000066/FMO3.2_1631_10000_0.486_0.3335_0.2942.png
                gene_name: FMO3
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.34 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.29 
    ci_joint_bounds_right: 0.30 

Current progress: 40 percent done.
FNBP4
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: 1.001251e-01	ci left: 1.262063e-01	ci right 1.396083e-01	k: 1328	n:10000
KS ci ratio: 1.648733e-01	ci left: 4.907401e-02	ci right 5.798834e-02	k: 534	n:10000
FNBP4   10000 perm   2 sec   (4567 perm/sec)   p_kst 5.340000e-02   p_cons 1.328000e-01   p_joint 1

Joint ci ratio: 2.564323e-02	ci left: 5.318612e-01	ci right 5.457276e-01	k: 10776	n:20000
Cons ci ratio: 7.069307e-02	ci left: 1.285194e-01	ci right 1.379875e-01	k: 2664	n:20000
KS ci ratio: 1.150598e-01	ci left: 5.168573e-02	ci right 5.804447e-02	k: 1096	n:20000
FNBP4   20000 perm   5 sec   (3981 perm/sec)   p_kst 5.480000e-02   p_cons 1.332000e-01   p_joint 5.388000e-01

Joint ci ratio: 3.051312e-02	ci left: 3.494499e-01	ci right 3.603115e-01	k: 10646	n:30000
Cons ci ratio: 5.836701e-02	ci left: 1.268720e-01	ci right 1.345330e-01	k: 3920	n:30000
KS ci ratio: 9.375085e-02	ci left: 5.247933e-02	ci right 5.767393e-02	k: 1651	n:30000
FNBP4   30000 perm   7 sec   (4035 perm/sec)   p_kst 5.503333e-02   p_cons 1.306667e-01   p_joint 3.548667e-01

Outputting figure to mutsig2_images.part000000000066/FNBP4.2_3122_30000_0.055033_0.13067_0.35487.png
                gene_name: FNBP4
               theta_stop: 0.094 
                    nperm: 30000 
                     p_ks: 0.055 
        ci_ks_bounds_left: 0.052 
       ci_ks_bounds_right: 0.058 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.35 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.36 

Current progress: 60 percent done.
FOLH1
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: 1.350161e-02	ci left: 8.878013e-01	ci right 8.999681e-01	k: 8940	n:10000
KS ci ratio: 1.199064e-02	ci left: 9.088480e-01	ci right 9.199092e-01	k: 9145	n:10000
FOLH1   10000 perm   2 sec   (5871 perm/sec)   p_kst 9.145000e-01   p_cons 8.940000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000066/FOLH1.2_2329_10000_0.9145_0.894_1.png
                gene_name: FOLH1
               theta_stop: 0.014 
                    nperm: 10000 
                     p_ks: 0.91 
        ci_ks_bounds_left: 0.91 
       ci_ks_bounds_right: 0.92 
                   p_cons: 0.89 
      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: 80 percent done.
FOXP2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.552184e-02	ci left: 8.576357e-01	ci right 8.711513e-01	k: 8645	n:10000
Cons ci ratio: 6.486675e-02	ci left: 2.587439e-01	ci right 2.761918e-01	k: 2674	n:10000
KS ci ratio: 7.786312e-02	ci left: 1.942671e-01	ci right 2.101068e-01	k: 2021	n:10000
FOXP2   10000 perm   2 sec   (4614 perm/sec)   p_kst 2.021000e-01   p_cons 2.674000e-01   p_joint 8.645000e-01

Outputting figure to mutsig2_images.part000000000066/FOXP2.2_2379_10000_0.2021_0.2674_0.8645.png
                gene_name: FOXP2
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.27 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.28 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

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.165.3896/
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/181708/iteration1/scatter.0000000066
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 66 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1532>
Subject: Job 1119873: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1532>, 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/181708/iteration1/scatter.0000000067> was used as the working directory.
Started at Wed Oct 10 10:42:59 2012
Results reported at Wed Oct 10 10:45:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000067.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000067.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 67  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    142.14 sec.
    Max Memory :      1303 MB
    Max Swap   :      3817 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.165.3896/
-whichjob
67
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 67: processing genes 5972 - 6061
Calculating significance of each gene.
Using projection method.
5972	FPR2	1
5973	FPR3	1
5974	FRA10AC1	1
5975	FRAS1	2.050092e-01
5976	FREM1	3.984355e-01
5977	FREM2	2.538880e-01
5978	FRG1	1
5979	FRG2B	1
5980	FRK	2.448262e-01
5981	FRMD1	1.582716e-01
5982	FRMD3	1
5983	FRMD4A	1
5984	FRMD4B	1
5985	FRMD5	1
5986	FRMD6	1.882973e-01
5987	FRMD7	1
5988	FRMD8	8.226682e-02
5989	FRMPD1	1
5990	FRMPD2	4.768345e-01
5991	FRMPD4	1
5992	FRRS1	2.653572e-01
5993	FRS2	1.578799e-02
5994	FRS3	1.874357e-01
5995	FRY	5.200356e-01
5996	FRYL	7.194100e-01
5997	FRZB	1
5998	FSCB	1
5999	FSCN1	1
6000/18094 6000	FSCN2	5.012766e-02
6001	FSCN3	1
6002	FSD1	1
6003	FSD2	1
6004	FSHB	1
6005	FSHR	9.660978e-02
6006	FSIP1	1.295238e-01
6007	FST	1.334293e-01
6008	FSTL1	1
6009	FSTL3	1
6010	FSTL4	1
6011	FSTL5	1
6012	FTCD	1
6013	FTH1	1
6014	FTHL17	4.408628e-02
6015	FTL	1
6016	FTMT	1
6017	FTO	1.847136e-01
6018	FTSJ1	1
6019	FTSJ2	1
6020	FTSJ3	1.397412e-01
6021	FTSJD1	1.555741e-01
6022	FTSJD2	1
6023	FUBP1	2.733430e-01
6024	FUBP3	1.718792e-01
6025	FUCA1	1
6026	FUCA2	7.445989e-02
6027	FUK	1
6028	FUNDC1	3.059649e-02
6029	FUNDC2	1
6030	FURIN	2.179873e-01
6031	FUS	1.336551e-01
6032	FUT1	1.306116e-01
6033	FUT10	1
6034	FUT11	1
6035	FUT2	1
6036	FUT3	1
6037	FUT4	1
6038	FUT5	1
6039	FUT6	1
6040	FUT7	1
6041	FUT8	1
6042	FUT9	1
6043	FUZ	1
6044	FXC1	1
6045	FXN	1
6046	FXR1	1
6047	FXR2	1
6048	FXYD1	1
6049	FXYD2	1
6050	FXYD3	1
6051	FXYD4	1
6052	FXYD5	1
6053	FXYD6	1
6054	FXYD7	1
6055	FYB	1
6056	FYCO1	1
6057	FYN	1
6058	FYTTD1	1
6059	FZD1	1
6060	FZD10	1.914419e-01
6061	FZD2	1
Done

Running MutSig 2:
Scatter job 67: processing genes 5972 - 6061
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: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.182907e-02	ci left: 9.110088e-01	ci right 9.219471e-01	k: 9166	n:10000
KS ci ratio: 1.914655e-02	ci left: 7.995320e-01	ci right 8.150886e-01	k: 8074	n:10000
FRAS1   10000 perm   5 sec   (1964 perm/sec)   p_kst 8.074000e-01   p_cons 9.166000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000067/FRAS1.4_12410_10000_0.8074_0.9166_1.png
                gene_name: FRAS1
               theta_stop: 0.019 
                    nperm: 10000 
                     p_ks: 0.81 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.92 
      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: 33 percent done.
FREM2
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: 9.768831e-03	ci left: 9.368238e-01	ci right 9.461169e-01	k: 9416	n:10000
KS ci ratio: 2.570989e-02	ci left: 6.901044e-01	ci right 7.081794e-01	k: 6992	n:10000
FREM2   10000 perm   3 sec   (2931 perm/sec)   p_kst 6.992000e-01   p_cons 9.416000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000067/FREM2.2_9606_10000_0.6992_0.9416_1.png
                gene_name: FREM2
               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: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
FRS2
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: 4.578402e-02	ci left: 4.131910e-01	ci right 4.326539e-01	k: 4229	n:10000
KS ci ratio: 1.851014e-02	ci left: 8.099906e-01	ci right 8.252239e-01	k: 8177	n:10000
FRS2   10000 perm   2 sec   (5069 perm/sec)   p_kst 8.177000e-01   p_cons 4.229000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000067/FRS2.2_1547_10000_0.8177_0.4229_1.png
                gene_name: FRS2
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.83 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000067
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 67 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119880: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000068> was used as the working directory.
Started at Wed Oct 10 10:43:04 2012
Results reported at Wed Oct 10 10:44:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000068.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000068.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 68  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    122.48 sec.
    Max Memory :      1364 MB
    Max Swap   :      3919 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.165.3896/
-whichjob
68
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 68: processing genes 6062 - 6152
Calculating significance of each gene.
Using projection method.
6062	FZD3	1
6063	FZD4	1
6064	FZD5	1
6065	FZD6	2.481399e-01
6066	FZD7	1
6067	FZD8	1.961088e-01
6068	FZD9	1
6069	FZR1	1
6070	G0S2	1
6071	G2E3	1
6072	G3BP1	1.946044e-01
6073	G3BP2	2.747452e-02
6074	G6PC	1
6075	G6PC2	1
6076	G6PC3	1
6077	G6PD	1
6078	GAA	1
6079	GAB1	1
6080	GAB2	1
6081	GAB3	1
6082	GAB4	1.765485e-01
6083	GABARAP	1
6084	GABARAPL1	1
6085	GABARAPL2	1
6086	GABBR1	1
6087	GABBR2	2.098527e-01
6088	GABPA	1
6089	GABPB1	1
6090	GABPB2	1
6091	GABRA1	5.815091e-02
6092	GABRA2	1
6093	GABRA3	1
6094	GABRA4	2.612301e-01
6095	GABRA5	1
6096	GABRA6	5.804773e-03
6097	GABRB1	1.798971e-01
6098	GABRB2	8.983016e-03
6099	GABRB3	1
6100	GABRD	1
6101	GABRE	1
6102	GABRG1	2.209152e-01
6103	GABRG2	1
6104	GABRG3	1
6105	GABRP	1
6106	GABRQ	1
6107	GABRR1	1
6108	GABRR2	1
6109	GABRR3	1
6110	GAD1	2.485766e-02
6111	GAD2	1
6112	GADD45A	1
6113	GADD45B	1
6114	GADD45G	1
6115	GADD45GIP1	1
6116	GADL1	1
6117	GAGE1	1
6118	GAGE10	1
6119	GAGE13	1
6120	GAK	4.725259e-01
6121	GAL	1
6122	GAL3ST1	1
6123	GAL3ST2	1
6124	GAL3ST3	1
6125	GAL3ST4	1
6126	GALC	1.871412e-01
6127	GALE	1
6128	GALK1	1
6129	GALK2	1
6130	GALM	1
6131	GALNS	1
6132	GALNT1	1
6133	GALNT10	1
6134	GALNT11	1
6135	GALNT12	1
6136	GALNT13	1
6137	GALNT14	1
6138	GALNT2	1
6139	GALNT3	1
6140	GALNT4	1
6141	GALNT5	8.431522e-02
6142	GALNT6	1
6143	GALNT7	1
6144	GALNT8	1.404303e-01
6145	GALNT9	1
6146	GALNTL1	1
6147	GALNTL2	1
6148	GALNTL4	1
6149	GALNTL5	1
6150	GALNTL6	1
6151	GALP	1
6152	GALR1	1
Done

Running MutSig 2:
Scatter job 68: processing genes 6062 - 6152
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
G3BP2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.884176e-02	ci left: 1.903270e-01	ci right 2.060492e-01	k: 1981	n:10000
Cons ci ratio: 9.294744e-02	ci left: 1.439367e-01	ci right 1.580673e-01	k: 1509	n:10000
KS ci ratio: 2.795794e-02	ci left: 6.534378e-01	ci right 6.720673e-01	k: 6628	n:10000
G3BP2   10000 perm   2 sec   (5751 perm/sec)   p_kst 6.628000e-01   p_cons 1.509000e-01   p_joint 1.981000e-01

Outputting figure to mutsig2_images.part000000000068/G3BP2.2_1493_10000_0.6628_0.1509_0.1981.png
                gene_name: G3BP2
               theta_stop: 0.093 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.16 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.21 

Current progress: 20 percent done.
GABRA6
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: 5.904794e-02	ci left: 2.967772e-01	ci right 3.149361e-01	k: 3058	n:10000
KS ci ratio: 3.423102e-02	ci left: 5.575209e-01	ci right 5.770399e-01	k: 5673	n:10000
GABRA6   10000 perm   2 sec   (6442 perm/sec)   p_kst 5.673000e-01   p_cons 3.058000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000068/GABRA6.2_1398_10000_0.5673_0.3058_1.png
                gene_name: GABRA6
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   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: 40 percent done.
GABRB2
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: 3.384225e-02	ci left: 5.631348e-01	ci right 5.826227e-01	k: 5729	n:10000
KS ci ratio: 3.890521e-02	ci left: 4.938506e-01	ci right 5.135473e-01	k: 5037	n:10000
GABRB2   10000 perm   2 sec   (6297 perm/sec)   p_kst 5.037000e-01   p_cons 5.729000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000068/GABRB2.2_1579_10000_0.5037_0.5729_1.png
                gene_name: GABRB2
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.57 
      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: 60 percent done.
GAD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.180359e-02	ci left: 5.933315e-01	ci right 6.126085e-01	k: 6030	n:10000
Cons ci ratio: 8.526847e-03	ci left: 9.506481e-01	ci right 9.588844e-01	k: 9549	n:10000
KS ci ratio: 3.691682e-02	ci left: 5.200602e-01	ci right 5.397224e-01	k: 5299	n:10000
GAD1   10000 perm   2 sec   (6088 perm/sec)   p_kst 5.299000e-01   p_cons 9.549000e-01   p_joint 6.030000e-01

Outputting figure to mutsig2_images.part000000000068/GAD1.2_1890_10000_0.5299_0.9549_0.603.png
                gene_name: GAD1
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.60 
     ci_joint_bounds_left: 0.59 
    ci_joint_bounds_right: 0.61 

Current progress: 80 percent done.
GALNT5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.157215e-02	ci left: 9.144065e-01	ci right 9.251474e-01	k: 9199	n:10000
Cons ci ratio: 3.202320e-02	ci left: 5.900191e-01	ci right 6.093228e-01	k: 5997	n:10000
KS ci ratio: 1.553508e-02	ci left: 8.574316e-01	ci right 8.709555e-01	k: 8643	n:10000
GALNT5   10000 perm   2 sec   (5918 perm/sec)   p_kst 8.643000e-01   p_cons 5.997000e-01   p_joint 9.199000e-01

Outputting figure to mutsig2_images.part000000000068/GALNT5.2_2863_10000_0.8643_0.5997_0.9199.png
                gene_name: GALNT5
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.87 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.92 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.93 

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.165.3896/
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/181708/iteration1/scatter.0000000068
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 68 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119888: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000069> was used as the working directory.
Started at Wed Oct 10 10:43:04 2012
Results reported at Wed Oct 10 10:45:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000069.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000069.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 69  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    184.27 sec.
    Max Memory :      1325 MB
    Max Swap   :      3861 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.165.3896/
-whichjob
69
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 69: processing genes 6153 - 6242
Calculating significance of each gene.
Using projection method.
6153	GALR2	9.736256e-02
6154	GALR3	1
6155	GALT	1
6156	GAMT	1
6157	GAN	1
6158	GANAB	1.146266e-01
6159	GANC	1
6160	GAP43	1
6161	GAPDH	1
6162	GAPDHS	1
6163	GAPT	1
6164	GAPVD1	5.674214e-01
6165	GAR1	1
6166	GARNL3	6.523437e-02
6167	GARS	2.471381e-01
6168	GART	1
6169	GAS1	1
6170	GAS2	1
6171	GAS2L1	1
6172	GAS2L2	1
6173	GAS2L3	1
6174	GAS6	1
6175	GAS7	1
6176	GAS8	1
6177	GAST	1
6178	GATA1	1
6179	GATA2	4.502609e-02
6180	GATA3	1
6181	GATA4	1
6182	GATA5	1
6183	GATA6	1
6184	GATAD1	1
6185	GATAD2A	1
6186	GATAD2B	2.181514e-02
6187	GATC	1
6188	GATM	1.820738e-01
6189	GATS	1
6190	GATSL3	1
6191	GBA	1.772854e-01
6192	GBA2	1
6193	GBA3	1.038853e-01
6194	GBAS	1
6195	GBE1	3.073951e-01
6196	GBF1	2.704556e-01
6197	GBGT1	1
6198	GBP1	1.626695e-01
6199	GBP2	1
6200	GBP3	1
6201	GBP4	1
6202	GBP5	1
6203	GBP6	1
6204	GBP7	1
6205	GBX1	1
6206	GBX2	1
6207	GC	1
6208	GCA	1
6209	GCAT	1
6210	GCC1	1
6211	GCC2	5.623205e-02
6212	GCDH	1
6213	GCET2	1
6214	GCFC1	1
6215	GCG	1
6216	GCH1	1
6217	GCHFR	1
6218	GCK	1
6219	GCKR	1
6220	GCLC	1
6221	GCLM	1
6222	GCM1	1
6223	GCM2	1
6224	GCN1L1	6.234844e-01
6225	GCNT1	4.682224e-02
6226	GCNT2	1
6227	GCNT3	1
6228	GCNT4	1
6229	GCOM1	1
6230	GCSH	1
6231	GDA	1
6232	GDAP1	1
6233	GDAP1L1	1
6234	GDAP2	1
6235	GDE1	1
6236	GDF10	1
6237	GDF11	8.051544e-02
6238	GDF15	1
6239	GDF2	1
6240	GDF3	1
6241	GDF5	1
6242	GDF6	1
Done

Running MutSig 2:
Scatter job 69: processing genes 6153 - 6242
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GCC2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.166900e-01	ci left: 9.545302e-02	ci right 1.073803e-01	k: 1013	n:10000
Cons ci ratio: 7.293884e-02	ci left: 2.158598e-01	ci right 2.323013e-01	k: 2240	n:10000
KS ci ratio: 1.305483e-01	ci left: 7.727681e-02	ci right 8.816773e-02	k: 826	n:10000
GCC2   10000 perm   2 sec   (4223 perm/sec)   p_kst 8.260000e-02   p_cons 2.240000e-01   p_joint 1.013000e-01

Joint ci ratio: 8.540206e-02	ci left: 9.121559e-02	ci right 9.940250e-02	k: 1905	n:20000
Cons ci ratio: 5.095377e-02	ci left: 2.224977e-01	ci right 2.341814e-01	k: 4566	n:20000
KS ci ratio: 9.144234e-02	ci left: 8.028925e-02	ci right 8.803215e-02	k: 1682	n:20000
GCC2   20000 perm   8 sec   (2407 perm/sec)   p_kst 8.410000e-02   p_cons 2.283000e-01   p_joint 9.525000e-02

Outputting figure to mutsig2_images.part000000000069/GCC2.3_5147_20000_0.0841_0.2283_0.09525.png
                gene_name: GCC2
               theta_stop: 0.091 
                    nperm: 20000 
                     p_ks: 0.084 
        ci_ks_bounds_left: 0.080 
       ci_ks_bounds_right: 0.088 
                   p_cons: 0.23 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.095 
     ci_joint_bounds_left: 0.091 
    ci_joint_bounds_right: 0.099 

Current progress: 20 percent done.
GARNL3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.252227e-01	ci left: 2.608227e-02	ci right 3.279558e-02	k: 293	n:10000
Cons ci ratio: 2.483822e-01	ci left: 2.127733e-02	ci right 2.740406e-02	k: 242	n:10000
KS ci ratio: 5.932719e-02	ci left: 2.947944e-01	ci right 3.129200e-01	k: 3038	n:10000
GARNL3   10000 perm   2 sec   (4598 perm/sec)   p_kst 3.038000e-01   p_cons 2.420000e-02   p_joint 2.930000e-02

Joint ci ratio: 1.340536e-01	ci left: 3.824541e-02	ci right 4.378904e-02	k: 819	n:20000
Cons ci ratio: 1.736334e-01	ci left: 2.268901e-02	ci right 2.705062e-02	k: 496	n:20000
KS ci ratio: 4.206011e-02	ci left: 2.963865e-01	ci right 3.091708e-01	k: 6055	n:20000
GARNL3   20000 perm   6 sec   (3254 perm/sec)   p_kst 3.027500e-01   p_cons 2.480000e-02   p_joint 4.095000e-02

Joint ci ratio: 1.318179e-01	ci left: 2.674297e-02	ci right 3.054904e-02	k: 858	n:30000
Cons ci ratio: 1.437114e-01	ci left: 2.245846e-02	ci right 2.596784e-02	k: 725	n:30000
KS ci ratio: 3.420151e-02	ci left: 2.992950e-01	ci right 3.097429e-01	k: 9135	n:30000
GARNL3   30000 perm   9 sec   (3289 perm/sec)   p_kst 3.045000e-01   p_cons 2.416667e-02   p_joint 2.860000e-02

Joint ci ratio: 1.363314e-01	ci left: 1.886790e-02	ci right 2.165236e-02	k: 809	n:40000
Cons ci ratio: 1.238044e-01	ci left: 2.293435e-02	ci right 2.598522e-02	k: 977	n:40000
KS ci ratio: 2.976218e-02	ci left: 2.979756e-01	ci right 3.070031e-01	k: 12099	n:40000
GARNL3   40000 perm   12 sec   (3427 perm/sec)   p_kst 3.024750e-01   p_cons 2.442500e-02   p_joint 2.022500e-02

Joint ci ratio: 1.204596e-01	ci left: 1.948932e-02	ci right 2.200675e-02	k: 1036	n:50000
Cons ci ratio: 1.092547e-01	ci left: 2.372702e-02	ci right 2.648849e-02	k: 1254	n:50000
KS ci ratio: 2.658609e-02	ci left: 2.989933e-01	ci right 3.070695e-01	k: 15151	n:50000
GARNL3   50000 perm   14 sec   (3481 perm/sec)   p_kst 3.030200e-01   p_cons 2.508000e-02   p_joint 2.072000e-02

Joint ci ratio: 1.190471e-01	ci left: 1.669233e-02	ci right 1.882135e-02	k: 1064	n:60000
Cons ci ratio: 1.008049e-01	ci left: 2.334273e-02	ci right 2.583688e-02	k: 1474	n:60000
KS ci ratio: 2.418414e-02	ci left: 3.008355e-01	ci right 3.082167e-01	k: 18271	n:60000
GARNL3   60000 perm   17 sec   (3510 perm/sec)   p_kst 3.045167e-01   p_cons 2.456667e-02   p_joint 1.773333e-02

Joint ci ratio: 1.016929e-01	ci left: 1.972767e-02	ci right 2.185517e-02	k: 1454	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: 2.237759e-02	ci left: 3.013482e-01	ci right 3.081822e-01	k: 21333	n:70000
GARNL3   70000 perm   20 sec   (3520 perm/sec)   p_kst 3.047571e-01   p_cons 2.438571e-02   p_joint 2.077143e-02

Joint ci ratio: 1.049180e-01	ci left: 1.624945e-02	ci right 1.806081e-02	k: 1371	n:80000
Cons ci ratio: 8.765840e-02	ci left: 2.331742e-02	ci right 2.546726e-02	k: 1950	n:80000
KS ci ratio: 2.090748e-02	ci left: 3.020722e-01	ci right 3.084669e-01	k: 24421	n:80000
GARNL3   80000 perm   23 sec   (3518 perm/sec)   p_kst 3.052625e-01   p_cons 2.437500e-02   p_joint 1.713750e-02

Joint ci ratio: 9.860940e-02	ci left: 1.640398e-02	ci right 1.811623e-02	k: 1552	n:90000
Cons ci ratio: 8.320791e-02	ci left: 2.306433e-02	ci right 2.507762e-02	k: 2165	n:90000
KS ci ratio: 1.972041e-02	ci left: 3.020704e-01	ci right 3.080977e-01	k: 27457	n:90000
GARNL3   90000 perm   26 sec   (3504 perm/sec)   p_kst 3.050778e-01   p_cons 2.405556e-02   p_joint 1.724444e-02

Outputting figure to mutsig2_images.part000000000069/GARNL3.2_3154_90000_0.30508_0.024056_0.017244.png
                gene_name: GARNL3
               theta_stop: 0.099 
                    nperm: 90000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.024 
      ci_cons_bounds_left: 0.023 
     ci_cons_bounds_right: 0.025 
                  p_joint: 0.017 
     ci_joint_bounds_left: 0.016 
    ci_joint_bounds_right: 0.018 

Current progress: 40 percent done.
GATAD2B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.656929e-01	ci left: 4.859368e-02	ci right 5.746898e-02	k: 529	n:10000
Cons ci ratio: 1.128281e-01	ci left: 1.015915e-01	ci right 1.138381e-01	k: 1076	n:10000
KS ci ratio: 6.256426e-02	ci left: 2.729972e-01	ci right 2.907301e-01	k: 2818	n:10000
GATAD2B   10000 perm   2 sec   (5851 perm/sec)   p_kst 2.818000e-01   p_cons 1.076000e-01   p_joint 5.290000e-02

Joint ci ratio: 1.184089e-01	ci left: 4.886604e-02	ci right 5.506504e-02	k: 1038	n:20000
Cons ci ratio: 7.988696e-02	ci left: 1.031412e-01	ci right 1.117733e-01	k: 2148	n:20000
KS ci ratio: 4.418528e-02	ci left: 2.761185e-01	ci right 2.886449e-01	k: 5647	n:20000
GATAD2B   20000 perm   4 sec   (5242 perm/sec)   p_kst 2.823500e-01   p_cons 1.074000e-01   p_joint 5.190000e-02

Joint ci ratio: 9.739180e-02	ci left: 4.873281e-02	ci right 5.375454e-02	k: 1536	n:30000
Cons ci ratio: 6.592305e-02	ci left: 1.019469e-01	ci right 1.089297e-01	k: 3162	n:30000
KS ci ratio: 3.598839e-02	ci left: 2.782719e-01	ci right 2.885034e-01	k: 8501	n:30000
GATAD2B   30000 perm   6 sec   (5013 perm/sec)   p_kst 2.833667e-01   p_cons 1.054000e-01   p_joint 5.120000e-02

Outputting figure to mutsig2_images.part000000000069/GATAD2B.2_1822_30000_0.28337_0.1054_0.0512.png
                gene_name: GATAD2B
               theta_stop: 0.097 
                    nperm: 30000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.051 
     ci_joint_bounds_left: 0.049 
    ci_joint_bounds_right: 0.054 

Current progress: 60 percent done.
GBF1
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: 6.609721e-02	ci left: 2.515227e-01	ci right 2.688172e-01	k: 2601	n:10000
KS ci ratio: 1.282976e-02	ci left: 8.973393e-01	ci right 9.090246e-01	k: 9033	n:10000
GBF1   10000 perm   2 sec   (4134 perm/sec)   p_kst 9.033000e-01   p_cons 2.601000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000069/GBF1.2_5736_10000_0.9033_0.2601_1.png
                gene_name: GBF1
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.90 
        ci_ks_bounds_left: 0.90 
       ci_ks_bounds_right: 0.91 
                   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: 80 percent done.
GCN1L1
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: 9.038022e-03	ci left: 9.451295e-01	ci right 9.538063e-01	k: 9496	n:10000
KS ci ratio: 7.842084e-03	ci left: 9.576469e-01	ci right 9.652813e-01	k: 9616	n:10000
GCN1L1   10000 perm   3 sec   (3419 perm/sec)   p_kst 9.616000e-01   p_cons 9.496000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000069/GCN1L1.2_8248_10000_0.9616_0.9496_1.png
                gene_name: GCN1L1
               theta_stop: 0.0090 
                    nperm: 10000 
                     p_ks: 0.96 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000069
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 69 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119894: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000070> was used as the working directory.
Started at Wed Oct 10 10:43:04 2012
Results reported at Wed Oct 10 10:44:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000070.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000070.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 70  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    122.60 sec.
    Max Memory :      1119 MB
    Max Swap   :      3803 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.165.3896/
-whichjob
70
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 70: processing genes 6243 - 6333
Calculating significance of each gene.
Using projection method.
6243	GDF7	1
6244	GDF9	1
6245	GDI1	1.716643e-01
6246	GDI2	6.268245e-02
6247	GDNF	1
6248	GDPD1	1
6249	GDPD2	1
6250	GDPD3	1
6251	GDPD4	1
6252	GDPD5	1
6253	GEFT	1
6254	GEM	1
6255	GEMIN4	1
6256	GEMIN5	1
6257	GEMIN6	1
6258	GEMIN7	1
6259	GEMIN8	1
6260	GEN1	1
6261	GET4	8.211073e-02
6262	GFAP	1.182529e-01
6263	GFER	1
6264	GFI1	1
6265	GFI1B	1
6266	GFM1	1.671145e-01
6267	GFM2	1
6268	GFOD1	1
6269	GFOD2	1
6270	GFPT1	1
6271	GFPT2	1
6272	GFRA1	1
6273	GFRA2	1
6274	GFRA3	1
6275	GFRAL	1
6276	GGA1	2.295466e-01
6277	GGA2	1
6278	GGA3	1.669891e-01
6279	GGCT	1
6280	GGCX	3.136630e-01
6281	GGH	1
6282	GGN	1.803091e-01
6283	GGNBP2	1
6284	GGPS1	1
6285	GGT1	1
6286	GGT5	1
6287	GGT6	1.436837e-01
6288	GGT7	1
6289	GGTLC1	1
6290	GGTLC2	1
6291	GH1	1
6292	GH2	1
6293	GHDC	1.669796e-02
6294	GHITM	1
6295	GHR	1
6296	GHRH	1
6297	GHRHR	1
6298	GHRL	1
6299	GHSR	8.642955e-02
6300	GIF	1
6301	GIGYF1	1.482533e-01
6302	GIGYF2	1
6303	GIMAP1	1
6304	GIMAP2	3.763859e-02
6305	GIMAP4	1
6306	GIMAP5	1.267419e-01
6307	GIMAP6	1
6308	GIMAP7	1
6309	GIMAP8	1
6310	GIN1	1
6311	GINS1	2.204681e-02
6312	GINS2	1
6313	GINS3	1
6314	GINS4	1
6315	GIP	1
6316	GIPC1	1
6317	GIPC2	1
6318	GIPC3	1
6319	GIPR	1
6320	GIT1	1.998048e-01
6321	GIT2	1
6322	GJA1	1
6323	GJA10	1.393746e-01
6324	GJA3	1
6325	GJA4	1
6326	GJA5	1
6327	GJA8	1
6328	GJA9	1.832947e-01
6329	GJB1	1
6330	GJB2	1
6331	GJB3	1
6332	GJB4	1
6333	GJB5	1
Done

Running MutSig 2:
Scatter job 70: processing genes 6243 - 6333
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GFM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.817468e-02	ci left: 1.307088e-01	ci right 1.443032e-01	k: 1374	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: 9.780389e-02	ci left: 1.315900e-01	ci right 1.452214e-01	k: 1383	n:10000
GFM1   10000 perm   2 sec   (5579 perm/sec)   p_kst 1.383000e-01   p_cons 7.430000e-02   p_joint 1.374000e-01

Joint ci ratio: 3.783232e-02	ci left: 3.426402e-01	ci right 3.559036e-01	k: 6985	n:20000
Cons ci ratio: 9.464079e-02	ci left: 7.524916e-02	ci right 8.277377e-02	k: 1579	n:20000
KS ci ratio: 6.968580e-02	ci left: 1.318193e-01	ci right 1.413866e-01	k: 2731	n:20000
GFM1   20000 perm   6 sec   (3243 perm/sec)   p_kst 1.365500e-01   p_cons 7.895000e-02   p_joint 3.492500e-01

Outputting figure to mutsig2_images.part000000000070/GFM1.2_2328_20000_0.13655_0.07895_0.34925.png
                gene_name: GFM1
               theta_stop: 0.095 
                    nperm: 20000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.079 
      ci_cons_bounds_left: 0.075 
     ci_cons_bounds_right: 0.083 
                  p_joint: 0.35 
     ci_joint_bounds_left: 0.34 
    ci_joint_bounds_right: 0.36 

Current progress: 33 percent done.
GHDC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.930512e-02	ci left: 3.776368e-01	ci right 3.968289e-01	k: 3872	n:10000
Cons ci ratio: 6.486675e-02	ci left: 2.587439e-01	ci right 2.761918e-01	k: 2674	n:10000
KS ci ratio: 1.601493e-02	ci left: 8.499848e-01	ci right 8.638066e-01	k: 8570	n:10000
GHDC   10000 perm   2 sec   (6056 perm/sec)   p_kst 8.570000e-01   p_cons 2.674000e-01   p_joint 3.872000e-01

Outputting figure to mutsig2_images.part000000000070/GHDC.2_1714_10000_0.857_0.2674_0.3872.png
                gene_name: GHDC
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.27 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.28 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 67 percent done.
GIMAP5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.460899e-02	ci left: 5.521087e-01	ci right 5.716552e-01	k: 5619	n:10000
Cons ci ratio: 4.641806e-02	ci left: 4.065144e-01	ci right 4.259345e-01	k: 4162	n:10000
KS ci ratio: 9.331165e-02	ci left: 1.429561e-01	ci right 1.570484e-01	k: 1499	n:10000
GIMAP5   10000 perm   2 sec   (6262 perm/sec)   p_kst 1.499000e-01   p_cons 4.162000e-01   p_joint 5.619000e-01

Outputting figure to mutsig2_images.part000000000070/GIMAP5.2_932_10000_0.1499_0.4162_0.5619.png
                gene_name: GIMAP5
               theta_stop: 0.093 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.56 
     ci_joint_bounds_left: 0.55 
    ci_joint_bounds_right: 0.57 

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.165.3896/
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/181708/iteration1/scatter.0000000070
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 70 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1529>
Subject: Job 1119903: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1529>, 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/181708/iteration1/scatter.0000000071> was used as the working directory.
Started at Wed Oct 10 10:43:04 2012
Results reported at Wed Oct 10 10:44:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000071.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000071.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 71  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    119.39 sec.
    Max Memory :       895 MB
    Max Swap   :      3761 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.165.3896/
-whichjob
71
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 71: processing genes 6334 - 6423
Calculating significance of each gene.
Using projection method.
6334	GJB6	1
6335	GJB7	1
6336	GJC1	1
6337	GJC2	1
6338	GJC3	1
6339	GJD2	1.399646e-01
6340	GJD4	1
6341	GK	1
6342	GK2	1
6343	GK5	1
6344	GKAP1	1
6345	GKN1	1
6346	GKN2	1
6347	GLA	1
6348	GLB1	5.439366e-02
6349	GLB1L	1
6350	GLB1L2	1.438514e-01
6351	GLB1L3	1
6352	GLCCI1	1
6353	GLCE	1
6354	GLDC	1
6355	GLDN	1
6356	GLE1	1
6357	GLG1	1
6358	GLI1	1
6359	GLI2	4.465661e-01
6360	GLI3	2.807915e-01
6361	GLI4	1
6362	GLIPR1	1
6363	GLIPR1L1	1
6364	GLIPR1L2	1
6365	GLIPR2	1
6366	GLIS1	5.326150e-02
6367	GLIS2	1.737549e-01
6368	GLIS3	1
6369	GLMN	1
6370	GLO1	1.935446e-02
6371	GLOD4	1
6372	GLOD5	1
6373	GLP1R	1
6374	GLP2R	1
6375	GLRA1	1
6376	GLRA2	1
6377	GLRA3	1
6378	GLRA4	1
6379	GLRB	1
6380	GLRX	1
6381	GLRX2	1
6382	GLRX3	1
6383	GLRX5	1
6384	GLS	1
6385	GLS2	1
6386	GLT1D1	6.417037e-02
6387	GLT25D1	1
6388	GLT25D2	1
6389	GLT6D1	1
6390	GLT8D1	1
6391	GLT8D2	1
6392	GLTP	1
6393	GLTPD1	1
6394	GLTPD2	1
6395	GLTSCR2	1
6396	GLUD1	1
6397	GLUD2	1.192846e-01
6398	GLUL	1
6399	GLYAT	1.378664e-01
6400	GLYATL1	1.725970e-01
6401	GLYATL2	1
6402	GLYCTK	2.102476e-01
6403	GLYR1	1.041458e-01
6404	GM2A	1
6405	GMCL1	1
6406	GMDS	1
6407	GMEB1	1
6408	GMEB2	1
6409	GMFB	1
6410	GMFG	1
6411	GMIP	3.148929e-01
6412	GML	1
6413	GMNN	1
6414	GMPPA	1
6415	GMPPB	1
6416	GMPR	1
6417	GMPR2	1
6418	GMPS	2.233920e-01
6419	GNA11	1
6420	GNA12	1
6421	GNA13	1
6422	GNA14	1
6423	GNA15	1.094463e-01
Done

Running MutSig 2:
Scatter job 71: processing genes 6334 - 6423
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GLIS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.280852e-02	ci left: 4.462022e-01	ci right 4.658234e-01	k: 4560	n:10000
Cons ci ratio: 2.594843e-02	ci left: 6.861727e-01	ci right 7.043134e-01	k: 6953	n:10000
KS ci ratio: 5.694681e-02	ci left: 3.122498e-01	ci right 3.306543e-01	k: 3214	n:10000
GLIS1   10000 perm   2 sec   (5047 perm/sec)   p_kst 3.214000e-01   p_cons 6.953000e-01   p_joint 4.560000e-01

Outputting figure to mutsig2_images.part000000000071/GLIS1.2_1895_10000_0.3214_0.6953_0.456.png
                gene_name: GLIS1
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.70 
                  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.165.3896/
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/181708/iteration1/scatter.0000000071
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 71 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119909: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000072> was used as the working directory.
Started at Wed Oct 10 10:43:04 2012
Results reported at Wed Oct 10 10:44:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000072.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000072.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 72  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    111.67 sec.
    Max Memory :      1173 MB
    Max Swap   :      3820 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.165.3896/
-whichjob
72
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 72: processing genes 6424 - 6514
Calculating significance of each gene.
Using projection method.
6424	GNAI1	1
6425	GNAI2	1
6426	GNAI3	1
6427	GNAL	1
6428	GNAO1	1
6429	GNAQ	1
6430	GNAS	4.214666e-01
6431	GNAT1	1
6432	GNAT2	1
6433	GNAT3	1
6434	GNAZ	1
6435	GNB1	1
6436	GNB1L	1
6437	GNB2	1
6438	GNB2L1	1
6439	GNB3	1
6440	GNB4	1
6441	GNB5	1
6442	GNE	1.759526e-01
6443	GNG10	1
6444	GNG11	1
6445	GNG12	1
6446	GNG13	1
6447	GNG2	2.743215e-02
6448	GNG3	2.458341e-02
6449	GNG4	1
6450	GNG5	1
6451	GNG7	1
6452	GNG8	1
6453	GNGT1	1
6454	GNGT2	1
6455	GNL1	1
6456	GNL2	1
6457	GNL3	1
6458	GNL3L	1.353121e-01
6459	GNLY	1
6460	GNMT	1
6461	GNPAT	1
6462	GNPDA1	1
6463	GNPDA2	1
6464	GNPNAT1	1
6465	GNPTAB	1
6466	GNPTG	1
6467	GNRH1	1
6468	GNRH2	1
6469	GNRHR	1
6470	GNS	1
6471	GOLGA1	1
6472	GOLGA2	1
6473	GOLGA2B	1
6474	GOLGA3	1
6475	GOLGA4	1
6476	GOLGA5	1
6477	GOLGA6A	5.806956e-02
6478	GOLGA6C	1
6479	GOLGA6D	1
6480	GOLGA7	1
6481	GOLGA7B	1
6482	GOLGB1	3.005402e-02
6483	GOLIM4	1.892473e-01
6484	GOLM1	1
6485	GOLPH3	1
6486	GOLPH3L	1
6487	GOLT1A	1
6488	GOLT1B	1
6489	GON4L	3.923613e-01
6490	GOPC	1
6491	GORAB	1
6492	GORASP1	1
6493	GORASP2	1
6494	GOSR1	1
6495	GOSR2	1
6496	GOT1	1
6497	GOT1L1	1
6498	GOT2	1
6499	GP2	1.058912e-01
6500	GP5	1.583843e-01
6501	GP6	1
6502	GP9	1
6503	GPA33	1
6504	GPAA1	1
6505	GPAM	1
6506	GPAT2	1
6507	GPATCH1	1
6508	GPATCH2	1
6509	GPATCH3	1
6510	GPATCH4	1
6511	GPATCH8	1
6512	GPBP1	2.338661e-01
6513	GPBP1L1	1
6514	GPC1	1
Done

Running MutSig 2:
Scatter job 72: processing genes 6424 - 6514
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: 4.068000e-02	ci left: 4.715636e-01	ci right 4.912473e-01	k: 4814	n:10000
Cons ci ratio: 3.719183e-02	ci left: 5.163572e-01	ci right 5.360275e-01	k: 5262	n:10000
KS ci ratio: 6.475109e-02	ci left: 2.594365e-01	ci right 2.768988e-01	k: 2681	n:10000
GOLGB1   10000 perm   3 sec   (3123 perm/sec)   p_kst 2.681000e-01   p_cons 5.262000e-01   p_joint 4.814000e-01

Outputting figure to mutsig2_images.part000000000072/GOLGB1.11_9864_10000_0.2681_0.5262_0.4814.png
                gene_name: GOLGB1
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

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.165.3896/
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/181708/iteration1/scatter.0000000072
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 72 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119916: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000073> was used as the working directory.
Started at Wed Oct 10 10:43:04 2012
Results reported at Wed Oct 10 10:44:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000073.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000073.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 73  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    132.33 sec.
    Max Memory :       626 MB
    Max Swap   :      3422 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.165.3896/
-whichjob
73
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 73: processing genes 6515 - 6604
Calculating significance of each gene.
Using projection method.
6515	GPC2	1
6516	GPC3	1
6517	GPC4	1
6518	GPC5	1.482853e-01
6519	GPC6	1.326200e-01
6520	GPCPD1	1
6521	GPD1	1
6522	GPD1L	1
6523	GPD2	1
6524	GPER	1
6525	GPHA2	1
6526	GPHB5	1
6527	GPHN	1
6528	GPI	1
6529	GPIHBP1	1
6530	GPKOW	1
6531	GPLD1	2.174781e-01
6532	GPM6A	1
6533	GPM6B	1
6534	GPN1	1
6535	GPN2	1.420810e-01
6536	GPN3	8.030283e-02
6537	GPNMB	1
6538	GPR1	1
6539	GPR101	5.341671e-02
6540	GPR107	1
6541	GPR108	4.756864e-02
6542	GPR109A	1
6543	GPR109B	1
6544	GPR110	1
6545	GPR111	7.903545e-02
6546	GPR112	3.456146e-01
6547	GPR113	1
6548	GPR114	1
6549	GPR115	1
6550	GPR116	3.198908e-01
6551	GPR119	1
6552	GPR12	1
6553	GPR120	1
6554	GPR123	1.024912e-01
6555	GPR124	1
6556	GPR125	1.977133e-01
6557	GPR126	1.022867e-01
6558	GPR128	1
6559	GPR132	1
6560	GPR133	1
6561	GPR135	5.850293e-02
6562	GPR137	1
6563	GPR137B	1
6564	GPR137C	1
6565	GPR139	1
6566	GPR141	9.559246e-02
6567	GPR142	1
6568	GPR143	1
6569	GPR146	1
6570	GPR148	1
6571	GPR149	2.040965e-01
6572	GPR15	1.643883e-01
6573	GPR150	1
6574	GPR151	4.386728e-02
6575	GPR152	1
6576	GPR153	1
6577	GPR155	6.185299e-02
6578	GPR156	1
6579	GPR157	1
6580	GPR158	1.408156e-01
6581	GPR160	1
6582	GPR161	1
6583	GPR162	1
6584	GPR17	1.461106e-02
6585	GPR171	2.969675e-02
6586	GPR172A	1
6587	GPR172B	1
6588	GPR173	1
6589	GPR174	1.095801e-01
6590	GPR176	1
6591	GPR179	1
6592	GPR18	1
6593	GPR180	7.827123e-03
6594	GPR182	1
6595	GPR183	1
6596	GPR19	1
6597	GPR20	1
6598	GPR21	2.395754e-02
6599	GPR22	1
6600	GPR25	1
6601	GPR26	1
6602	GPR27	1
6603	GPR3	1
6604	GPR31	1
Done

Running MutSig 2:
Scatter job 73: processing genes 6515 - 6604
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: 4.720332e-03	ci left: 9.832843e-01	ci right 9.880266e-01	k: 9858	n:10000
Cons ci ratio: 1.766047e-02	ci left: 8.238140e-01	ci right 8.385925e-01	k: 8313	n:10000
KS ci ratio: 6.298409e-02	ci left: 2.703238e-01	ci right 2.880050e-01	k: 2791	n:10000
GPR112   10000 perm   3 sec   (3446 perm/sec)   p_kst 2.791000e-01   p_cons 8.313000e-01   p_joint 9.858000e-01

Outputting figure to mutsig2_images.part000000000073/GPR112.2_9335_10000_0.2791_0.8313_0.9858.png
                gene_name: GPR112
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.84 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.99 

Current progress: 20 percent done.
GPR126
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.789910e-02	ci left: 8.199499e-01	ci right 8.348589e-01	k: 8275	n:10000
Cons ci ratio: 4.702498e-02	ci left: 4.002380e-01	ci right 4.196145e-01	k: 4099	n:10000
KS ci ratio: 7.889140e-02	ci left: 1.901300e-01	ci right 2.058463e-01	k: 1979	n:10000
GPR126   10000 perm   2 sec   (5415 perm/sec)   p_kst 1.979000e-01   p_cons 4.099000e-01   p_joint 8.275000e-01

Outputting figure to mutsig2_images.part000000000073/GPR126.2_3903_10000_0.1979_0.4099_0.8275.png
                gene_name: GPR126
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.83 
     ci_joint_bounds_left: 0.82 
    ci_joint_bounds_right: 0.83 

Current progress: 40 percent done.
GPR155
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.197341e-02	ci left: 3.530692e-01	ci right 3.720109e-01	k: 3625	n:10000
Cons ci ratio: 1.594356e-01	ci left: 5.243929e-02	ci right 6.162089e-02	k: 569	n:10000
KS ci ratio: 3.025127e-02	ci left: 6.171342e-01	ci right 6.361919e-01	k: 6267	n:10000
GPR155   10000 perm   2 sec   (5997 perm/sec)   p_kst 6.267000e-01   p_cons 5.690000e-02   p_joint 3.625000e-01

Joint ci ratio: 7.046446e-02	ci left: 1.292581e-01	ci right 1.387486e-01	k: 2679	n:20000
Cons ci ratio: 1.126881e-01	ci left: 5.382647e-02	ci right 6.030306e-02	k: 1140	n:20000
KS ci ratio: 2.134850e-02	ci left: 6.209069e-01	ci right 6.343559e-01	k: 12553	n:20000
GPR155   20000 perm   4 sec   (5317 perm/sec)   p_kst 6.276500e-01   p_cons 5.700000e-02   p_joint 1.339500e-01

Joint ci ratio: 4.307932e-02	ci left: 2.116189e-01	ci right 2.209694e-01	k: 6488	n:30000
Cons ci ratio: 9.205290e-02	ci left: 5.437022e-02	ci right 5.964931e-02	k: 1709	n:30000
KS ci ratio: 1.740950e-02	ci left: 6.227358e-01	ci right 6.337061e-01	k: 18847	n:30000
GPR155   30000 perm   6 sec   (5035 perm/sec)   p_kst 6.282333e-01   p_cons 5.696667e-02   p_joint 2.162667e-01

Outputting figure to mutsig2_images.part000000000073/GPR155.2_2673_30000_0.62823_0.056967_0.21627.png
                gene_name: GPR155
               theta_stop: 0.092 
                    nperm: 30000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.057 
      ci_cons_bounds_left: 0.054 
     ci_cons_bounds_right: 0.060 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 60 percent done.
GPR17
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.779247e-02	ci left: 8.216784e-01	ci right 8.365294e-01	k: 8292	n:10000
Cons ci ratio: 3.569007e-02	ci left: 5.368806e-01	ci right 5.564922e-01	k: 5467	n:10000
KS ci ratio: 8.597494e-02	ci left: 1.646498e-01	ci right 1.795417e-01	k: 1720	n:10000
GPR17   10000 perm   2 sec   (6555 perm/sec)   p_kst 1.720000e-01   p_cons 5.467000e-01   p_joint 8.292000e-01

Outputting figure to mutsig2_images.part000000000073/GPR17.2_1112_10000_0.172_0.5467_0.8292.png
                gene_name: GPR17
               theta_stop: 0.086 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.55 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.83 
     ci_joint_bounds_left: 0.82 
    ci_joint_bounds_right: 0.84 

Current progress: 80 percent done.
GPR180
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.128802e-02	ci left: 6.011627e-01	ci right 6.203727e-01	k: 6108	n:10000
Cons ci ratio: 6.204299e-02	ci left: 2.763642e-01	ci right 2.941611e-01	k: 2852	n:10000
KS ci ratio: 9.913811e-02	ci left: 1.284572e-01	ci right 1.419561e-01	k: 1351	n:10000
GPR180   10000 perm   2 sec   (6312 perm/sec)   p_kst 1.351000e-01   p_cons 2.852000e-01   p_joint 6.108000e-01

Outputting figure to mutsig2_images.part000000000073/GPR180.2_1359_10000_0.1351_0.2852_0.6108.png
                gene_name: GPR180
               theta_stop: 0.099 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.28 
     ci_cons_bounds_right: 0.29 
                  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.165.3896/
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/181708/iteration1/scatter.0000000073
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 73 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1699>
Subject: Job 1119922: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, 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/181708/iteration1/scatter.0000000074> was used as the working directory.
Started at Wed Oct 10 10:43:04 2012
Results reported at Wed Oct 10 10:44:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000074.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000074.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 74  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    127.23 sec.
    Max Memory :      1073 MB
    Max Swap   :      3796 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.165.3896/
-whichjob
74
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 74: processing genes 6605 - 6695
Calculating significance of each gene.
Using projection method.
6605	GPR32	1
6606	GPR34	1
6607	GPR35	1
6608	GPR37	1
6609	GPR37L1	1
6610	GPR39	8.758995e-02
6611	GPR4	1
6612	GPR45	9.288903e-02
6613	GPR50	1
6614	GPR52	1
6615	GPR55	2.495941e-02
6616	GPR56	1
6617	GPR6	1
6618	GPR61	2.910472e-02
6619	GPR62	1
6620	GPR63	7.141549e-02
6621	GPR64	1
6622	GPR65	1
6623	GPR68	1
6624	GPR75	1
6625	GPR77	1
6626	GPR78	1
6627	GPR81	1
6628	GPR82	1
6629	GPR83	1
6630	GPR84	1
6631	GPR85	1
6632	GPR87	1
6633	GPR88	1
6634	GPR89A	1
6635	GPR89B	1
6636	GPR97	1
6637	GPR98	1
6638	GPRASP1	2.983361e-01
6639	GPRASP2	1
6640	GPRC5A	1
6641	GPRC5B	1
6642	GPRC5C	1
6643	GPRC5D	1.417624e-01
6644	GPRC6A	1
6645	GPRIN1	1.099770e-01
6646	GPRIN2	1
6647	GPRIN3	1
6648	GPS1	1
6649	GPS2	1.556248e-05
6650	GPSM1	1
6651	GPSM2	1
6652	GPSM3	1
6653	GPT	1
6654	GPT2	1
6655	GPX1	1
6656	GPX2	1
6657	GPX3	1
6658	GPX4	1
6659	GPX5	1
6660	GPX6	1
6661	GPX7	1
6662	GPX8	1
6663	GRAMD1A	1
6664	GRAMD1B	1
6665	GRAMD1C	1
6666	GRAMD2	1
6667	GRAMD3	1
6668	GRAMD4	1
6669	GRAP	3.330288e-02
6670	GRAP2	1
6671	GRASP	1
6672	GRB10	1
6673	GRB14	1
6674	GRB2	1
6675	GRB7	2.313167e-01
6676	GREB1	1
6677	GREM1	1
6678	GREM2	1
6679	GRHL1	1
6680	GRHL2	1.048416e-01
6681	GRHL3	1
6682	GRHPR	1.450394e-01
6683	GRIA1	1.713156e-01
6684	GRIA2	2.876475e-01
6685	GRIA3	1
6686	GRIA4	1.287282e-02
6687	GRID1	1
6688	GRID2	1.192096e-01
6689	GRIK1	3.686423e-01
6690	GRIK2	1.457710e-01
6691	GRIK3	3.914186e-01
6692	GRIK4	3.462085e-01
6693	GRIK5	1
6694	GRIN1	2.148283e-01
6695	GRIN2A	2.570387e-01
Done

Running MutSig 2:
Scatter job 74: processing genes 6605 - 6695
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: 6.367975e-02	ci left: 2.659681e-01	ci right 2.835633e-01	k: 2747	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: 3.089463e-02	ci left: 6.071884e-01	ci right 6.263435e-01	k: 6168	n:10000
GPR98   10000 perm   4 sec   (2567 perm/sec)   p_kst 6.168000e-01   p_cons 1.623000e-01   p_joint 2.747000e-01

Outputting figure to mutsig2_images.part000000000074/GPR98.4_19281_10000_0.6168_0.1623_0.2747.png
                gene_name: GPR98
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.27 
     ci_joint_bounds_left: 0.27 
    ci_joint_bounds_right: 0.28 

Current progress: 33 percent done.
GRIA4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.388548e-02	ci left: 4.339301e-01	ci right 4.535027e-01	k: 4437	n:10000
Cons ci ratio: 1.288838e-02	ci left: 8.965182e-01	ci right 9.082462e-01	k: 9025	n:10000
KS ci ratio: 4.884086e-02	ci left: 3.821155e-01	ci right 4.013476e-01	k: 3917	n:10000
GRIA4   10000 perm   2 sec   (4677 perm/sec)   p_kst 3.917000e-01   p_cons 9.025000e-01   p_joint 4.437000e-01

Outputting figure to mutsig2_images.part000000000074/GRIA4.4_3040_10000_0.3917_0.9025_0.4437.png
                gene_name: GRIA4
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.91 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.45 

Current progress: 67 percent done.
GPS2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.022542e-02	ci left: 6.175362e-01	ci right 6.365898e-01	k: 6271	n:10000
Cons ci ratio: 4.741593e-02	ci left: 3.962539e-01	ci right 4.156010e-01	k: 4059	n:10000
KS ci ratio: 4.896405e-02	ci left: 3.809211e-01	ci right 4.001427e-01	k: 3905	n:10000
GPS2   10000 perm   2 sec   (6010 perm/sec)   p_kst 3.905000e-01   p_cons 4.059000e-01   p_joint 6.271000e-01

Outputting figure to mutsig2_images.part000000000074/GPS2.3_1024_10000_0.3905_0.4059_0.6271.png
                gene_name: GPS2
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.64 

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.165.3896/
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/181708/iteration1/scatter.0000000074
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 74 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1534>
Subject: Job 1119928: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1534>, 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/181708/iteration1/scatter.0000000075> was used as the working directory.
Started at Wed Oct 10 10:43:04 2012
Results reported at Wed Oct 10 10:45:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000075.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000075.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 75  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    137.45 sec.
    Max Memory :       895 MB
    Max Swap   :      3632 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.165.3896/
-whichjob
75
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 75: processing genes 6696 - 6785
Calculating significance of each gene.
Using projection method.
6696	GRIN2B	1
6697	GRIN2C	1.334863e-01
6698	GRIN2D	1
6699	GRIN3A	1
6700	GRIN3B	1
6701	GRINA	1
6702	GRINL1A	1
6703	GRIP1	1
6704	GRIP2	1
6705	GRIPAP1	1
6706	GRK1	1
6707	GRK4	1
6708	GRK5	1.078895e-01
6709	GRK6	1
6710	GRK7	1
6711	GRLF1	1.473042e-01
6712	GRM1	1.873330e-01
6713	GRM2	1
6714	GRM3	1
6715	GRM4	5.539311e-02
6716	GRM5	1.056366e-01
6717	GRM6	1.930983e-01
6718	GRM7	2.946239e-02
6719	GRM8	1.977430e-01
6720	GRN	2.968284e-02
6721	GRP	1
6722	GRPEL1	1
6723	GRPEL2	1
6724	GRPR	1
6725	GRSF1	1
6726	GRTP1	1
6727	GRWD1	1
6728	GRXCR1	1
6729	GRXCR2	1
6730	GSDMA	1
6731	GSDMB	1
6732	GSDMC	1
6733	GSDMD	1
6734	GSG1	1.300512e-01
6735	GSG1L	1
6736	GSG2	1
6737	GSK3A	1.595765e-01
6738	GSK3B	1
6739	GSN	1
6740	GSPT1	1
6741	GSPT2	1
6742	GSR	6.721941e-02
6743	GSS	1
6744	GSTA1	1
6745	GSTA2	2.837553e-02
6746	GSTA3	1
6747	GSTA4	9.877217e-02
6748	GSTA5	1.338253e-02
6749	GSTCD	1
6750	GSTK1	1
6751	GSTM1	1
6752	GSTM2	1
6753	GSTM3	1
6754	GSTM4	1
6755	GSTM5	1
6756	GSTO1	1
6757	GSTO2	1
6758	GSTP1	1
6759	GSTZ1	1
6760	GSX1	1
6761	GSX2	1
6762	GTDC1	1
6763	GTF2A1	1
6764	GTF2A1L	1
6765	GTF2A2	1
6766	GTF2B	1
6767	GTF2E1	1
6768	GTF2E2	8.929783e-02
6769	GTF2F1	1
6770	GTF2F2	1
6771	GTF2H1	2.090472e-01
6772	GTF2H2C	1
6773	GTF2H2D	1
6774	GTF2H3	1.392606e-01
6775	GTF2H4	1
6776	GTF2H5	1
6777	GTF2I	1
6778	GTF2IRD1	3.339123e-01
6779	GTF2IRD2	1
6780	GTF2IRD2B	1
6781	GTF3A	1
6782	GTF3C1	1
6783	GTF3C2	3.757265e-01
6784	GTF3C3	2.809865e-03
6785	GTF3C4	1
Done

Running MutSig 2:
Scatter job 75: processing genes 6696 - 6785
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GTF3C3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.961818e-02	ci left: 3.746515e-01	ci right 3.938160e-01	k: 3842	n:10000
Cons ci ratio: 2.043634e-02	ci left: 7.781330e-01	ci right 7.943000e-01	k: 7863	n:10000
KS ci ratio: 7.904075e-02	ci left: 1.895391e-01	ci right 2.052376e-01	k: 1973	n:10000
GTF3C3   10000 perm   2 sec   (4725 perm/sec)   p_kst 1.973000e-01   p_cons 7.863000e-01   p_joint 3.842000e-01

Outputting figure to mutsig2_images.part000000000075/GTF3C3.3_2733_10000_0.1973_0.7863_0.3842.png
                gene_name: GTF3C3
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 25 percent done.
GRM4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.972347e-02	ci left: 6.253754e-01	ci right 6.443460e-01	k: 6349	n:10000
Cons ci ratio: 2.210680e-02	ci left: 7.501892e-01	ci right 7.670598e-01	k: 7587	n:10000
KS ci ratio: 5.317518e-02	ci left: 3.426336e-01	ci right 3.614527e-01	k: 3520	n:10000
GRM4   10000 perm   2 sec   (5588 perm/sec)   p_kst 3.520000e-01   p_cons 7.587000e-01   p_joint 6.349000e-01

Outputting figure to mutsig2_images.part000000000075/GRM4.2_2779_10000_0.352_0.7587_0.6349.png
                gene_name: GRM4
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.34 
       ci_ks_bounds_right: 0.36 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.64 

Current progress: 50 percent done.
GRM7
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: 6.827759e-02	ci left: 2.393626e-01	ci right 2.563846e-01	k: 2478	n:10000
KS ci ratio: 1.093240e-02	ci left: 9.226548e-01	ci right 9.328943e-01	k: 9279	n:10000
GRM7   10000 perm   2 sec   (4739 perm/sec)   p_kst 9.279000e-01   p_cons 2.478000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000075/GRM7.2_2863_10000_0.9279_0.2478_1.png
                gene_name: GRM7
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   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: 75 percent done.
GRN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.762478e-02	ci left: 2.429207e-01	ci right 2.600243e-01	k: 2514	n:10000
Cons ci ratio: 1.204951e-01	ci left: 8.990526e-02	ci right 1.015315e-01	k: 956	n:10000
KS ci ratio: 1.920191e-02	ci left: 7.986185e-01	ci right 8.142026e-01	k: 8065	n:10000
GRN   10000 perm   2 sec   (5569 perm/sec)   p_kst 8.065000e-01   p_cons 9.560000e-02   p_joint 2.514000e-01

Joint ci ratio: 7.681736e-02	ci left: 1.107573e-01	ci right 1.196549e-01	k: 2303	n:20000
Cons ci ratio: 8.047557e-02	ci left: 1.017662e-01	ci right 1.103488e-01	k: 2120	n:20000
KS ci ratio: 1.379890e-02	ci left: 7.958024e-01	ci right 8.069099e-01	k: 16028	n:20000
GRN   20000 perm   4 sec   (5097 perm/sec)   p_kst 8.014000e-01   p_cons 1.060000e-01   p_joint 1.151500e-01

Outputting figure to mutsig2_images.part000000000075/GRN.2_1830_20000_0.8014_0.106_0.11515.png
                gene_name: GRN
               theta_stop: 0.080 
                    nperm: 20000 
                     p_ks: 0.80 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.12 

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.165.3896/
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/181708/iteration1/scatter.0000000075
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 75 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119934: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000076> was used as the working directory.
Started at Wed Oct 10 10:43:14 2012
Results reported at Wed Oct 10 10:45:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000076.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000076.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 76  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    112.65 sec.
    Max Memory :      1220 MB
    Max Swap   :      3853 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.165.3896/
-whichjob
76
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 76: processing genes 6786 - 6876
Calculating significance of each gene.
Using projection method.
6786	GTF3C5	1
6787	GTF3C6	1
6788	GTPBP1	1
6789	GTPBP10	1
6790	GTPBP2	1.939939e-01
6791	GTPBP3	1
6792	GTPBP4	1
6793	GTPBP5	1
6794	GTPBP8	1
6795	GTSE1	1
6796	GTSF1	1
6797	GTSF1L	1
6798	GUCA1A	1
6799	GUCA1B	1
6800	GUCA1C	1
6801	GUCA2A	1
6802	GUCA2B	1
6803	GUCY1A2	1.896004e-02
6804	GUCY1A3	1.750537e-01
6805	GUCY1B3	1.950197e-01
6806	GUCY2C	2.530972e-01
6807	GUCY2D	1
6808	GUCY2F	1
6809	GUF1	1
6810	GUK1	1
6811	GULP1	1
6812	GUSB	1
6813	GXYLT1	1
6814	GXYLT2	1.647713e-01
6815	GYG1	1
6816	GYG2	1
6817	GYLTL1B	1
6818	GYPA	1
6819	GYPB	1
6820	GYPC	1
6821	GYPE	1
6822	GYS1	2.791615e-01
6823	GYS2	1.586680e-01
6824	GZF1	2.829990e-01
6825	GZMA	1
6826	GZMB	5.421134e-02
6827	GZMH	1
6828	GZMK	1
6829	GZMM	1
6830	H1F0	6.155521e-03
6831	H1FNT	1
6832	H1FOO	1
6833	H1FX	8.214068e-03
6834	H2AFB1	1
6835	H2AFB3	1
6836	H2AFJ	1
6837	H2AFV	1
6838	H2AFX	1
6839	H2AFY	1.414174e-01
6840	H2AFY2	1
6841	H2AFZ	1
6842	H2BFWT	1
6843	H3F3A	8.289759e-03
6844	H3F3B	1
6845	H3F3C	1
6846	H6PD	1
6847	HAAO	1.479727e-02
6848	HABP2	1
6849	HABP4	1
6850	HACE1	1
6851	HACL1	1
6852	HADH	1
6853	HADHA	1
6854	HADHB	1
6855	HAGH	1
6856	HAGHL	1
6857	HAL	1
6858	HAMP	1
6859	HAND1	1
6860	HAND2	1
6861	HAO1	1
6862	HAO2	1
6863	HAP1	1
6864	HAPLN1	1
6865	HAPLN2	9.569257e-02
6866	HAPLN3	1
6867	HAPLN4	1
6868	HARBI1	1
6869	HARS	1
6870	HARS2	1
6871	HAS1	1
6872	HAS2	1
6873	HAS3	3.222598e-02
6874	HAT1	1
6875	HAUS1	1
6876	HAUS2	1
Done

Running MutSig 2:
Scatter job 76: processing genes 6786 - 6876
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
GUCY1A2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.059430e-02	ci left: 7.754984e-01	ci right 7.917361e-01	k: 7837	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: 4.071259e-02	ci left: 4.711640e-01	ci right 4.908471e-01	k: 4810	n:10000
GUCY1A2   10000 perm   2 sec   (5164 perm/sec)   p_kst 4.810000e-01   p_cons 1.230000e-01   p_joint 7.837000e-01

Joint ci ratio: 1.463737e-02	ci left: 7.761615e-01	ci right 7.876564e-01	k: 15639	n:20000
Cons ci ratio: 7.372326e-02	ci left: 1.192654e-01	ci right 1.284443e-01	k: 2476	n:20000
KS ci ratio: 2.904824e-02	ci left: 4.696069e-01	ci right 4.834999e-01	k: 9531	n:20000
GUCY1A2   20000 perm   7 sec   (3018 perm/sec)   p_kst 4.765500e-01   p_cons 1.238000e-01   p_joint 7.819500e-01

Outputting figure to mutsig2_images.part000000000076/GUCY1A2.2_2231_20000_0.47655_0.1238_0.78195.png
                gene_name: GUCY1A2
               theta_stop: 0.074 
                    nperm: 20000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.79 

Current progress: 33 percent done.
H1FX
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.268173e-01	ci left: 2.570435e-02	ci right 3.237377e-02	k: 289	n:10000
Cons ci ratio: 6.233328e-02	ci left: 2.744825e-01	ci right 2.922438e-01	k: 2833	n:10000
KS ci ratio: 2.155899e-01	ci left: 2.854258e-02	ci right 3.553353e-02	k: 319	n:10000
H1FX   10000 perm   2 sec   (5294 perm/sec)   p_kst 3.190000e-02   p_cons 2.833000e-01   p_joint 2.890000e-02

Joint ci ratio: 1.354374e-01	ci left: 3.747135e-02	ci right 4.296335e-02	k: 803	n:20000
Cons ci ratio: 4.455333e-02	ci left: 2.727916e-01	ci right 2.852727e-01	k: 5580	n:20000
KS ci ratio: 1.496921e-01	ci left: 3.066372e-02	ci right 3.567321e-02	k: 662	n:20000
H1FX   20000 perm   4 sec   (5329 perm/sec)   p_kst 3.310000e-02   p_cons 2.790000e-01   p_joint 4.015000e-02

Joint ci ratio: 9.715883e-02	ci left: 4.896076e-02	ci right 5.399322e-02	k: 1543	n:30000
Cons ci ratio: 3.638826e-02	ci left: 2.738302e-01	ci right 2.840126e-01	k: 8367	n:30000
KS ci ratio: 1.205723e-01	ci left: 3.197780e-02	ci right 3.611308e-02	k: 1020	n:30000
H1FX   30000 perm   6 sec   (5185 perm/sec)   p_kst 3.400000e-02   p_cons 2.789000e-01   p_joint 5.143333e-02

Joint ci ratio: 7.986914e-02	ci left: 5.452694e-02	ci right 5.908767e-02	k: 2271	n:40000
Cons ci ratio: 3.149818e-02	ci left: 2.747079e-01	ci right 2.835242e-01	k: 11164	n:40000
KS ci ratio: 1.041948e-01	ci left: 3.239160e-02	ci right 3.597644e-02	k: 1366	n:40000
H1FX   40000 perm   8 sec   (5080 perm/sec)   p_kst 3.415000e-02   p_cons 2.791000e-01   p_joint 5.677500e-02

Joint ci ratio: 9.944430e-02	ci left: 2.863920e-02	ci right 3.165568e-02	k: 1506	n:50000
Cons ci ratio: 2.824337e-02	ci left: 2.741756e-01	ci right 2.820502e-01	k: 13905	n:50000
KS ci ratio: 9.296276e-02	ci left: 3.274138e-02	ci right 3.595298e-02	k: 1716	n:50000
H1FX   50000 perm   10 sec   (5038 perm/sec)   p_kst 3.432000e-02   p_cons 2.781000e-01   p_joint 3.012000e-02

Outputting figure to mutsig2_images.part000000000076/H1FX.2_646_50000_0.03432_0.2781_0.03012.png
                gene_name: H1FX
               theta_stop: 0.099 
                    nperm: 50000 
                     p_ks: 0.034 
        ci_ks_bounds_left: 0.033 
       ci_ks_bounds_right: 0.036 
                   p_cons: 0.28 
      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: 0.032 

Current progress: 67 percent done.
HAS3
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: 8.090944e-02	ci left: 1.823522e-01	ci right 1.978288e-01	k: 1900	n:10000
KS ci ratio: 4.081873e-02	ci left: 4.698654e-01	ci right 4.895465e-01	k: 4797	n:10000
HAS3   10000 perm   2 sec   (6127 perm/sec)   p_kst 4.797000e-01   p_cons 1.900000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000076/HAS3.2_1786_10000_0.4797_0.19_1.png
                gene_name: HAS3
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   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.165.3896/
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/181708/iteration1/scatter.0000000076
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 76 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1645>
Subject: Job 1119942: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1645>, 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/181708/iteration1/scatter.0000000077> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:46:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000077.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000077.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 77  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    174.97 sec.
    Max Memory :      1545 MB
    Max Swap   :      3875 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.165.3896/
-whichjob
77
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 77: processing genes 6877 - 6966
Calculating significance of each gene.
Using projection method.
6877	HAUS3	2.914967e-02
6878	HAUS4	1
6879	HAUS5	1
6880	HAUS6	3.015722e-01
6881	HAUS7	1
6882	HAUS8	1
6883	HAVCR1	1
6884	HAVCR2	1
6885	HAX1	1
6886	HBA1	1
6887	HBA2	1
6888	HBB	1
6889	HBD	1
6890	HBE1	1
6891	HBEGF	1
6892	HBG1	1
6893	HBG2	1
6894	HBM	1
6895	HBP1	1
6896	HBQ1	1
6897	HBS1L	1
6898	HBXIP	1
6899	HCCS	1
6900	HCFC1	4.441889e-01
6901	HCFC1R1	1
6902	HCFC2	1
6903	HCK	1
6904	HCLS1	5.290061e-02
6905	HCN1	2.463335e-05
6906	HCN2	1
6907	HCN3	1
6908	HCN4	3.689154e-01
6909	HCP5	1
6910	HCRT	3.504362e-03
6911	HCRTR1	1
6912	HCRTR2	1.091032e-01
6913	HCST	1
6914	HDAC1	1
6915	HDAC10	1
6916	HDAC11	1
6917	HDAC2	1
6918	HDAC3	1
6919	HDAC4	1.102779e-01
6920	HDAC5	1
6921	HDAC6	4.753736e-02
6922	HDAC7	1
6923	HDAC8	1
6924	HDAC9	2.463858e-01
6925	HDC	2.001846e-01
6926	HDDC2	1
6927	HDDC3	1
6928	HDGF	1
6929	HDGFL1	1
6930	HDGFRP2	1
6931	HDGFRP3	1
6932	HDHD1A	1
6933	HDHD2	1
6934	HDHD3	1
6935	HDLBP	4.234192e-01
6936	HDX	3.104623e-01
6937	HEATR1	1
6938	HEATR2	1
6939	HEATR3	2.373395e-01
6940	HEATR4	1
6941	HEATR5A	1
6942	HEATR5B	2.832524e-01
6943	HEATR6	4.682108e-01
6944	HEATR7B2	1
6945	HEBP1	5.440850e-02
6946	HEBP2	1
6947	HECA	1
6948	HECTD1	2.440991e-01
6949	HECTD2	1
6950	HECTD3	1
6951	HECW1	1
6952	HECW2	4.111653e-01
6953	HEG1	7.953635e-04
6954	HELB	1
6955	HELLS	1
6956	HELQ	1
6957	HELT	1.227821e-01
6958	HELZ	5.213935e-01
6959	HEMGN	1
6960	HEMK1	1
6961	HEPACAM	1
6962	HEPACAM2	1
6963	HEPH	1
6964	HEPHL1	8.780044e-02
6965	HEPN1	1
6966	HERC1	6.270741e-01
Done

Running MutSig 2:
Scatter job 77: processing genes 6877 - 6966
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HCN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.708334e-02	ci left: 3.996404e-01	ci right 4.190125e-01	k: 4093	n:10000
Cons ci ratio: 2.750894e-02	ci left: 6.606855e-01	ci right 6.792154e-01	k: 6700	n:10000
KS ci ratio: 6.494961e-02	ci left: 2.582492e-01	ci right 2.756868e-01	k: 2669	n:10000
HCN1   10000 perm   2 sec   (4390 perm/sec)   p_kst 2.669000e-01   p_cons 6.700000e-01   p_joint 4.093000e-01

Outputting figure to mutsig2_images.part000000000077/HCN1.4_2705_10000_0.2669_0.67_0.4093.png
                gene_name: HCN1
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.42 

Current progress: 11 percent done.
HEG1
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: 3.244499e-02	ci left: 5.836966e-01	ci right 6.030490e-01	k: 5934	n:10000
KS ci ratio: 2.255332e-02	ci left: 7.427054e-01	ci right 7.597480e-01	k: 7513	n:10000
HEG1   10000 perm   2 sec   (4924 perm/sec)   p_kst 7.513000e-01   p_cons 5.934000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000077/HEG1.4_4214_10000_0.7513_0.5934_1.png
                gene_name: HEG1
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.76 
                   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: 22 percent done.
HAUS3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.020242e-02	ci left: 4.774582e-01	ci right 4.971492e-01	k: 4873	n:10000
Cons ci ratio: 3.755887e-02	ci left: 5.114541e-01	ci right 5.311335e-01	k: 5213	n:10000
KS ci ratio: 7.281323e-02	ci left: 2.164518e-01	ci right 2.329089e-01	k: 2246	n:10000
HAUS3   10000 perm   2 sec   (6252 perm/sec)   p_kst 2.246000e-01   p_cons 5.213000e-01   p_joint 4.873000e-01

Outputting figure to mutsig2_images.part000000000077/HAUS3.2_1828_10000_0.2246_0.5213_0.4873.png
                gene_name: HAUS3
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 33 percent done.
HDAC4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.372124e-02	ci left: 8.846253e-01	ci right 8.969460e-01	k: 8909	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: 2.482671e-02	ci left: 7.047290e-01	ci right 7.225464e-01	k: 7137	n:10000
HDAC4   10000 perm   2 sec   (4094 perm/sec)   p_kst 7.137000e-01   p_cons 4.379000e-01   p_joint 8.909000e-01

Outputting figure to mutsig2_images.part000000000077/HDAC4.2_3359_10000_0.7137_0.4379_0.8909.png
                gene_name: HDAC4
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.45 
                  p_joint: 0.89 
     ci_joint_bounds_left: 0.88 
    ci_joint_bounds_right: 0.90 

Current progress: 44 percent done.
HDAC6
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: 3.054934e-02	ci left: 6.125124e-01	ci right 6.316164e-01	k: 6221	n:10000
KS ci ratio: 1.412003e-02	ci left: 8.787895e-01	ci right 8.913852e-01	k: 8852	n:10000
HDAC6   10000 perm   2 sec   (5220 perm/sec)   p_kst 8.852000e-01   p_cons 6.221000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000077/HDAC6.2_3760_10000_0.8852_0.6221_1.png
                gene_name: HDAC6
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   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: 56 percent done.
HEATR5B
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: 2.675337e-02	ci left: 6.729719e-01	ci right 6.913219e-01	k: 6822	n:10000
KS ci ratio: 1.016747e-01	ci left: 1.227823e-01	ci right 1.360344e-01	k: 1293	n:10000
HEATR5B   10000 perm   2 sec   (4914 perm/sec)   p_kst 1.293000e-01   p_cons 6.822000e-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: 1.889849e-02	ci left: 6.761482e-01	ci right 6.890987e-01	k: 13653	n:20000
KS ci ratio: 7.026779e-02	ci left: 1.298983e-01	ci right 1.394082e-01	k: 2692	n:20000
HEATR5B   20000 perm   4 sec   (4476 perm/sec)   p_kst 1.346000e-01   p_cons 6.826500e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000077/HEATR5B.2_6356_20000_0.1346_0.68265_1.png
                gene_name: HEATR5B
               theta_stop: 0.070 
                    nperm: 20000 
                     p_ks: 0.13 
        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: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 67 percent done.
HECTD1
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: 3.400848e-02	ci left: 5.607287e-01	ci right 5.802302e-01	k: 5705	n:10000
KS ci ratio: 9.953727e-03	ci left: 9.346478e-01	ci right 9.440942e-01	k: 9395	n:10000
HECTD1   10000 perm   2 sec   (4350 perm/sec)   p_kst 9.395000e-01   p_cons 5.705000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000077/HECTD1.2_8001_10000_0.9395_0.5705_1.png
                gene_name: HECTD1
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   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: 78 percent done.
HEPHL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.018666e-02	ci left: 6.181391e-01	ci right 6.371865e-01	k: 6277	n:10000
Cons ci ratio: 1.383594e-01	ci left: 6.913757e-02	ci right 7.951204e-02	k: 742	n:10000
KS ci ratio: 6.760723e-03	ci left: 9.677317e-01	ci right 9.743901e-01	k: 9712	n:10000
HEPHL1   10000 perm   2 sec   (5492 perm/sec)   p_kst 9.712000e-01   p_cons 7.420000e-02   p_joint 6.277000e-01

Joint ci ratio: 1.080788e-02	ci left: 8.632811e-01	ci right 8.727117e-01	k: 17361	n:20000
Cons ci ratio: 1.013035e-01	ci left: 6.611102e-02	ci right 7.321471e-02	k: 1392	n:20000
KS ci ratio: 4.785415e-03	ci left: 9.686837e-01	ci right 9.733781e-01	k: 19422	n:20000
HEPHL1   20000 perm   4 sec   (4943 perm/sec)   p_kst 9.711000e-01   p_cons 6.960000e-02   p_joint 8.680500e-01

Joint ci ratio: 1.306580e-04	ci left: 9.998770e-01	ci right 1	k: 30000	n:30000
Cons ci ratio: 8.272519e-02	ci left: 6.674555e-02	ci right 7.253813e-02	k: 2088	n:30000
KS ci ratio: 3.901645e-03	ci left: 9.692102e-01	ci right 9.730312e-01	k: 29135	n:30000
HEPHL1   30000 perm   6 sec   (4769 perm/sec)   p_kst 9.711667e-01   p_cons 6.960000e-02   p_joint 1

Outputting figure to mutsig2_images.part000000000077/HEPHL1.2_3560_30000_0.97117_0.0696_1.png
                gene_name: HEPHL1
               theta_stop: 0.083 
                    nperm: 30000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.070 
      ci_cons_bounds_left: 0.067 
     ci_cons_bounds_right: 0.073 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 89 percent done.
HERC1
Processing conservation and coverage...
67% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.346729e-02	ci left: 1.731041e-01	ci right 1.882824e-01	k: 1806	n:10000
Cons ci ratio: 7.577795e-02	ci left: 2.030380e-01	ci right 2.191306e-01	k: 2110	n:10000
KS ci ratio: 8.951618e-02	ci left: 1.536497e-01	ci right 1.681484e-01	k: 1608	n:10000
HERC1   10000 perm   3 sec   (3219 perm/sec)   p_kst 1.608000e-01   p_cons 2.110000e-01   p_joint 1.806000e-01

Outputting figure to mutsig2_images.part000000000077/HERC1.2_14894_10000_0.1608_0.211_0.1806.png
                gene_name: HERC1
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.21 
      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: 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.165.3896/
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/181708/iteration1/scatter.0000000077
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 77 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1726>
Subject: Job 1119948: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1726>, 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/181708/iteration1/scatter.0000000078> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:44:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000078.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000078.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 78  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     67.32 sec.
    Max Memory :      1138 MB
    Max Swap   :      3924 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.165.3896/
-whichjob
78
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 78: processing genes 6967 - 7057
Calculating significance of each gene.
Using projection method.
6967	HERC2	8.353689e-01
6968	HERC3	1
6969	HERC4	1
6970	HERC5	1
6971	HERC6	1
6972	HERPUD1	1
6973	HERPUD2	1
6974	HES1	1
6975	HES3	1
6976	HES4	1
6977	HES5	1
6978	HES6	1
6979	HES7	1
6980	HESX1	1
6981	HEXA	1.545251e-01
6982	HEXB	1
6983	HEXDC	1
6984	HEXIM1	1.466868e-01
6985	HEXIM2	1
6986	HEY1	1
6987	HEY2	1
6988	HEYL	1
6989	HFE	1.526903e-01
6990	HFE2	1
6991	HFM1	2.970483e-01
6992	HGD	1
6993	HGF	1.038372e-01
6994	HGFAC	1
6995	HGS	1
6996	HGSNAT	1
6997	HHAT	1
6998	HHATL	1
6999	HHEX	1
7000/18094 7000	HHIP	1
7001	HHIPL1	1
7002	HHIPL2	7.317116e-02
7003	HHLA2	1
7004	HHLA3	1
7005	HIAT1	1
7006	HIATL1	1
7007	HIBADH	1
7008	HIBCH	1
7009	HIC1	1
7010	HIC2	1
7011	HIF1A	1
7012	HIF1AN	1.416840e-01
7013	HIF3A	1
7014	HIGD1A	1
7015	HIGD1B	1
7016	HIGD1C	1
7017	HIGD2A	1
7018	HINFP	1
7019	HINT1	1
7020	HINT2	1
7021	HINT3	1
7022	HIP1	2.415502e-01
7023	HIP1R	5.883001e-02
7024	HIPK1	1
7025	HIPK2	3.409571e-01
7026	HIPK3	1.890180e-01
7027	HIPK4	1
7028	HIRA	1
7029	HIRIP3	1
7030	HIST1H1A	1
7031	HIST1H1B	1
7032	HIST1H1C	1
7033	HIST1H1D	1
7034	HIST1H1E	1
7035	HIST1H1T	1
7036	HIST1H2AA	1
7037	HIST1H2AB	1
7038	HIST1H2AC	1
7039	HIST1H2AD	1
7040	HIST1H2AE	1
7041	HIST1H2AG	5.943878e-03
7042	HIST1H2AH	1
7043	HIST1H2AI	1
7044	HIST1H2AJ	1
7045	HIST1H2AK	1
7046	HIST1H2AL	1
7047	HIST1H2AM	1
7048	HIST1H2BA	1.932120e-02
7049	HIST1H2BB	1
7050	HIST1H2BC	1
7051	HIST1H2BD	1
7052	HIST1H2BE	1
7053	HIST1H2BF	1
7054	HIST1H2BG	1
7055	HIST1H2BH	1
7056	HIST1H2BI	1
7057	HIST1H2BJ	1
Done

Running MutSig 2:
Scatter job 78: processing genes 6967 - 7057
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HIP1R
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.952147e-02	ci left: 1.275764e-01	ci right 1.410375e-01	k: 1342	n:10000
Cons ci ratio: 2.383317e-02	ci left: 7.212834e-01	ci right 7.387824e-01	k: 7301	n:10000
KS ci ratio: 1.881451e-01	ci left: 3.767505e-02	ci right 4.559480e-02	k: 415	n:10000
HIP1R   10000 perm   2 sec   (5367 perm/sec)   p_kst 4.150000e-02   p_cons 7.301000e-01   p_joint 1.342000e-01

Joint ci ratio: 4.344482e-02	ci left: 2.829721e-01	ci right 2.955892e-01	k: 5785	n:20000
Cons ci ratio: 1.665843e-02	ci left: 7.284721e-01	ci right 7.407596e-01	k: 14693	n:20000
KS ci ratio: 1.356132e-01	ci left: 3.737462e-02	ci right 4.286011e-02	k: 801	n:20000
HIP1R   20000 perm   6 sec   (3397 perm/sec)   p_kst 4.005000e-02   p_cons 7.346500e-01   p_joint 2.892500e-01

Joint ci ratio: 7.837486e-02	ci left: 7.394222e-02	ci right 8.000667e-02	k: 2308	n:30000
Cons ci ratio: 1.358708e-02	ci left: 7.300337e-01	ci right 7.400540e-01	k: 22052	n:30000
KS ci ratio: 1.108246e-01	ci left: 3.781053e-02	ci right 4.227910e-02	k: 1200	n:30000
HIP1R   30000 perm   8 sec   (3679 perm/sec)   p_kst 4.000000e-02   p_cons 7.350667e-01   p_joint 7.693333e-02

Joint ci ratio: 3.043687e-02	ci left: 2.886419e-01	ci right 2.975881e-01	k: 11724	n:40000
Cons ci ratio: 1.181261e-02	ci left: 7.291881e-01	ci right 7.378779e-01	k: 29342	n:40000
KS ci ratio: 9.512444e-02	ci left: 3.878452e-02	ci right 4.268252e-02	k: 1628	n:40000
HIP1R   40000 perm   10 sec   (3823 perm/sec)   p_kst 4.070000e-02   p_cons 7.335500e-01   p_joint 2.931000e-01

Outputting figure to mutsig2_images.part000000000078/HIP1R.2_3335_40000_0.0407_0.73355_0.2931.png
                gene_name: HIP1R
               theta_stop: 0.095 
                    nperm: 40000 
                     p_ks: 0.041 
        ci_ks_bounds_left: 0.039 
       ci_ks_bounds_right: 0.043 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.74 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.29 
    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.165.3896/
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/181708/iteration1/scatter.0000000078
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 78 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119953: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000079> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:45:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000079.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000079.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 79  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    115.42 sec.
    Max Memory :      1299 MB
    Max Swap   :      4049 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.165.3896/
-whichjob
79
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 79: processing genes 7058 - 7147
Calculating significance of each gene.
Using projection method.
7058	HIST1H2BK	1
7059	HIST1H2BL	2.005502e-02
7060	HIST1H2BM	1
7061	HIST1H2BN	1
7062	HIST1H2BO	1
7063	HIST1H3A	2.982496e-02
7064	HIST1H3B	1
7065	HIST1H3C	1
7066	HIST1H3D	1
7067	HIST1H3E	1
7068	HIST1H3F	3.587576e-02
7069	HIST1H3G	1
7070	HIST1H3H	1
7071	HIST1H3I	1
7072	HIST1H3J	1
7073	HIST1H4A	1
7074	HIST1H4B	1
7075	HIST1H4C	1
7076	HIST1H4D	1
7077	HIST1H4E	1
7078	HIST1H4F	1
7079	HIST1H4G	1
7080	HIST1H4H	1
7081	HIST1H4I	4.696064e-02
7082	HIST1H4J	1
7083	HIST1H4K	1
7084	HIST1H4L	1.137958e-02
7085	HIST2H2AB	1
7086	HIST2H2AC	1
7087	HIST2H2BE	1
7088	HIST2H2BF	3.537119e-02
7089	HIST2H3D	1
7090	HIST3H2A	1
7091	HIST3H2BB	3.278267e-02
7092	HIST3H3	1
7093	HIST4H4	1
7094	HIVEP1	1.514818e-01
7095	HIVEP2	5.067402e-01
7096	HIVEP3	1
7097	HJURP	5.625169e-02
7098	HK1	7.527361e-02
7099	HK2	4.031297e-01
7100	HK3	4.413509e-02
7101	HKDC1	1
7102	HKR1	1
7103	HLA-A	1.431143e-04
7104	HLA-B	1
7105	HLA-C	1
7106	HLA-DMA	1
7107	HLA-DMB	1
7108	HLA-DOA	1
7109	HLA-DOB	1
7110	HLA-DPA1	1
7111	HLA-DPB1	1
7112	HLA-DQA1	1
7113	HLA-DQA2	1
7114	HLA-DQB1	1
7115	HLA-DRA	1
7116	HLA-DRB1	1
7117	HLA-DRB5	1
7118	HLA-E	1
7119	HLA-F	1
7120	HLA-G	1
7121	HLCS	1
7122	HLF	1.190676e-01
7123	HLTF	1
7124	HLX	2.284362e-01
7125	HM13	1
7126	HMBOX1	1
7127	HMBS	1
7128	HMCN1	2.804933e-03
7129	HMG20A	1
7130	HMG20B	1
7131	HMGA1	1
7132	HMGA2	1
7133	HMGB1	1
7134	HMGB2	2.806956e-03
7135	HMGB3	1
7136	HMGB4	2.041774e-02
7137	HMGCL	1
7138	HMGCLL1	1
7139	HMGCR	1
7140	HMGCS1	1
7141	HMGCS2	1
7142	HMGN1	1
7143	HMGN2	1
7144	HMGN3	1
7145	HMGN4	1
7146	HMGN5	1
7147	HMGXB4	1
Done

Running MutSig 2:
Scatter job 79: processing genes 7058 - 7147
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HMCN1
Processing conservation and coverage...
57% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.550139e-01	ci left: 5.542402e-02	ci right 6.483425e-02	k: 600	n:10000
Cons ci ratio: 2.111979e-01	ci left: 2.977507e-02	ci right 3.690017e-02	k: 332	n:10000
KS ci ratio: 6.485020e-02	ci left: 2.588428e-01	ci right 2.762928e-01	k: 2675	n:10000
HMCN1   10000 perm   4 sec   (2596 perm/sec)   p_kst 2.675000e-01   p_cons 3.320000e-02   p_joint 6.000000e-02

Joint ci ratio: 1.396534e-01	ci left: 3.524760e-02	ci right 4.058782e-02	k: 757	n:20000
Cons ci ratio: 1.480826e-01	ci left: 3.133844e-02	ci right 3.639826e-02	k: 676	n:20000
KS ci ratio: 4.550795e-02	ci left: 2.644019e-01	ci right 2.767649e-01	k: 5411	n:20000
HMCN1   20000 perm   10 sec   (1957 perm/sec)   p_kst 2.705500e-01   p_cons 3.380000e-02   p_joint 3.785000e-02

Joint ci ratio: 9.336273e-02	ci left: 5.290307e-02	ci right 5.811676e-02	k: 1664	n:30000
Cons ci ratio: 1.213745e-01	ci left: 3.155716e-02	ci right 3.566714e-02	k: 1007	n:30000
KS ci ratio: 3.727044e-02	ci left: 2.643525e-01	ci right 2.744256e-01	k: 8081	n:30000
HMCN1   30000 perm   15 sec   (2052 perm/sec)   p_kst 2.693667e-01   p_cons 3.356667e-02   p_joint 5.546667e-02

Joint ci ratio: 8.653209e-02	ci left: 4.668446e-02	ci right 5.093134e-02	k: 1951	n:40000
Cons ci ratio: 1.047915e-01	ci left: 3.202608e-02	ci right 3.559202e-02	k: 1351	n:40000
KS ci ratio: 3.228129e-02	ci left: 2.649821e-01	ci right 2.737014e-01	k: 10773	n:40000
HMCN1   40000 perm   19 sec   (2096 perm/sec)   p_kst 2.693250e-01   p_cons 3.377500e-02   p_joint 4.877500e-02

Joint ci ratio: 6.628151e-02	ci left: 6.320887e-02	ci right 6.756176e-02	k: 3268	n:50000
Cons ci ratio: 9.304697e-02	ci left: 3.268272e-02	ci right 3.589164e-02	k: 1713	n:50000
KS ci ratio: 2.879791e-02	ci left: 2.664704e-01	ci right 2.742763e-01	k: 13518	n:50000
HMCN1   50000 perm   24 sec   (2116 perm/sec)   p_kst 2.703600e-01   p_cons 3.426000e-02   p_joint 6.536000e-02

Outputting figure to mutsig2_images.part000000000079/HMCN1.9_17336_50000_0.27036_0.03426_0.06536.png
                gene_name: HMCN1
               theta_stop: 0.093 
                    nperm: 50000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.034 
      ci_cons_bounds_left: 0.033 
     ci_cons_bounds_right: 0.036 
                  p_joint: 0.065 
     ci_joint_bounds_left: 0.063 
    ci_joint_bounds_right: 0.068 

Current progress: 14 percent done.
HLA-A
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: 2.772690e-02	ci left: 6.571620e-01	ci right 6.757409e-01	k: 6665	n:10000
KS ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
HLA-A   10000 perm   2 sec   (6240 perm/sec)   p_kst 1   p_cons 6.665000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000079/HLA-A.3_1130_10000_1_0.6665_1.png
                gene_name: HLA-A
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 1 
        ci_ks_bounds_left: 1.00 
       ci_ks_bounds_right: 1 
                   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: 29 percent done.
HIVEP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.504170e-02	ci left: 4.211655e-01	ci right 4.406747e-01	k: 4309	n:10000
Cons ci ratio: 9.687168e-02	ci left: 1.338424e-01	ci right 1.475676e-01	k: 1406	n:10000
KS ci ratio: 4.234563e-02	ci left: 4.515919e-01	ci right 4.712306e-01	k: 4614	n:10000
HIVEP1   10000 perm   2 sec   (4298 perm/sec)   p_kst 4.614000e-01   p_cons 1.406000e-01   p_joint 4.309000e-01

Outputting figure to mutsig2_images.part000000000079/HIVEP1.2_8189_10000_0.4614_0.1406_0.4309.png
                gene_name: HIVEP1
               theta_stop: 0.097 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 43 percent done.
HJURP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.536657e-02	ci left: 3.245569e-01	ci right 3.431400e-01	k: 3338	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: 9.627528e-02	ci left: 1.353117e-01	ci right 1.490975e-01	k: 1421	n:10000
HJURP   10000 perm   2 sec   (6508 perm/sec)   p_kst 1.421000e-01   p_cons 3.054000e-01   p_joint 3.338000e-01

Outputting figure to mutsig2_images.part000000000079/HJURP.2_2283_10000_0.1421_0.3054_0.3338.png
                gene_name: HJURP
               theta_stop: 0.096 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.31 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 57 percent done.
HK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.906018e-02	ci left: 6.358318e-01	ci right 6.546835e-01	k: 6453	n:10000
Cons ci ratio: 7.465850e-02	ci left: 2.079681e-01	ci right 2.241977e-01	k: 2160	n:10000
KS ci ratio: 7.783900e-02	ci left: 1.943656e-01	ci right 2.102082e-01	k: 2022	n:10000
HK1   10000 perm   2 sec   (6061 perm/sec)   p_kst 2.022000e-01   p_cons 2.160000e-01   p_joint 6.453000e-01

Outputting figure to mutsig2_images.part000000000079/HK1.2_3004_10000_0.2022_0.216_0.6453.png
                gene_name: HK1
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.65 
     ci_joint_bounds_left: 0.64 
    ci_joint_bounds_right: 0.65 

Current progress: 71 percent done.
HK3
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: 3.413353e-02	ci left: 5.589243e-01	ci right 5.784357e-01	k: 5687	n:10000
KS ci ratio: 4.208421e-03	ci left: 9.864298e-01	ci right 9.906784e-01	k: 9887	n:10000
HK3   10000 perm   2 sec   (6005 perm/sec)   p_kst 9.887000e-01   p_cons 5.687000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000079/HK3.2_2844_10000_0.9887_0.5687_1.png
                gene_name: HK3
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.99 
        ci_ks_bounds_left: 0.99 
       ci_ks_bounds_right: 0.99 
                   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: 86 percent done.
HMGB2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.404318e-02	ci left: 5.602275e-01	ci right 5.797317e-01	k: 5700	n:10000
Cons ci ratio: 4.444986e-02	ci left: 4.276467e-01	ci right 4.471898e-01	k: 4374	n:10000
KS ci ratio: 6.628658e-02	ci left: 2.504348e-01	ci right 2.677057e-01	k: 2590	n:10000
HMGB2   10000 perm   1 sec   (7060 perm/sec)   p_kst 2.590000e-01   p_cons 4.374000e-01   p_joint 5.700000e-01

Outputting figure to mutsig2_images.part000000000079/HMGB2.2_646_10000_0.259_0.4374_0.57.png
                gene_name: HMGB2
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.44 
      ci_cons_bounds_left: 0.43 
     ci_cons_bounds_right: 0.45 
                  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.165.3896/
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/181708/iteration1/scatter.0000000079
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 79 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119957: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000080> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:44:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000080.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000080.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 80  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     65.17 sec.
    Max Memory :       538 MB
    Max Swap   :      3429 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.165.3896/
-whichjob
80
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 80: processing genes 7148 - 7238
Calculating significance of each gene.
Using projection method.
7148	HMHA1	1
7149	HMHB1	1
7150	HMMR	1
7151	HMOX1	1
7152	HMOX2	1
7153	HMP19	1
7154	HMSD	1
7155	HMX2	1
7156	HMX3	1
7157	HN1	1
7158	HN1L	1
7159	HNF1A	1
7160	HNF1B	1
7161	HNF4A	2.244322e-01
7162	HNF4G	2.440196e-03
7163	HNMT	1.242471e-01
7164	HNRNPA0	1
7165	HNRNPA1	1
7166	HNRNPA1L2	1
7167	HNRNPA2B1	1
7168	HNRNPA3	8.756291e-02
7169	HNRNPAB	4.644827e-02
7170	HNRNPC	1
7171	HNRNPCL1	1
7172	HNRNPD	1
7173	HNRNPF	1.882516e-01
7174	HNRNPH1	1
7175	HNRNPH2	1
7176	HNRNPH3	1
7177	HNRNPK	1
7178	HNRNPL	1
7179	HNRNPM	1
7180	HNRNPR	1
7181	HNRNPU	8.438674e-02
7182	HNRNPUL1	2.318237e-01
7183	HNRNPUL2	1
7184	HNRPDL	3.534359e-02
7185	HNRPLL	1
7186	HOMER1	1
7187	HOMER2	1
7188	HOMER3	1
7189	HOMEZ	1
7190	HOOK1	1.710094e-01
7191	HOOK2	1
7192	HOOK3	1
7193	HOPX	1
7194	HORMAD1	1
7195	HORMAD2	1
7196	HOXA1	1
7197	HOXA10	1
7198	HOXA11	1
7199	HOXA13	1
7200	HOXA2	1
7201	HOXA3	1
7202	HOXA4	1
7203	HOXA5	1
7204	HOXA6	1
7205	HOXA7	1
7206	HOXA9	1
7207	HOXB1	1
7208	HOXB13	1
7209	HOXB2	1
7210	HOXB3	1
7211	HOXB4	1.670378e-03
7212	HOXB5	1
7213	HOXB6	1
7214	HOXB7	1
7215	HOXB8	1
7216	HOXB9	1
7217	HOXC10	1
7218	HOXC11	1
7219	HOXC12	1
7220	HOXC13	1
7221	HOXC4	1
7222	HOXC5	1
7223	HOXC6	1
7224	HOXC8	1
7225	HOXC9	1
7226	HOXD1	1
7227	HOXD10	1
7228	HOXD11	1
7229	HOXD12	1
7230	HOXD13	1
7231	HOXD3	1
7232	HOXD4	1
7233	HOXD8	1
7234	HOXD9	1
7235	HP	1
7236	HP1BP3	2.267674e-01
7237	HPCA	1
7238	HPCAL1	1
Done

Running MutSig 2:
Scatter job 80: processing genes 7148 - 7238
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HNF4G
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.853489e-02	ci left: 2.379790e-01	ci right 2.549689e-01	k: 2464	n:10000
Cons ci ratio: 1.076335e-01	ci left: 1.107625e-01	ci right 1.234615e-01	k: 1170	n:10000
KS ci ratio: 3.392529e-02	ci left: 5.619317e-01	ci right 5.814265e-01	k: 5717	n:10000
HNF4G   10000 perm   2 sec   (6387 perm/sec)   p_kst 5.717000e-01   p_cons 1.170000e-01   p_joint 2.464000e-01

Joint ci ratio: 5.287016e-02	ci left: 2.098678e-01	ci right 2.213150e-01	k: 4311	n:20000
Cons ci ratio: 7.486609e-02	ci left: 1.160187e-01	ci right 1.250920e-01	k: 2410	n:20000
KS ci ratio: 2.374622e-02	ci left: 5.698168e-01	ci right 5.835609e-01	k: 11534	n:20000
HNF4G   20000 perm   5 sec   (3703 perm/sec)   p_kst 5.767000e-01   p_cons 1.205000e-01   p_joint 2.155500e-01

Outputting figure to mutsig2_images.part000000000080/HNF4G.2_1378_20000_0.5767_0.1205_0.21555.png
                gene_name: HNF4G
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 0.58 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 50 percent done.
HOXB4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.717362e-02	ci left: 8.316480e-01	ci right 8.461540e-01	k: 8390	n:10000
Cons ci ratio: 6.997954e-03	ci left: 9.656240e-01	ci right 9.724991e-01	k: 9692	n:10000
KS ci ratio: 8.773547e-02	ci left: 1.590500e-01	ci right 1.737448e-01	k: 1663	n:10000
HOXB4   10000 perm   1 sec   (7182 perm/sec)   p_kst 1.663000e-01   p_cons 9.692000e-01   p_joint 8.390000e-01

Outputting figure to mutsig2_images.part000000000080/HOXB4.2_764_10000_0.1663_0.9692_0.839.png
                gene_name: HOXB4
               theta_stop: 0.088 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.84 
     ci_joint_bounds_left: 0.83 
    ci_joint_bounds_right: 0.85 

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.165.3896/
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/181708/iteration1/scatter.0000000080
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 80 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1653>
Subject: Job 1119961: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1653>, 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/181708/iteration1/scatter.0000000081> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:45:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000081.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000081.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 81  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    155.06 sec.
    Max Memory :      1483 MB
    Max Swap   :      3830 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.165.3896/
-whichjob
81
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 81: processing genes 7239 - 7328
Calculating significance of each gene.
Using projection method.
7239	HPCAL4	1
7240	HPD	7.372741e-02
7241	HPDL	1
7242	HPGD	1
7243	HPGDS	9.854496e-02
7244	HPN	1
7245	HPR	1.106651e-01
7246	HPRT1	1
7247	HPS1	1
7248	HPS3	1
7249	HPS4	1
7250	HPS5	1
7251	HPS6	1
7252	HPSE	2.206952e-01
7253	HPSE2	1
7254	HPX	1
7255	HR	1
7256	HRAS	1
7257	HRASLS	1
7258	HRASLS2	1
7259	HRASLS5	2.144114e-02
7260	HRC	3.276872e-01
7261	HRCT1	1
7262	HRG	1.337094e-01
7263	HRH1	1.221598e-02
7264	HRH2	1
7265	HRH3	1
7266	HRH4	8.955839e-02
7267	HRNR	2.010729e-04
7268	HRSP12	4.016803e-02
7269	HS1BP3	1
7270	HS2ST1	1
7271	HS3ST1	1
7272	HS3ST2	1
7273	HS3ST3A1	1
7274	HS3ST3B1	1
7275	HS3ST4	1
7276	HS3ST5	1
7277	HS3ST6	1
7278	HS6ST1	1
7279	HS6ST2	1
7280	HS6ST3	1
7281	HSBP1	1
7282	HSCB	1
7283	HSD11B1	1
7284	HSD11B1L	1
7285	HSD11B2	1
7286	HSD17B1	1
7287	HSD17B10	1
7288	HSD17B11	1
7289	HSD17B12	1
7290	HSD17B13	5.068756e-02
7291	HSD17B14	1
7292	HSD17B2	1
7293	HSD17B3	1
7294	HSD17B4	2.236311e-01
7295	HSD17B6	1
7296	HSD17B7	1
7297	HSD17B8	9.638368e-02
7298	HSD3B1	1
7299	HSD3B2	1
7300	HSD3B7	1
7301	HSDL1	1
7302	HSDL2	1
7303	HSF1	1.214479e-02
7304	HSF2	1
7305	HSF2BP	1
7306	HSF4	1
7307	HSF5	1
7308	HSH2D	1
7309	HSP90AA1	1
7310	HSP90AB1	2.020761e-02
7311	HSP90B1	7.512709e-03
7312	HSPA12A	1
7313	HSPA12B	1
7314	HSPA13	1
7315	HSPA14	1
7316	HSPA1A	1
7317	HSPA1B	1
7318	HSPA1L	1
7319	HSPA2	1
7320	HSPA4	1
7321	HSPA4L	1
7322	HSPA5	1
7323	HSPA6	1
7324	HSPA8	1
7325	HSPA9	1
7326	HSPB1	1
7327	HSPB11	2.412122e-02
7328	HSPB2	6.345818e-02
Done

Running MutSig 2:
Scatter job 81: processing genes 7239 - 7328
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HRNR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.508232e-02	ci left: 5.453952e-01	ci right 5.649726e-01	k: 5552	n:10000
Cons ci ratio: 4.314654e-02	ci left: 4.423104e-01	ci right 4.619175e-01	k: 4521	n:10000
KS ci ratio: 4.465815e-02	ci left: 4.253532e-01	ci right 4.448846e-01	k: 4351	n:10000
HRNR   10000 perm   5 sec   (2071 perm/sec)   p_kst 4.351000e-01   p_cons 4.521000e-01   p_joint 5.552000e-01

Outputting figure to mutsig2_images.part000000000081/HRNR.6_8561_10000_0.4351_0.4521_0.5552.png
                gene_name: HRNR
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.56 
     ci_joint_bounds_left: 0.55 
    ci_joint_bounds_right: 0.56 

Current progress: 14 percent done.
HSP90B1
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: 7.681687e-02	ci left: 1.986025e-01	ci right 2.145687e-01	k: 2065	n:10000
KS ci ratio: 3.173059e-02	ci left: 5.944357e-01	ci right 6.137036e-01	k: 6041	n:10000
HSP90B1   10000 perm   2 sec   (4801 perm/sec)   p_kst 6.041000e-01   p_cons 2.065000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000081/HSP90B1.3_2484_10000_0.6041_0.2065_1.png
                gene_name: HSP90B1
               theta_stop: 0.077 
                    nperm: 10000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 29 percent done.
HPSE
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.823153e-02	ci left: 3.880884e-01	ci right 4.073712e-01	k: 3977	n:10000
Cons ci ratio: 3.374555e-02	ci left: 5.645385e-01	ci right 5.840182e-01	k: 5743	n:10000
KS ci ratio: 1.207044e-01	ci left: 8.961344e-02	ci right 1.012235e-01	k: 953	n:10000
HPSE   10000 perm   2 sec   (6411 perm/sec)   p_kst 9.530000e-02   p_cons 5.743000e-01   p_joint 3.977000e-01

Joint ci ratio: 2.595177e-02	ci left: 5.259061e-01	ci right 5.397843e-01	k: 10657	n:20000
Cons ci ratio: 2.371462e-02	ci left: 5.704681e-01	ci right 5.842094e-01	k: 11547	n:20000
KS ci ratio: 8.457082e-02	ci left: 9.288305e-02	ci right 1.011345e-01	k: 1939	n:20000
HPSE   20000 perm   4 sec   (4965 perm/sec)   p_kst 9.695000e-02   p_cons 5.773500e-01   p_joint 5.328500e-01

Outputting figure to mutsig2_images.part000000000081/HPSE.2_1680_20000_0.09695_0.57735_0.53285.png
                gene_name: HPSE
               theta_stop: 0.085 
                    nperm: 20000 
                     p_ks: 0.097 
        ci_ks_bounds_left: 0.093 
       ci_ks_bounds_right: 0.10 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.58 
                  p_joint: 0.53 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.54 

Current progress: 43 percent done.
HRH1
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: 3.876542e-02	ci left: 4.956504e-01	ci right 5.153464e-01	k: 5055	n:10000
KS ci ratio: 3.476387e-02	ci left: 5.499041e-01	ci right 5.694611e-01	k: 5597	n:10000
HRH1   10000 perm   2 sec   (6205 perm/sec)   p_kst 5.597000e-01   p_cons 5.055000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000081/HRH1.2_1468_10000_0.5597_0.5055_1.png
                gene_name: HRH1
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   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: 57 percent done.
HSD17B8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.958604e-03	ci left: 9.878505e-01	ci right 9.918564e-01	k: 9900	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: 2.211887e-02	ci left: 7.499869e-01	ci right 7.668623e-01	k: 7585	n:10000
HSD17B8   10000 perm   2 sec   (5574 perm/sec)   p_kst 7.585000e-01   p_cons 7.989000e-01   p_joint 9.900000e-01

Outputting figure to mutsig2_images.part000000000081/HSD17B8.2_822_10000_0.7585_0.7989_0.99.png
                gene_name: HSD17B8
               theta_stop: 0.022 
                    nperm: 10000 
                     p_ks: 0.76 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.77 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.81 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 71 percent done.
HSF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.607094e-02	ci left: 3.189980e-01	ci right 3.375022e-01	k: 3282	n:10000
Cons ci ratio: 6.364781e-02	ci left: 2.661660e-01	ci right 2.837652e-01	k: 2749	n:10000
KS ci ratio: 3.170407e-02	ci left: 5.948373e-01	ci right 6.141018e-01	k: 6045	n:10000
HSF1   10000 perm   3 sec   (3478 perm/sec)   p_kst 6.045000e-01   p_cons 2.749000e-01   p_joint 3.282000e-01

Outputting figure to mutsig2_images.part000000000081/HSF1.2_1642_10000_0.6045_0.2749_0.3282.png
                gene_name: HSF1
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.27 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.28 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 86 percent done.
HSP90AB1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.051569e-01	ci left: 1.155484e-01	ci right 1.284727e-01	k: 1219	n:10000
Cons ci ratio: 5.395232e-03	ci left: 9.786643e-01	ci right 9.840501e-01	k: 9815	n:10000
KS ci ratio: 1.462753e-01	ci left: 6.207973e-02	ci right 7.197432e-02	k: 669	n:10000
HSP90AB1   10000 perm   3 sec   (3964 perm/sec)   p_kst 6.690000e-02   p_cons 9.815000e-01   p_joint 1.219000e-01

Joint ci ratio: 8.246861e-02	ci left: 9.729878e-02	ci right 1.057175e-01	k: 2029	n:20000
Cons ci ratio: 3.898264e-03	ci left: 9.786445e-01	ci right 9.825140e-01	k: 19613	n:20000
KS ci ratio: 1.037668e-01	ci left: 6.313395e-02	ci right 7.009269e-02	k: 1331	n:20000
HSP90AB1   20000 perm   5 sec   (4299 perm/sec)   p_kst 6.655000e-02   p_cons 9.806500e-01   p_joint 1.014500e-01

Joint ci ratio: 6.733577e-02	ci left: 9.807193e-02	ci right 1.049388e-01	k: 3044	n:30000
Cons ci ratio: 3.092628e-03	ci left: 9.801191e-01	ci right 9.831866e-01	k: 29451	n:30000
KS ci ratio: 8.434209e-02	ci left: 6.432686e-02	ci right 7.002398e-02	k: 2014	n:30000
HSP90AB1   30000 perm   7 sec   (4362 perm/sec)   p_kst 6.713333e-02   p_cons 9.817000e-01   p_joint 1.014667e-01

Outputting figure to mutsig2_images.part000000000081/HSP90AB1.2_2219_30000_0.067133_0.9817_0.10147.png
                gene_name: HSP90AB1
               theta_stop: 0.084 
                    nperm: 30000 
                     p_ks: 0.067 
        ci_ks_bounds_left: 0.064 
       ci_ks_bounds_right: 0.070 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.10 
     ci_joint_bounds_left: 0.098 
    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.165.3896/
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/181708/iteration1/scatter.0000000081
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 81 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119965: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000082> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:45:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000082.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000082.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 82  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    123.21 sec.
    Max Memory :      1113 MB
    Max Swap   :      3853 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.165.3896/
-whichjob
82
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 82: processing genes 7329 - 7419
Calculating significance of each gene.
Using projection method.
7329	HSPB3	1
7330	HSPB7	1
7331	HSPB8	1
7332	HSPB9	1
7333	HSPBAP1	1.538192e-01
7334	HSPBP1	2.573790e-02
7335	HSPC159	1
7336	HSPD1	1
7337	HSPE1	1
7338	HSPG2	1
7339	HSPH1	1
7340	HTATIP2	5.319529e-02
7341	HTATSF1	1
7342	HTN1	1
7343	HTN3	1
7344	HTR1A	1
7345	HTR1B	1
7346	HTR1D	1
7347	HTR1E	1
7348	HTR1F	1
7349	HTR2A	1
7350	HTR2B	6.886325e-02
7351	HTR2C	1
7352	HTR3A	1
7353	HTR3B	1
7354	HTR3C	1
7355	HTR3D	1
7356	HTR3E	1
7357	HTR4	2.067375e-01
7358	HTR5A	1
7359	HTR6	1
7360	HTR7	1
7361	HTRA1	1
7362	HTRA2	1
7363	HTRA3	3.587621e-02
7364	HTRA4	1
7365	HTT	1
7366	HUNK	1
7367	HUS1	1
7368	HUS1B	1
7369	HUWE1	1
7370	HVCN1	1
7371	HYAL1	1
7372	HYAL2	1
7373	HYAL3	5.715875e-02
7374	HYAL4	1
7375	HYDIN	1
7376	HYI	1.637053e-03
7377	HYLS1	1
7378	HYOU1	1
7379	IAH1	1
7380	IAPP	1
7381	IARS	1
7382	IARS2	1
7383	IBSP	1
7384	IBTK	3.259858e-01
7385	ICA1	1.402255e-01
7386	ICA1L	9.361246e-02
7387	ICAM1	2.069946e-01
7388	ICAM2	1
7389	ICAM3	1
7390	ICAM4	1
7391	ICAM5	1
7392	ICK	1
7393	ICMT	1
7394	ICOS	1
7395	ICOSLG	3.118751e-02
7396	ICT1	1
7397	ID1	1
7398	ID2	1
7399	ID3	1
7400	IDE	6.377112e-02
7401	IDH1	1.028834e-01
7402	IDH2	1
7403	IDH3A	1
7404	IDH3B	1
7405	IDH3G	1
7406	IDI1	1
7407	IDI2	1
7408	IDO1	1
7409	IDO2	1.015308e-01
7410	IDS	1
7411	IDUA	1
7412	IER2	1
7413	IER3	1
7414	IER3IP1	1
7415	IER5	3.352245e-02
7416	IER5L	1
7417	IFFO1	1
7418	IFI16	1
7419	IFI27	1
Done

Running MutSig 2:
Scatter job 82: processing genes 7329 - 7419
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
HYI
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.229731e-02	ci left: 5.859043e-01	ci right 6.052400e-01	k: 5956	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: 2.613506e-01	ci left: 1.912136e-02	ci right 2.496169e-02	k: 219	n:10000
HYI   10000 perm   2 sec   (6649 perm/sec)   p_kst 2.190000e-02   p_cons 8.012000e-01   p_joint 5.956000e-01

Joint ci ratio: 1.908840e-01	ci left: 1.867638e-02	ci right 2.266469e-02	k: 412	n:20000
Cons ci ratio: 1.396989e-02	ci left: 7.918120e-01	ci right 8.030014e-01	k: 15949	n:20000
KS ci ratio: 1.908840e-01	ci left: 1.867638e-02	ci right 2.266469e-02	k: 412	n:20000
HYI   20000 perm   7 sec   (2745 perm/sec)   p_kst 2.060000e-02   p_cons 7.974500e-01   p_joint 2.060000e-02

Joint ci ratio: 1.597865e-01	ci left: 1.809339e-02	ci right 2.126726e-02	k: 589	n:30000
Cons ci ratio: 1.137275e-02	ci left: 7.938147e-01	ci right 8.029275e-01	k: 23952	n:30000
KS ci ratio: 1.597865e-01	ci left: 1.809339e-02	ci right 2.126726e-02	k: 589	n:30000
HYI   30000 perm   10 sec   (3107 perm/sec)   p_kst 1.963333e-02   p_cons 7.984000e-01   p_joint 1.963333e-02

Joint ci ratio: 1.368497e-01	ci left: 1.872293e-02	ci right 2.149735e-02	k: 803	n:40000
Cons ci ratio: 9.797795e-03	ci left: 7.961214e-01	ci right 8.039850e-01	k: 32003	n:40000
KS ci ratio: 1.368497e-01	ci left: 1.872293e-02	ci right 2.149735e-02	k: 803	n:40000
HYI   40000 perm   12 sec   (3435 perm/sec)   p_kst 2.007500e-02   p_cons 8.000750e-01   p_joint 2.007500e-02

Joint ci ratio: 1.236000e-01	ci left: 1.849986e-02	ci right 2.095634e-02	k: 985	n:50000
Cons ci ratio: 8.742987e-03	ci left: 7.972919e-01	ci right 8.043131e-01	k: 40041	n:50000
KS ci ratio: 1.236000e-01	ci left: 1.849986e-02	ci right 2.095634e-02	k: 985	n:50000
HYI   50000 perm   14 sec   (3659 perm/sec)   p_kst 1.970000e-02   p_cons 8.008200e-01   p_joint 1.970000e-02

Joint ci ratio: 1.134290e-01	ci left: 1.840855e-02	ci right 2.063827e-02	k: 1170	n:60000
Cons ci ratio: 7.960022e-03	ci left: 7.984532e-01	ci right 8.048509e-01	k: 48100	n:60000
KS ci ratio: 1.134290e-01	ci left: 1.840855e-02	ci right 2.063827e-02	k: 1170	n:60000
HYI   60000 perm   16 sec   (3790 perm/sec)   p_kst 1.950000e-02   p_cons 8.016667e-01   p_joint 1.950000e-02

Joint ci ratio: 5.260336e-02	ci left: 7.156330e-02	ci right 7.544357e-02	k: 5144	n:70000
Cons ci ratio: 7.363803e-03	ci left: 7.989422e-01	ci right 8.048614e-01	k: 56134	n:70000
KS ci ratio: 1.058143e-01	ci left: 1.821016e-02	ci right 2.025854e-02	k: 1345	n:70000
HYI   70000 perm   19 sec   (3746 perm/sec)   p_kst 1.921429e-02   p_cons 8.019143e-01   p_joint 7.348571e-02

Joint ci ratio: 9.908827e-02	ci left: 1.823590e-02	ci right 2.014919e-02	k: 1534	n:80000
Cons ci ratio: 6.881736e-03	ci left: 7.994351e-01	ci right 8.049680e-01	k: 64177	n:80000
KS ci ratio: 9.908827e-02	ci left: 1.823590e-02	ci right 2.014919e-02	k: 1534	n:80000
HYI   80000 perm   21 sec   (3802 perm/sec)   p_kst 1.917500e-02   p_cons 8.022125e-01   p_joint 1.917500e-02

Outputting figure to mutsig2_images.part000000000082/HYI.2_866_80000_0.019175_0.80221_0.019175.png
                gene_name: HYI
               theta_stop: 0.099 
                    nperm: 80000 
                     p_ks: 0.019 
        ci_ks_bounds_left: 0.018 
       ci_ks_bounds_right: 0.020 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.80 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.019 
     ci_joint_bounds_left: 0.018 
    ci_joint_bounds_right: 0.020 

Current progress: 50 percent done.
IDE
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: 2.589946e-02	ci left: 6.869792e-01	ci right 7.051065e-01	k: 6961	n:10000
KS ci ratio: 6.798590e-02	ci left: 2.409439e-01	ci right 2.580023e-01	k: 2494	n:10000
IDE   10000 perm   2 sec   (5353 perm/sec)   p_kst 2.494000e-01   p_cons 6.961000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000082/IDE.2_3160_10000_0.2494_0.6961_1.png
                gene_name: IDE
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.70 
      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.165.3896/
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/181708/iteration1/scatter.0000000082
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 82 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1119970: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000083> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:47:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000083.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000083.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 83  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    275.67 sec.
    Max Memory :      1119 MB
    Max Swap   :      3789 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.165.3896/
-whichjob
83
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 83: processing genes 7420 - 7509
Calculating significance of each gene.
Using projection method.
7420	IFI27L1	1
7421	IFI27L2	1
7422	IFI30	1
7423	IFI35	1
7424	IFI44	1
7425	IFI44L	1
7426	IFI6	1
7427	IFIH1	1.553989e-02
7428	IFIT1	1
7429	IFIT1B	1
7430	IFIT2	1
7431	IFIT3	9.797442e-02
7432	IFIT5	1
7433	IFITM1	1
7434	IFITM2	1
7435	IFITM3	1
7436	IFITM5	1.882336e-02
7437	IFLTD1	1
7438	IFNA1	1
7439	IFNA10	1
7440	IFNA13	1
7441	IFNA14	1
7442	IFNA16	1
7443	IFNA17	1
7444	IFNA2	1
7445	IFNA21	1
7446	IFNA4	3.267210e-02
7447	IFNA5	1
7448	IFNA6	1
7449	IFNA7	1
7450	IFNA8	1
7451	IFNAR1	1
7452	IFNAR2	1
7453	IFNB1	1
7454	IFNE	1
7455	IFNG	1
7456	IFNGR1	1
7457	IFNGR2	1.488807e-02
7458	IFNK	1
7459	IFNW1	1
7460	IFRD1	2.185214e-01
7461	IFRD2	1
7462	IFT122	3.955176e-01
7463	IFT140	2.926342e-01
7464	IFT172	1
7465	IFT20	1
7466	IFT27	1
7467	IFT46	1
7468	IFT52	1.799714e-01
7469	IFT57	1
7470	IFT74	1
7471	IFT80	2.212998e-01
7472	IFT81	1
7473	IFT88	2.618543e-01
7474	IGBP1	1
7475	IGDCC3	1
7476	IGDCC4	1
7477	IGF1	1
7478	IGF1R	1
7479	IGF2	1.220887e-01
7480	IGF2BP1	1
7481	IGF2BP2	1
7482	IGF2BP3	1
7483	IGF2R	1
7484	IGFALS	1
7485	IGFBP1	1
7486	IGFBP2	1
7487	IGFBP3	1
7488	IGFBP4	1
7489	IGFBP5	1
7490	IGFBP6	1
7491	IGFBP7	1
7492	IGFBPL1	1
7493	IGFL1	1
7494	IGFL2	1
7495	IGFL3	1
7496	IGFL4	1
7497	IGHMBP2	1
7498	IGJ	1
7499	IGLL1	1
7500	IGLL5	1
7501	IGLON5	1
7502	IGSF1	1
7503	IGSF10	3.681935e-01
7504	IGSF11	6.012952e-02
7505	IGSF21	1
7506	IGSF22	1
7507	IGSF3	1
7508	IGSF5	1
7509	IGSF6	1
Done

Running MutSig 2:
Scatter job 83: processing genes 7420 - 7509
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
IGSF10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.527287e-01	ci left: 5.706232e-02	ci right 6.659491e-02	k: 617	n:10000
Cons ci ratio: 1.126343e-02	ci left: 9.184254e-01	ci right 9.289262e-01	k: 9238	n:10000
KS ci ratio: 5.319759e-01	ci left: 3.972510e-03	ci right 6.926868e-03	k: 53	n:10000
IGSF10   10000 perm   4 sec   (2531 perm/sec)   p_kst 5.300000e-03   p_cons 9.238000e-01   p_joint 6.170000e-02

Joint ci ratio: 1.659200e-01	ci left: 2.489359e-02	ci right 2.944527e-02	k: 542	n:20000
Cons ci ratio: 7.456631e-03	ci left: 9.289858e-01	ci right 9.359878e-01	k: 18651	n:20000
KS ci ratio: 3.949987e-01	ci left: 3.934731e-03	ci right 5.913431e-03	k: 97	n:20000
IGSF10   20000 perm   10 sec   (1914 perm/sec)   p_kst 4.850000e-03   p_cons 9.325500e-01   p_joint 2.710000e-02

Joint ci ratio: 1.337539e-01	ci left: 2.596885e-02	ci right 2.972334e-02	k: 834	n:30000
Cons ci ratio: 6.107899e-03	ci left: 9.292285e-01	ci right 9.349542e-01	k: 27964	n:30000
KS ci ratio: 3.043262e-01	ci left: 4.663813e-03	ci right 6.367437e-03	k: 164	n:30000
IGSF10   30000 perm   14 sec   (2164 perm/sec)   p_kst 5.466667e-03   p_cons 9.321333e-01   p_joint 2.780000e-02

Joint ci ratio: 9.552247e-02	ci left: 3.846696e-02	ci right 4.235012e-02	k: 1615	n:40000
Cons ci ratio: 5.230965e-03	ci left: 9.310396e-01	ci right 9.359472e-01	k: 37341	n:40000
KS ci ratio: 2.724118e-01	ci left: 4.448864e-03	ci right 5.874430e-03	k: 205	n:40000
IGSF10   40000 perm   18 sec   (2269 perm/sec)   p_kst 5.125000e-03   p_cons 9.335250e-01   p_joint 4.037500e-02

Joint ci ratio: 9.349981e-02	ci left: 3.236994e-02	ci right 3.556446e-02	k: 1697	n:50000
Cons ci ratio: 4.671236e-03	ci left: 9.315042e-01	ci right 9.358853e-01	k: 46686	n:50000
KS ci ratio: 2.438912e-01	ci left: 4.513293e-03	ci right 5.785203e-03	k: 256	n:50000
IGSF10   50000 perm   21 sec   (2337 perm/sec)   p_kst 5.120000e-03   p_cons 9.337200e-01   p_joint 3.394000e-02

Joint ci ratio: 8.823150e-02	ci left: 3.044296e-02	ci right 3.326922e-02	k: 1910	n:60000
Cons ci ratio: 4.265420e-03	ci left: 9.316629e-01	ci right 9.356617e-01	k: 56021	n:60000
KS ci ratio: 2.250004e-01	ci left: 4.467073e-03	ci right 5.614940e-03	k: 301	n:60000
IGSF10   60000 perm   25 sec   (2368 perm/sec)   p_kst 5.016667e-03   p_cons 9.336833e-01   p_joint 3.183333e-02

Joint ci ratio: 8.137608e-02	ci left: 3.077850e-02	ci right 3.340333e-02	k: 2245	n:70000
Cons ci ratio: 3.953437e-03	ci left: 9.316725e-01	ci right 9.353772e-01	k: 65348	n:70000
KS ci ratio: 2.063570e-01	ci left: 4.599324e-03	ci right 5.670900e-03	k: 358	n:70000
IGSF10   70000 perm   30 sec   (2354 perm/sec)   p_kst 5.114286e-03   p_cons 9.335429e-01   p_joint 3.207143e-02

Joint ci ratio: 8.337672e-02	ci left: 2.576530e-02	ci right 2.801918e-02	k: 2150	n:80000
Cons ci ratio: 3.702692e-03	ci left: 9.316376e-01	ci right 9.351059e-01	k: 74671	n:80000
KS ci ratio: 1.907725e-01	ci left: 4.749083e-03	ci right 5.762305e-03	k: 419	n:80000
IGSF10   80000 perm   34 sec   (2363 perm/sec)   p_kst 5.237500e-03   p_cons 9.333875e-01   p_joint 2.687500e-02

Joint ci ratio: 6.372773e-02	ci left: 3.905727e-02	ci right 4.163913e-02	k: 3630	n:90000
Cons ci ratio: 3.486186e-03	ci left: 9.319088e-01	ci right 9.351743e-01	k: 84020	n:90000
KS ci ratio: 1.764229e-01	ci left: 4.974137e-03	ci right 5.947045e-03	k: 490	n:90000
IGSF10   90000 perm   38 sec   (2382 perm/sec)   p_kst 5.444444e-03   p_cons 9.335556e-01   p_joint 4.033333e-02

Joint ci ratio: 6.039855e-02	ci left: 3.919785e-02	ci right 4.164890e-02	k: 4041	n:100000
Cons ci ratio: 3.310878e-03	ci left: 9.318573e-01	ci right 9.349575e-01	k: 93342	n:100000
KS ci ratio: 1.669938e-01	ci left: 5.022250e-03	ci right 5.946789e-03	k: 547	n:100000
IGSF10   100000 perm   42 sec   (2394 perm/sec)   p_kst 5.470000e-03   p_cons 9.334200e-01   p_joint 4.041000e-02

Joint ci ratio: 6.025920e-02	ci left: 3.592802e-02	ci right 3.816920e-02	k: 4074	n:110000
Cons ci ratio: 3.156367e-03	ci left: 9.319473e-01	ci right 9.349025e-01	k: 102678	n:110000
KS ci ratio: 1.581445e-01	ci left: 5.115140e-03	ci right 6.002144e-03	k: 610	n:110000
IGSF10   110000 perm   46 sec   (2393 perm/sec)   p_kst 5.545455e-03   p_cons 9.334364e-01   p_joint 3.703636e-02

Joint ci ratio: 5.150899e-02	ci left: 4.485449e-02	ci right 4.723418e-02	k: 5524	n:120000
Cons ci ratio: 3.029341e-03	ci left: 9.317054e-01	ci right 9.345403e-01	k: 111976	n:120000
KS ci ratio: 1.514742e-01	ci left: 5.129465e-03	ci right 5.978033e-03	k: 665	n:120000
IGSF10   120000 perm   51 sec   (2354 perm/sec)   p_kst 5.541667e-03   p_cons 9.331333e-01   p_joint 4.603333e-02

Joint ci ratio: 4.665452e-02	ci left: 5.030474e-02	ci right 5.271532e-02	k: 6695	n:130000
Cons ci ratio: 2.910905e-03	ci left: 9.317438e-01	ci right 9.344676e-01	k: 121305	n:130000
KS ci ratio: 1.456841e-01	ci left: 5.134836e-03	ci right 5.948997e-03	k: 719	n:130000
IGSF10   130000 perm   55 sec   (2347 perm/sec)   p_kst 5.530769e-03   p_cons 9.331154e-01   p_joint 5.150000e-02

Joint ci ratio: 4.452002e-02	ci left: 5.130207e-02	ci right 5.364508e-02	k: 7345	n:140000
Cons ci ratio: 2.807762e-03	ci left: 9.316706e-01	ci right 9.342972e-01	k: 130619	n:140000
KS ci ratio: 1.404198e-01	ci left: 5.146863e-03	ci right 5.930973e-03	k: 774	n:140000
IGSF10   140000 perm   60 sec   (2347 perm/sec)   p_kst 5.528571e-03   p_cons 9.329929e-01   p_joint 5.246429e-02

Joint ci ratio: 4.382357e-02	ci left: 4.952917e-02	ci right 5.175491e-02	k: 7595	n:150000
Cons ci ratio: 2.706025e-03	ci left: 9.320189e-01	ci right 9.345510e-01	k: 139994	n:150000
KS ci ratio: 1.347925e-01	ci left: 5.228610e-03	ci right 5.990692e-03	k: 840	n:150000
IGSF10   150000 perm   64 sec   (2343 perm/sec)   p_kst 5.600000e-03   p_cons 9.332933e-01   p_joint 5.063333e-02

Joint ci ratio: 4.681854e-02	ci left: 4.099141e-02	ci right 4.296273e-02	k: 6715	n:160000
Cons ci ratio: 2.622580e-03	ci left: 9.319404e-01	ci right 9.343939e-01	k: 149308	n:160000
KS ci ratio: 1.319297e-01	ci left: 5.125338e-03	ci right 5.855257e-03	k: 877	n:160000
IGSF10   160000 perm   68 sec   (2336 perm/sec)   p_kst 5.481250e-03   p_cons 9.331750e-01   p_joint 4.196875e-02

Joint ci ratio: 4.569795e-02	ci left: 4.053935e-02	ci right 4.244103e-02	k: 7052	n:170000
Cons ci ratio: 2.544002e-03	ci left: 9.319909e-01	ci right 9.343707e-01	k: 158642	n:170000
KS ci ratio: 1.266245e-01	ci left: 5.250781e-03	ci right 5.966238e-03	k: 952	n:170000
IGSF10   170000 perm   73 sec   (2326 perm/sec)   p_kst 5.600000e-03   p_cons 9.331882e-01   p_joint 4.148235e-02

Joint ci ratio: 4.575962e-02	ci left: 3.827514e-02	ci right 4.007307e-02	k: 7050	n:180000
Cons ci ratio: 2.469553e-03	ci left: 9.321656e-01	ci right 9.344760e-01	k: 167999	n:180000
KS ci ratio: 1.240535e-01	ci left: 5.174313e-03	ci right 5.863982e-03	k: 992	n:180000
IGSF10   180000 perm   78 sec   (2314 perm/sec)   p_kst 5.511111e-03   p_cons 9.333278e-01   p_joint 3.916667e-02

Joint ci ratio: 5.720798e-02	ci left: 2.342544e-02	ci right 2.481019e-02	k: 4581	n:190000
Cons ci ratio: 2.401067e-03	ci left: 9.323333e-01	ci right 9.345798e-01	k: 177358	n:190000
KS ci ratio: 1.206966e-01	ci left: 5.187698e-03	ci right 5.859104e-03	k: 1048	n:190000
IGSF10   190000 perm   83 sec   (2303 perm/sec)   p_kst 5.515789e-03   p_cons 9.334632e-01   p_joint 2.411053e-02

Joint ci ratio: 5.663899e-02	ci left: 2.272710e-02	ci right 2.405676e-02	k: 4677	n:200000
Cons ci ratio: 2.340704e-03	ci left: 9.323388e-01	ci right 9.345286e-01	k: 186688	n:200000
KS ci ratio: 1.183000e-01	ci left: 5.136878e-03	ci right 5.787582e-03	k: 1091	n:200000
IGSF10   200000 perm   87 sec   (2291 perm/sec)   p_kst 5.455000e-03   p_cons 9.334400e-01   p_joint 2.338500e-02

Joint ci ratio: 5.825770e-02	ci left: 2.048956e-02	ci right 2.172371e-02	k: 4431	n:210000
Cons ci ratio: 2.282136e-03	ci left: 9.324836e-01	ci right 9.346187e-01	k: 196047	n:210000
KS ci ratio: 1.157845e-01	ci left: 5.114141e-03	ci right 5.747248e-03	k: 1139	n:210000
IGSF10   210000 perm   92 sec   (2278 perm/sec)   p_kst 5.423810e-03   p_cons 9.335571e-01   p_joint 2.110000e-02

Joint ci ratio: 5.693109e-02	ci left: 2.049453e-02	ci right 2.169995e-02	k: 4640	n:220000
Cons ci ratio: 2.227585e-03	ci left: 9.326249e-01	ci right 9.347092e-01	k: 205408	n:220000
KS ci ratio: 1.136155e-01	ci left: 5.075936e-03	ci right 5.691752e-03	k: 1183	n:220000
IGSF10   220000 perm   97 sec   (2260 perm/sec)   p_kst 5.377273e-03   p_cons 9.336727e-01   p_joint 2.109091e-02

Joint ci ratio: 5.563261e-02	ci left: 2.054225e-02	ci right 2.172203e-02	k: 4859	n:230000
Cons ci ratio: 2.178904e-03	ci left: 9.326317e-01	ci right 9.346704e-01	k: 214741	n:230000
KS ci ratio: 1.114726e-01	ci left: 5.049609e-03	ci right 5.649917e-03	k: 1229	n:230000
IGSF10   230000 perm   103 sec   (2238 perm/sec)   p_kst 5.343478e-03   p_cons 9.336565e-01   p_joint 2.112609e-02

Joint ci ratio: 5.765727e-02	ci left: 1.835073e-02	ci right 1.944427e-02	k: 4534	n:240000
Cons ci ratio: 2.132348e-03	ci left: 9.326931e-01	ci right 9.346881e-01	k: 224087	n:240000
KS ci ratio: 1.093605e-01	ci left: 5.033683e-03	ci right 5.620028e-03	k: 1277	n:240000
IGSF10   240000 perm   108 sec   (2219 perm/sec)   p_kst 5.320833e-03   p_cons 9.336958e-01   p_joint 1.889167e-02

Joint ci ratio: 5.643734e-02	ci left: 1.839741e-02	ci right 1.946978e-02	k: 4732	n:250000
Cons ci ratio: 2.093106e-03	ci left: 9.324841e-01	ci right 9.344419e-01	k: 233367	n:250000
KS ci ratio: 1.071206e-01	ci left: 5.042489e-03	ci right 5.617071e-03	k: 1331	n:250000
IGSF10   250000 perm   114 sec   (2195 perm/sec)   p_kst 5.324000e-03   p_cons 9.334680e-01   p_joint 1.892800e-02

Joint ci ratio: 5.087674e-02	ci left: 2.175483e-02	ci right 2.289431e-02	k: 5803	n:260000
Cons ci ratio: 2.051865e-03	ci left: 9.325394e-01	ci right 9.344586e-01	k: 242711	n:260000
KS ci ratio: 1.054730e-01	ci left: 5.005786e-03	ci right 5.566867e-03	k: 1373	n:260000
IGSF10   260000 perm   120 sec   (2169 perm/sec)   p_kst 5.280769e-03   p_cons 9.335038e-01   p_joint 2.231923e-02

Joint ci ratio: 5.321693e-02	ci left: 1.917547e-02	ci right 2.022746e-02	k: 5318	n:270000
Cons ci ratio: 2.011647e-03	ci left: 9.326730e-01	ci right 9.345547e-01	k: 252077	n:270000
KS ci ratio: 1.036785e-01	ci left: 4.993513e-03	ci right 5.543115e-03	k: 1421	n:270000
IGSF10   270000 perm   125 sec   (2153 perm/sec)   p_kst 5.262963e-03   p_cons 9.336185e-01   p_joint 1.969630e-02

Joint ci ratio: 4.814113e-02	ci left: 2.257497e-02	ci right 2.369207e-02	k: 6476	n:280000
Cons ci ratio: 1.975919e-03	ci left: 9.326571e-01	ci right 9.345053e-01	k: 261404	n:280000
KS ci ratio: 1.019378e-01	ci left: 4.985672e-03	ci right 5.524647e-03	k: 1470	n:280000
IGSF10   280000 perm   131 sec   (2132 perm/sec)   p_kst 5.250000e-03   p_cons 9.335857e-01   p_joint 2.312857e-02

Joint ci ratio: 4.800184e-02	ci left: 2.193944e-02	ci right 2.302186e-02	k: 6518	n:290000
Cons ci ratio: 1.940626e-03	ci left: 9.327329e-01	ci right 9.345481e-01	k: 270757	n:290000
KS ci ratio: 9.988626e-02	ci left: 5.018793e-03	ci right 5.549788e-03	k: 1531	n:290000
IGSF10   290000 perm   137 sec   (2118 perm/sec)   p_kst 5.279310e-03   p_cons 9.336448e-01   p_joint 2.247586e-02

Outputting figure to mutsig2_images.part000000000083/IGSF10.3_7944_290000_0.0052793_0.93364_0.022476.png
                gene_name: IGSF10
               theta_stop: 0.100 
                    nperm: 290000 
                     p_ks: 0.0053 
        ci_ks_bounds_left: 0.0050 
       ci_ks_bounds_right: 0.0055 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.022 
     ci_joint_bounds_left: 0.022 
    ci_joint_bounds_right: 0.023 

Current progress: 50 percent done.
IFIH1
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: 2.833421e-03	ci left: 9.932998e-01	ci right 9.962004e-01	k: 9949	n:10000
KS ci ratio: 2.175058e-02	ci left: 7.561585e-01	ci right 7.728871e-01	k: 7646	n:10000
IFIH1   10000 perm   2 sec   (4775 perm/sec)   p_kst 7.646000e-01   p_cons 9.949000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000083/IFIH1.2_3142_10000_0.7646_0.9949_1.png
                gene_name: IFIH1
               theta_stop: 0.022 
                    nperm: 10000 
                     p_ks: 0.76 
        ci_ks_bounds_left: 0.76 
       ci_ks_bounds_right: 0.77 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 1.00 
                  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.165.3896/
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/181708/iteration1/scatter.0000000083
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 83 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1542>
Subject: Job 1119975: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1542>, 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/181708/iteration1/scatter.0000000084> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:45:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000084.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000084.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 84  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    133.23 sec.
    Max Memory :      1289 MB
    Max Swap   :      3973 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.165.3896/
-whichjob
84
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 84: processing genes 7510 - 7599
Calculating significance of each gene.
Using projection method.
7510	IGSF8	1
7511	IGSF9	1
7512	IGSF9B	3.363684e-01
7513	IHH	1
7514	IK	1
7515	IKBIP	1
7516	IKBKAP	4.861130e-02
7517	IKBKB	1
7518	IKBKE	1
7519	IKZF1	1
7520	IKZF2	1.029853e-01
7521	IKZF3	1
7522	IKZF4	1
7523	IKZF5	1
7524	IL10	1
7525	IL10RA	1
7526	IL10RB	1.231047e-01
7527	IL11RA	1
7528	IL12A	1
7529	IL12B	1
7530	IL12RB1	1
7531	IL12RB2	1
7532	IL13	1
7533	IL13RA1	1
7534	IL13RA2	1
7535	IL15	1
7536	IL15RA	1
7537	IL16	3.148229e-01
7538	IL17A	1
7539	IL17B	1.477105e-02
7540	IL17C	1
7541	IL17D	1
7542	IL17F	1
7543	IL17RA	1
7544	IL17RB	1
7545	IL17RC	4.275380e-02
7546	IL17RD	1
7547	IL17RE	1
7548	IL17REL	1
7549	IL18	1
7550	IL18BP	1
7551	IL18R1	1
7552	IL18RAP	1.862394e-01
7553	IL19	1
7554	IL1A	1
7555	IL1B	1
7556	IL1F10	1
7557	IL1F5	1
7558	IL1F6	1
7559	IL1F7	1
7560	IL1F8	1
7561	IL1F9	1
7562	IL1R1	1
7563	IL1R2	1
7564	IL1RAP	1
7565	IL1RAPL1	7.078852e-02
7566	IL1RAPL2	2.127289e-01
7567	IL1RL1	2.533467e-01
7568	IL1RL2	1
7569	IL1RN	1
7570	IL2	1
7571	IL20	1
7572	IL20RA	1
7573	IL20RB	1
7574	IL21	1
7575	IL21R	7.560246e-02
7576	IL22	1
7577	IL22RA1	1
7578	IL22RA2	1
7579	IL23A	1
7580	IL23R	5.071621e-02
7581	IL24	1
7582	IL25	1
7583	IL26	5.816881e-02
7584	IL27	1
7585	IL27RA	1
7586	IL28A	1
7587	IL28B	1
7588	IL28RA	1
7589	IL29	1
7590	IL2RA	1
7591	IL2RB	1
7592	IL2RG	6.627453e-02
7593	IL3	1
7594	IL31	1
7595	IL31RA	1
7596	IL32	1
7597	IL33	1.149269e-02
7598	IL34	7.644046e-04
7599	IL3RA	1.184265e-01
Done

Running MutSig 2:
Scatter job 84: processing genes 7510 - 7599
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
IKBKAP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.286084e-01	ci left: 7.950840e-02	ci right 9.053475e-02	k: 849	n:10000
Cons ci ratio: 1.307207e-01	ci left: 7.708281e-02	ci right 8.796184e-02	k: 824	n:10000
KS ci ratio: 9.251487e-02	ci left: 1.451135e-01	ci right 1.592898e-01	k: 1521	n:10000
IKBKAP   10000 perm   2 sec   (4657 perm/sec)   p_kst 1.521000e-01   p_cons 8.240000e-02   p_joint 8.490000e-02

Joint ci ratio: 3.294403e-02	ci left: 4.076105e-01	ci right 4.213144e-01	k: 8289	n:20000
Cons ci ratio: 9.204076e-02	ci left: 7.931024e-02	ci right 8.701145e-02	k: 1662	n:20000
KS ci ratio: 6.543162e-02	ci left: 1.471488e-01	ci right 1.571526e-01	k: 3042	n:20000
IKBKAP   20000 perm   8 sec   (2642 perm/sec)   p_kst 1.521000e-01   p_cons 8.310000e-02   p_joint 4.144500e-01

Outputting figure to mutsig2_images.part000000000084/IKBKAP.2_4143_20000_0.1521_0.0831_0.41445.png
                gene_name: IKBKAP
               theta_stop: 0.092 
                    nperm: 20000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.083 
      ci_cons_bounds_left: 0.079 
     ci_cons_bounds_right: 0.087 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.42 

Current progress: 25 percent done.
IL17RC
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: 5.153763e-03	ci left: 9.803783e-01	ci right 9.855349e-01	k: 9831	n:10000
KS ci ratio: 3.169081e-02	ci left: 5.950381e-01	ci right 6.143009e-01	k: 6047	n:10000
IL17RC   10000 perm   2 sec   (5666 perm/sec)   p_kst 6.047000e-01   p_cons 9.831000e-01   p_joint 9.361000e-01

Outputting figure to mutsig2_images.part000000000084/IL17RC.2_2452_10000_0.6047_0.9831_0.9361.png
                gene_name: IL17RC
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.94 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 50 percent done.
IL18RAP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.519441e-01	ci left: 5.764078e-02	ci right 6.721608e-02	k: 623	n:10000
Cons ci ratio: 1.235896e-01	ci left: 8.572423e-02	ci right 9.711508e-02	k: 913	n:10000
KS ci ratio: 1.236641e-01	ci left: 8.562704e-02	ci right 9.701233e-02	k: 912	n:10000
IL18RAP   10000 perm   2 sec   (6291 perm/sec)   p_kst 9.120000e-02   p_cons 9.130000e-02   p_joint 6.230000e-02

Joint ci ratio: 6.715852e-02	ci left: 1.406400e-01	ci right 1.504633e-01	k: 2910	n:20000
Cons ci ratio: 8.361947e-02	ci left: 9.484527e-02	ci right 1.031717e-01	k: 1979	n:20000
KS ci ratio: 8.707860e-02	ci left: 8.797988e-02	ci right 9.603919e-02	k: 1839	n:20000
IL18RAP   20000 perm   4 sec   (5500 perm/sec)   p_kst 9.195000e-02   p_cons 9.895000e-02   p_joint 1.455000e-01

Outputting figure to mutsig2_images.part000000000084/IL18RAP.2_1840_20000_0.09195_0.09895_0.1455.png
                gene_name: IL18RAP
               theta_stop: 0.087 
                    nperm: 20000 
                     p_ks: 0.092 
        ci_ks_bounds_left: 0.088 
       ci_ks_bounds_right: 0.096 
                   p_cons: 0.099 
      ci_cons_bounds_left: 0.095 
     ci_cons_bounds_right: 0.10 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.14 
    ci_joint_bounds_right: 0.15 

Current progress: 75 percent done.
IL34
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.814273e-02	ci left: 3.033218e-01	ci right 3.215876e-01	k: 3124	n:10000
Cons ci ratio: 3.070229e-03	ci left: 9.922835e-01	ci right 9.954183e-01	k: 9940	n:10000
KS ci ratio: 8.754621e-02	ci left: 1.596393e-01	ci right 1.743552e-01	k: 1669	n:10000
IL34   10000 perm   1 sec   (6729 perm/sec)   p_kst 1.669000e-01   p_cons 9.940000e-01   p_joint 3.124000e-01

Outputting figure to mutsig2_images.part000000000084/IL34.2_753_10000_0.1669_0.994_0.3124.png
                gene_name: IL34
               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: 1.00 
                  p_joint: 0.31 
     ci_joint_bounds_left: 0.30 
    ci_joint_bounds_right: 0.32 

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.165.3896/
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/181708/iteration1/scatter.0000000084
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 84 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1551>
Subject: Job 1119978: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1551>, 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/181708/iteration1/scatter.0000000085> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:46:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000085.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000085.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 85  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    163.98 sec.
    Max Memory :      1381 MB
    Max Swap   :      3824 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.165.3896/
-whichjob
85
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 85: processing genes 7600 - 7690
Calculating significance of each gene.
Using projection method.
7600	IL4	1
7601	IL4I1	1
7602	IL4R	1
7603	IL5	1
7604	IL5RA	1
7605	IL6	1
7606	IL6R	1
7607	IL6ST	2.736183e-01
7608	IL7	1
7609	IL7R	1
7610	IL8	5.126837e-02
7611	IL9	1
7612	IL9R	1
7613	ILDR1	2.194224e-01
7614	ILDR2	1
7615	ILF2	1
7616	ILF3	1
7617	ILK	1
7618	ILKAP	1
7619	ILVBL	1
7620	IMMP1L	1
7621	IMMP2L	1
7622	IMMT	1
7623	IMP3	1
7624	IMP4	3.118429e-02
7625	IMP5	1
7626	IMPA1	1
7627	IMPA2	6.918365e-02
7628	IMPACT	1
7629	IMPAD1	3.322548e-02
7630	IMPDH1	1
7631	IMPDH2	1
7632	IMPG1	1.811828e-01
7633	IMPG2	7.003604e-02
7634	INA	1
7635	INADL	1
7636	INCA1	1
7637	INCENP	1
7638	INF2	4.868850e-02
7639	ING1	1
7640	ING2	1
7641	ING3	1.148471e-01
7642	ING4	1
7643	ING5	1
7644	INHA	1
7645	INHBA	1
7646	INHBB	1
7647	INHBC	1
7648	INHBE	1
7649	INMT	1
7650	INO80	9.748841e-02
7651	INO80B	1
7652	INO80C	1
7653	INO80D	3.930662e-02
7654	INO80E	1
7655	INPP1	1.296814e-01
7656	INPP4A	1
7657	INPP4B	9.790808e-02
7658	INPP5A	3.534308e-02
7659	INPP5B	1
7660	INPP5D	1
7661	INPP5E	1
7662	INPP5F	4.703338e-02
7663	INPP5J	1
7664	INPP5K	1
7665	INPPL1	2.424500e-01
7666	INS	1
7667	INS-IGF2	1
7668	INSC	1
7669	INSIG1	1
7670	INSIG2	1
7671	INSL3	1
7672	INSL4	4.155017e-02
7673	INSL5	1
7674	INSL6	1
7675	INSM1	1
7676	INSM2	1.514840e-01
7677	INSR	1.661311e-01
7678	INSRR	2.805345e-01
7679	INTS1	7.600613e-02
7680	INTS10	2.400110e-01
7681	INTS12	1.866054e-01
7682	INTS2	1
7683	INTS3	2.070177e-01
7684	INTS4	1
7685	INTS5	1
7686	INTS6	1
7687	INTS7	1
7688	INTS8	1
7689	INTS9	1.934561e-02
7690	INTU	1.646696e-01
Done

Running MutSig 2:
Scatter job 85: processing genes 7600 - 7690
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
IMPG2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.377574e-02	ci left: 2.653742e-01	ci right 2.829575e-01	k: 2741	n:10000
Cons ci ratio: 8.304689e-02	ci left: 1.745794e-01	ci right 1.898062e-01	k: 1821	n:10000
KS ci ratio: 1.926953e-02	ci left: 7.975022e-01	ci right 8.131196e-01	k: 8054	n:10000
IMPG2   10000 perm   2 sec   (4496 perm/sec)   p_kst 8.054000e-01   p_cons 1.821000e-01   p_joint 2.741000e-01

Outputting figure to mutsig2_images.part000000000085/IMPG2.2_3802_10000_0.8054_0.1821_0.2741.png
                gene_name: IMPG2
               theta_stop: 0.083 
                    nperm: 10000 
                     p_ks: 0.81 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.27 
     ci_joint_bounds_left: 0.27 
    ci_joint_bounds_right: 0.28 

Current progress: 12 percent done.
INF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.306014e-02	ci left: 7.342143e-01	ci right 7.514440e-01	k: 7429	n:10000
Cons ci ratio: 4.561562e-02	ci left: 4.149851e-01	ci right 4.344588e-01	k: 4247	n:10000
KS ci ratio: 8.407617e-03	ci left: 9.518996e-01	ci right 9.600321e-01	k: 9561	n:10000
INF2   10000 perm   2 sec   (4193 perm/sec)   p_kst 9.561000e-01   p_cons 4.247000e-01   p_joint 7.429000e-01

Outputting figure to mutsig2_images.part000000000085/INF2.2_3871_10000_0.9561_0.4247_0.7429.png
                gene_name: INF2
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.96 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.96 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.74 
     ci_joint_bounds_left: 0.73 
    ci_joint_bounds_right: 0.75 

Current progress: 25 percent done.
INO80
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: 1.769821e-02	ci left: 8.232038e-01	ci right 8.380031e-01	k: 8307	n:10000
KS ci ratio: 6.250251e-02	ci left: 2.733932e-01	ci right 2.911338e-01	k: 2822	n:10000
INO80   10000 perm   2 sec   (4281 perm/sec)   p_kst 2.822000e-01   p_cons 8.307000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000085/INO80.2_4811_10000_0.2822_0.8307_1.png
                gene_name: INO80
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.83 
      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: 38 percent done.
INO80D
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: 2.905383e-02	ci left: 6.359324e-01	ci right 6.547828e-01	k: 6454	n:10000
KS ci ratio: 5.239198e-02	ci left: 3.493913e-01	ci right 3.682910e-01	k: 3588	n:10000
INO80D   10000 perm   2 sec   (5376 perm/sec)   p_kst 3.588000e-01   p_cons 6.454000e-01   p_joint 8.598000e-01

Outputting figure to mutsig2_images.part000000000085/INO80D.2_3120_10000_0.3588_0.6454_0.8598.png
                gene_name: INO80D
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.87 

Current progress: 50 percent done.
INPP5F
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.953258e-02	ci left: 4.858530e-01	ci right 5.055495e-01	k: 4957	n:10000
Cons ci ratio: 7.959375e-02	ci left: 1.873727e-01	ci right 2.030052e-01	k: 1951	n:10000
KS ci ratio: 9.079719e-02	ci left: 1.499203e-01	ci right 1.642801e-01	k: 1570	n:10000
INPP5F   10000 perm   2 sec   (4991 perm/sec)   p_kst 1.570000e-01   p_cons 1.951000e-01   p_joint 4.957000e-01

Outputting figure to mutsig2_images.part000000000085/INPP5F.2_3479_10000_0.157_0.1951_0.4957.png
                gene_name: INPP5F
               theta_stop: 0.091 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    ci_joint_bounds_right: 0.51 

Current progress: 62 percent done.
INSR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.573964e-02	ci left: 8.542685e-01	ci right 8.679204e-01	k: 8612	n:10000
Cons ci ratio: 6.907414e-02	ci left: 2.351136e-01	ci right 2.520360e-01	k: 2435	n:10000
KS ci ratio: 5.917331e-02	ci left: 2.958849e-01	ci right 3.140289e-01	k: 3049	n:10000
INSR   10000 perm   2 sec   (4914 perm/sec)   p_kst 3.049000e-01   p_cons 2.435000e-01   p_joint 8.612000e-01

Outputting figure to mutsig2_images.part000000000085/INSR.2_4237_10000_0.3049_0.2435_0.8612.png
                gene_name: INSR
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.87 

Current progress: 75 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: 2.299980e-02	ci left: 7.352249e-01	ci right 7.524328e-01	k: 7439	n:10000
KS ci ratio: 2.075816e-02	ci left: 7.727630e-01	ci right 7.890731e-01	k: 7810	n:10000
INTS1   10000 perm   2 sec   (4014 perm/sec)   p_kst 7.810000e-01   p_cons 7.439000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000085/INTS1.2_6761_10000_0.781_0.7439_1.png
                gene_name: INTS1
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.79 
                   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: 88 percent done.
INTS9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.172899e-02	ci left: 4.588797e-01	ci right 4.785385e-01	k: 4687	n:10000
Cons ci ratio: 7.979698e-02	ci left: 1.865851e-01	ci right 2.021934e-01	k: 1943	n:10000
KS ci ratio: 4.838285e-02	ci left: 3.865951e-01	ci right 4.058654e-01	k: 3962	n:10000
INTS9   10000 perm   2 sec   (5703 perm/sec)   p_kst 3.962000e-01   p_cons 1.943000e-01   p_joint 4.687000e-01

Outputting figure to mutsig2_images.part000000000085/INTS9.2_2045_10000_0.3962_0.1943_0.4687.png
                gene_name: INTS9
               theta_stop: 0.080 
                    nperm: 10000 
                     p_ks: 0.40 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.41 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    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.165.3896/
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/181708/iteration1/scatter.0000000085
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 85 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1642>
Subject: Job 1119981: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, 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/181708/iteration1/scatter.0000000086> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:44:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000086.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000086.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 86  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    112.48 sec.
    Max Memory :       896 MB
    Max Swap   :      3781 MB

    Max Processes  :         7
    Max Threads    :        91

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/
-whichjob
86
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 86: processing genes 7691 - 7780
Calculating significance of each gene.
Using projection method.
7691	INVS	1
7692	IP6K1	1
7693	IP6K2	1
7694	IP6K3	1
7695	IPCEF1	1
7696	IPMK	1
7697	IPO11	1
7698	IPO13	3.843676e-01
7699	IPO4	1
7700	IPO5	1
7701	IPO7	3.837485e-01
7702	IPO8	3.876113e-02
7703	IPO9	1
7704	IPP	1
7705	IPPK	1.115535e-01
7706	IQCA1	1
7707	IQCB1	1
7708	IQCC	5.449277e-02
7709	IQCD	9.839150e-02
7710	IQCE	1.560010e-01
7711	IQCF1	1
7712	IQCF2	1
7713	IQCF3	1
7714	IQCG	1.601323e-01
7715	IQCH	1
7716	IQCJ	1
7717	IQCK	1
7718	IQGAP1	1
7719	IQGAP2	1
7720	IQGAP3	1.392590e-01
7721	IQSEC1	2.077607e-01
7722	IQSEC2	1
7723	IQSEC3	1
7724	IQUB	1
7725	IRAK1	1
7726	IRAK1BP1	1
7727	IRAK2	1
7728	IRAK3	1
7729	IRAK4	1.175128e-01
7730	IREB2	2.588419e-01
7731	IRF1	1
7732	IRF2	1
7733	IRF2BP1	1
7734	IRF2BP2	1
7735	IRF3	1
7736	IRF4	1
7737	IRF5	1
7738	IRF6	1
7739	IRF7	7.909728e-02
7740	IRF8	1
7741	IRF9	4.989579e-02
7742	IRGC	1
7743	IRGQ	1
7744	IRS1	2.072598e-01
7745	IRS2	1
7746	IRS4	1
7747	IRX1	6.679843e-02
7748	IRX2	1
7749	IRX3	1
7750	IRX4	9.733331e-03
7751	IRX5	1
7752	IRX6	1
7753	ISCA1	1
7754	ISCA1P1	1
7755	ISCA2	1
7756	ISCU	1.890972e-02
7757	ISG15	1
7758	ISG20	1
7759	ISG20L2	1
7760	ISL1	1
7761	ISL2	1
7762	ISLR	1
7763	ISLR2	1
7764	ISM1	1.228791e-01
7765	ISM2	1.696601e-01
7766	ISOC1	1
7767	ISOC2	1
7768	ISPD	1
7769	ISX	1
7770	ISY1	1
7771	ISYNA1	1
7772	ITCH	1
7773	ITFG1	1.208507e-01
7774	ITFG2	1
7775	ITFG3	1.451525e-01
7776	ITGA1	1
7777	ITGA10	1
7778	ITGA11	4.008845e-02
7779	ITGA2	1
7780	ITGA2B	1
Done

Running MutSig 2:
Scatter job 86: processing genes 7691 - 7780
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
IPO8
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: 5.214247e-02	ci left: 3.515781e-01	ci right 3.705029e-01	k: 3610	n:10000
KS ci ratio: 2.892703e-02	ci left: 6.379438e-01	ci right 6.567703e-01	k: 6474	n:10000
IPO8   10000 perm   2 sec   (5391 perm/sec)   p_kst 6.474000e-01   p_cons 3.610000e-01   p_joint 7.100000e-01

Outputting figure to mutsig2_images.part000000000086/IPO8.2_3214_10000_0.6474_0.361_0.71.png
                gene_name: IPO8
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.71 
     ci_joint_bounds_left: 0.70 
    ci_joint_bounds_right: 0.72 

Current progress: 33 percent done.
IQGAP3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.872833e-02	ci left: 3.832104e-01	ci right 4.024520e-01	k: 3928	n:10000
Cons ci ratio: 4.150350e-02	ci left: 4.615758e-01	ci right 4.812409e-01	k: 4714	n:10000
KS ci ratio: 5.420475e-02	ci left: 3.339906e-01	ci right 3.527007e-01	k: 3433	n:10000
IQGAP3   10000 perm   2 sec   (4949 perm/sec)   p_kst 3.433000e-01   p_cons 4.714000e-01   p_joint 3.928000e-01

Outputting figure to mutsig2_images.part000000000086/IQGAP3.2_5048_10000_0.3433_0.4714_0.3928.png
                gene_name: IQGAP3
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.34 
        ci_ks_bounds_left: 0.33 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.48 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 67 percent done.
ITGA11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.837967e-02	ci left: 5.006505e-01	ci right 5.203434e-01	k: 5105	n:10000
Cons ci ratio: 1.081572e-01	ci left: 1.097862e-01	ci right 1.224384e-01	k: 1160	n:10000
KS ci ratio: 3.485564e-02	ci left: 5.486014e-01	ci right 5.681645e-01	k: 5584	n:10000
ITGA11   10000 perm   2 sec   (5059 perm/sec)   p_kst 5.584000e-01   p_cons 1.160000e-01   p_joint 5.105000e-01

Joint ci ratio: 3.592636e-02	ci left: 3.663912e-01	ci right 3.798457e-01	k: 7462	n:20000
Cons ci ratio: 7.670452e-02	ci left: 1.110523e-01	ci right 1.199599e-01	k: 2309	n:20000
KS ci ratio: 2.468822e-02	ci left: 5.506837e-01	ci right 5.644996e-01	k: 11152	n:20000
ITGA11   20000 perm   4 sec   (4502 perm/sec)   p_kst 5.576000e-01   p_cons 1.154500e-01   p_joint 3.731000e-01

Outputting figure to mutsig2_images.part000000000086/ITGA11.2_3687_20000_0.5576_0.11545_0.3731.png
                gene_name: ITGA11
               theta_stop: 0.077 
                    nperm: 20000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.37 
    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.165.3896/
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/181708/iteration1/scatter.0000000086
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 86 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1701>
Subject: Job 1120011: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1701>, 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/181708/iteration1/scatter.0000000087> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:45:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000087.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000087.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 87  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    127.60 sec.
    Max Memory :      1165 MB
    Max Swap   :      3817 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.165.3896/
-whichjob
87
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 87: processing genes 7781 - 7871
Calculating significance of each gene.
Using projection method.
7781	ITGA3	1
7782	ITGA4	3.439445e-02
7783	ITGA5	1
7784	ITGA6	1
7785	ITGA7	1.674708e-01
7786	ITGA8	2.894641e-02
7787	ITGA9	4.584729e-02
7788	ITGAD	3.539670e-01
7789	ITGAE	1
7790	ITGAL	1
7791	ITGAM	1
7792	ITGAV	1
7793	ITGAX	1
7794	ITGB1	1
7795	ITGB1BP1	1
7796	ITGB1BP2	1
7797	ITGB1BP3	1
7798	ITGB2	1
7799	ITGB3	3.467004e-01
7800	ITGB3BP	1
7801	ITGB4	1
7802	ITGB5	1
7803	ITGB6	1
7804	ITGB7	1
7805	ITGB8	2.715367e-01
7806	ITGBL1	1
7807	ITIH1	1
7808	ITIH2	3.296057e-01
7809	ITIH3	2.079768e-01
7810	ITIH4	1
7811	ITIH5	3.082935e-01
7812	ITIH5L	1
7813	ITK	1
7814	ITLN1	1
7815	ITLN2	9.104316e-02
7816	ITM2A	1
7817	ITM2B	1
7818	ITM2C	1
7819	ITPA	1
7820	ITPK1	1
7821	ITPKA	1
7822	ITPKB	1
7823	ITPKC	1
7824	ITPR1	1
7825	ITPR2	6.663247e-01
7826	ITPR3	7.757571e-01
7827	ITPRIP	1
7828	ITPRIPL1	1.697796e-01
7829	ITPRIPL2	2.053033e-01
7830	ITSN1	1.052472e-01
7831	ITSN2	1
7832	IVD	1
7833	IVL	1
7834	IVNS1ABP	1
7835	IWS1	3.458264e-01
7836	IYD	4.791792e-02
7837	IZUMO1	1
7838	JAG1	3.237631e-01
7839	JAG2	1
7840	JAGN1	1
7841	JAK1	1.629006e-01
7842	JAK2	3.604837e-01
7843	JAK3	1
7844	JAKMIP1	1
7845	JAKMIP2	1
7846	JAKMIP3	1
7847	JAM2	6.861589e-02
7848	JAM3	1
7849	JARID2	1
7850	JAZF1	1
7851	JDP2	1
7852	JHDM1D	1
7853	JKAMP	1
7854	JMJD1C	1
7855	JMJD4	1
7856	JMJD5	1
7857	JMJD6	1
7858	JMJD7	1
7859	JMJD7-PLA2G4B	2.769543e-01
7860	JMJD8	1
7861	JMY	1
7862	JOSD1	1
7863	JOSD2	1
7864	JPH1	1
7865	JPH2	1
7866	JPH3	1
7867	JPH4	1
7868	JRK	1
7869	JRKL	1
7870	JSRP1	8.656768e-02
7871	JTB	1
Done

Running MutSig 2:
Scatter job 87: processing genes 7781 - 7871
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ITGA4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.437322e-02	ci left: 2.092502e-01	ci right 2.255148e-01	k: 2173	n:10000
Cons ci ratio: 5.881241e-02	ci left: 2.984627e-01	ci right 3.166495e-01	k: 3075	n:10000
KS ci ratio: 9.371625e-02	ci left: 1.418777e-01	ci right 1.559275e-01	k: 1488	n:10000
ITGA4   10000 perm   2 sec   (5259 perm/sec)   p_kst 1.488000e-01   p_cons 3.075000e-01   p_joint 2.173000e-01

Outputting figure to mutsig2_images.part000000000087/ITGA4.3_3211_10000_0.1488_0.3075_0.2173.png
                gene_name: ITGA4
               theta_stop: 0.094 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.23 

Current progress: 25 percent done.
ITGA8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.896187e-02	ci left: 2.357064e-01	ci right 2.526429e-01	k: 2441	n:10000
Cons ci ratio: 5.215104e-03	ci left: 9.799492e-01	ci right 9.851642e-01	k: 9827	n:10000
KS ci ratio: 1.855993e-01	ci left: 3.872553e-02	ci right 4.674361e-02	k: 426	n:10000
ITGA8   10000 perm   2 sec   (5478 perm/sec)   p_kst 4.260000e-02   p_cons 9.827000e-01   p_joint 2.441000e-01

Joint ci ratio: 1.188358e-02	ci left: 8.396560e-01	ci right 8.497436e-01	k: 16895	n:20000
Cons ci ratio: 3.939051e-03	ci left: 9.782253e-01	ci right 9.821333e-01	k: 19605	n:20000
KS ci ratio: 1.302882e-01	ci left: 4.047238e-02	ci right 4.616135e-02	k: 865	n:20000
ITGA8   20000 perm   4 sec   (4765 perm/sec)   p_kst 4.325000e-02   p_cons 9.802500e-01   p_joint 8.447500e-01

Joint ci ratio: 6.001057e-03	ci left: 9.314714e-01	ci right 9.371108e-01	k: 28030	n:30000
Cons ci ratio: 3.216357e-03	ci left: 9.785942e-01	ci right 9.817785e-01	k: 29407	n:30000
KS ci ratio: 1.063807e-01	ci left: 4.099204e-02	ci right 4.563026e-02	k: 1298	n:30000
ITGA8   30000 perm   6 sec   (4618 perm/sec)   p_kst 4.326667e-02   p_cons 9.802333e-01   p_joint 9.343333e-01

Joint ci ratio: 5.211980e-03	ci left: 9.314973e-01	ci right 9.363895e-01	k: 37359	n:40000
Cons ci ratio: 2.743956e-03	ci left: 9.794073e-01	ci right 9.821223e-01	k: 39232	n:40000
KS ci ratio: 9.320256e-02	ci left: 4.037279e-02	ci right 4.434399e-02	k: 1693	n:40000
ITGA8   40000 perm   9 sec   (4519 perm/sec)   p_kst 4.232500e-02   p_cons 9.808000e-01   p_joint 9.339750e-01

Outputting figure to mutsig2_images.part000000000087/ITGA8.2_3312_40000_0.042325_0.9808_0.93397.png
                gene_name: ITGA8
               theta_stop: 0.093 
                    nperm: 40000 
                     p_ks: 0.042 
        ci_ks_bounds_left: 0.040 
       ci_ks_bounds_right: 0.044 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 50 percent done.
ITGA9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.211914e-02	ci left: 2.758690e-01	ci right 2.936566e-01	k: 2847	n:10000
Cons ci ratio: 7.448267e-02	ci left: 2.087570e-01	ci right 2.250082e-01	k: 2168	n:10000
KS ci ratio: 3.725154e-02	ci left: 5.155566e-01	ci right 5.352286e-01	k: 5254	n:10000
ITGA9   10000 perm   2 sec   (5545 perm/sec)   p_kst 5.254000e-01   p_cons 2.168000e-01   p_joint 2.847000e-01

Outputting figure to mutsig2_images.part000000000087/ITGA9.2_3220_10000_0.5254_0.2168_0.2847.png
                gene_name: ITGA9
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.28 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.29 

Current progress: 75 percent done.
ITSN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.438252e-02	ci left: 8.749018e-01	ci right 8.876752e-01	k: 8814	n:10000
Cons ci ratio: 7.762261e-02	ci left: 1.952523e-01	ci right 2.111210e-01	k: 2031	n:10000
KS ci ratio: 1.842321e-02	ci left: 8.114128e-01	ci right 8.266008e-01	k: 8191	n:10000
ITSN1   10000 perm   2 sec   (4878 perm/sec)   p_kst 8.191000e-01   p_cons 2.031000e-01   p_joint 8.814000e-01

Outputting figure to mutsig2_images.part000000000087/ITSN1.2_5328_10000_0.8191_0.2031_0.8814.png
                gene_name: ITSN1
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.88 
     ci_joint_bounds_left: 0.87 
    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.165.3896/
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/181708/iteration1/scatter.0000000087
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 87 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1702>
Subject: Job 1120014: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1702>, 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/181708/iteration1/scatter.0000000088> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:46:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000088.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000088.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 88  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    171.70 sec.
    Max Memory :      1279 MB
    Max Swap   :      3938 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.165.3896/
-whichjob
88
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 88: processing genes 7872 - 7961
Calculating significance of each gene.
Using projection method.
7872	JUB	1
7873	JUN	1
7874	JUNB	1
7875	JUND	1
7876	JUP	1
7877	KAAG1	1
7878	KAL1	2.126004e-01
7879	KALRN	7.501606e-01
7880	KANK1	1
7881	KANK2	1
7882	KANK3	3.575497e-02
7883	KANK4	1
7884	KARS	1
7885	KAT2A	5.869563e-02
7886	KAT2B	3.438988e-01
7887	KAT5	1
7888	KATNA1	1.240223e-01
7889	KATNAL1	1
7890	KATNAL2	2.177174e-01
7891	KATNB1	1
7892	KAZ	1
7893	KAZALD1	1
7894	KBTBD10	2.453953e-01
7895	KBTBD12	1
7896	KBTBD2	1
7897	KBTBD3	1
7898	KBTBD4	1
7899	KBTBD5	2.772317e-01
7900	KBTBD6	3.991720e-02
7901	KBTBD7	1
7902	KBTBD8	1
7903	KCMF1	1
7904	KCNA1	1
7905	KCNA10	1.986970e-01
7906	KCNA2	1.488692e-01
7907	KCNA3	1
7908	KCNA4	1
7909	KCNA5	1
7910	KCNA6	1
7911	KCNA7	1
7912	KCNAB1	1.015078e-01
7913	KCNAB2	1
7914	KCNAB3	1
7915	KCNB1	1
7916	KCNB2	1
7917	KCNC1	1
7918	KCNC2	2.447605e-01
7919	KCNC3	1
7920	KCNC4	1
7921	KCND1	1
7922	KCND2	1
7923	KCND3	1.949007e-01
7924	KCNE1	1
7925	KCNE1L	1
7926	KCNE2	1
7927	KCNE3	1
7928	KCNE4	1
7929	KCNF1	1.137693e-01
7930	KCNG1	1.105383e-01
7931	KCNG2	1
7932	KCNG3	1
7933	KCNG4	1
7934	KCNH1	1
7935	KCNH2	1
7936	KCNH3	1
7937	KCNH4	1.895868e-01
7938	KCNH5	1
7939	KCNH6	2.734224e-01
7940	KCNH7	2.931496e-02
7941	KCNH8	3.768457e-02
7942	KCNIP1	1
7943	KCNIP2	1
7944	KCNIP3	1
7945	KCNIP4	1
7946	KCNJ1	1
7947	KCNJ10	1
7948	KCNJ11	1
7949	KCNJ12	1
7950	KCNJ13	7.923656e-02
7951	KCNJ14	1.419907e-01
7952	KCNJ15	9.594868e-02
7953	KCNJ16	1.170917e-02
7954	KCNJ2	1
7955	KCNJ3	1
7956	KCNJ4	1
7957	KCNJ5	1
7958	KCNJ6	1.328958e-01
7959	KCNJ8	1
7960	KCNJ9	1
7961	KCNK1	1
Done

Running MutSig 2:
Scatter job 88: processing genes 7872 - 7961
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KBTBD6
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: 2.313764e-01	ci left: 2.466595e-02	ci right 3.121293e-02	k: 278	n:10000
KS ci ratio: 2.655618e-02	ci left: 6.761958e-01	ci right 6.944962e-01	k: 6854	n:10000
KBTBD6   10000 perm   2 sec   (5479 perm/sec)   p_kst 6.854000e-01   p_cons 2.780000e-02   p_joint 2.026000e-01

Joint ci ratio: 5.868446e-02	ci left: 1.770200e-01	ci right 1.877725e-01	k: 3647	n:20000
Cons ci ratio: 1.630116e-01	ci left: 2.580547e-02	ci right 3.043309e-02	k: 561	n:20000
KS ci ratio: 1.882003e-02	ci left: 6.779578e-01	ci right 6.908886e-01	k: 13689	n:20000
KBTBD6   20000 perm   6 sec   (3208 perm/sec)   p_kst 6.844500e-01   p_cons 2.805000e-02   p_joint 1.823500e-01

Joint ci ratio: 4.175976e-02	ci left: 2.222698e-01	ci right 2.317831e-01	k: 6810	n:30000
Cons ci ratio: 1.308024e-01	ci left: 2.716245e-02	ci right 3.099614e-02	k: 871	n:30000
KS ci ratio: 1.550377e-02	ci left: 6.752901e-01	ci right 6.858749e-01	k: 20418	n:30000
KBTBD6   30000 perm   9 sec   (3501 perm/sec)   p_kst 6.806000e-01   p_cons 2.903333e-02   p_joint 2.270000e-01

Joint ci ratio: 4.139933e-02	ci left: 1.792957e-01	ci right 1.869003e-01	k: 7323	n:40000
Cons ci ratio: 1.135640e-01	ci left: 2.728005e-02	ci right 3.058881e-02	k: 1156	n:40000
KS ci ratio: 1.344681e-02	ci left: 6.753530e-01	ci right 6.845209e-01	k: 27198	n:40000
KBTBD6   40000 perm   11 sec   (3700 perm/sec)   p_kst 6.799500e-01   p_cons 2.890000e-02   p_joint 1.830750e-01

Joint ci ratio: 3.175343e-02	ci left: 2.298769e-01	ci right 2.373140e-01	k: 11679	n:50000
Cons ci ratio: 1.028732e-01	ci left: 2.676641e-02	ci right 2.968870e-02	k: 1410	n:50000
KS ci ratio: 1.202806e-02	ci left: 6.758106e-01	ci right 6.840085e-01	k: 33996	n:50000
KBTBD6   50000 perm   13 sec   (3804 perm/sec)   p_kst 6.799200e-01   p_cons 2.820000e-02   p_joint 2.335800e-01

Joint ci ratio: 3.310536e-02	ci left: 1.862715e-01	ci right 1.925585e-01	k: 11364	n:60000
Cons ci ratio: 9.394441e-02	ci left: 2.687364e-02	ci right 2.953893e-02	k: 1691	n:60000
KS ci ratio: 1.097723e-02	ci left: 6.762839e-01	ci right 6.837653e-01	k: 40802	n:60000
KBTBD6   60000 perm   16 sec   (3842 perm/sec)   p_kst 6.800333e-01   p_cons 2.818333e-02   p_joint 1.894000e-01

Outputting figure to mutsig2_images.part000000000088/KBTBD6.4_2029_60000_0.68003_0.028183_0.1894.png
                gene_name: KBTBD6
               theta_stop: 0.094 
                    nperm: 60000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.68 
                   p_cons: 0.028 
      ci_cons_bounds_left: 0.027 
     ci_cons_bounds_right: 0.030 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.19 

Current progress: 17 percent done.
KALRN
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: 2.521293e-01	ci left: 2.062036e-02	ci right 2.666153e-02	k: 235	n:10000
KS ci ratio: 4.414416e-02	ci left: 4.310375e-01	ci right 4.505970e-01	k: 4408	n:10000
KALRN   10000 perm   3 sec   (3911 perm/sec)   p_kst 4.408000e-01   p_cons 2.350000e-02   p_joint 3.647000e-01

Joint ci ratio: 3.607658e-02	ci left: 3.644487e-01	ci right 3.778888e-01	k: 7423	n:20000
Cons ci ratio: 1.736334e-01	ci left: 2.268901e-02	ci right 2.705062e-02	k: 496	n:20000
KS ci ratio: 3.094655e-02	ci left: 4.381958e-01	ci right 4.520202e-01	k: 8902	n:20000
KALRN   20000 perm   6 sec   (3247 perm/sec)   p_kst 4.451000e-01   p_cons 2.480000e-02   p_joint 3.711500e-01

Joint ci ratio: 2.963596e-02	ci left: 3.628714e-01	ci right 3.738208e-01	k: 11050	n:30000
Cons ci ratio: 1.431066e-01	ci left: 2.265144e-02	ci right 2.617482e-02	k: 731	n:30000
KS ci ratio: 2.528212e-02	ci left: 4.391989e-01	ci right 4.504785e-01	k: 13345	n:30000
KALRN   30000 perm   9 sec   (3213 perm/sec)   p_kst 4.448333e-01   p_cons 2.436667e-02   p_joint 3.683333e-01

Joint ci ratio: 2.554002e-02	ci left: 3.658890e-01	ci right 3.753798e-01	k: 14825	n:40000
Cons ci ratio: 1.247889e-01	ci left: 2.257075e-02	ci right 2.559888e-02	k: 962	n:40000
KS ci ratio: 2.193781e-02	ci left: 4.389978e-01	ci right 4.487604e-01	k: 17755	n:40000
KALRN   40000 perm   13 sec   (3187 perm/sec)   p_kst 4.438750e-01   p_cons 2.405000e-02   p_joint 3.706250e-01

Joint ci ratio: 2.276992e-02	ci left: 3.679006e-01	ci right 3.763942e-01	k: 18607	n:50000
Cons ci ratio: 1.111310e-01	ci left: 2.292910e-02	ci right 2.564652e-02	k: 1213	n:50000
KS ci ratio: 1.951085e-02	ci left: 4.423156e-01	ci right 4.510506e-01	k: 22334	n:50000
KALRN   50000 perm   16 sec   (3150 perm/sec)   p_kst 4.466800e-01   p_cons 2.426000e-02   p_joint 3.721400e-01

Joint ci ratio: 2.039975e-02	ci left: 3.770618e-01	ci right 3.848497e-01	k: 22857	n:60000
Cons ci ratio: 1.008049e-01	ci left: 2.334273e-02	ci right 2.583688e-02	k: 1474	n:60000
KS ci ratio: 1.787345e-02	ci left: 4.409680e-01	ci right 4.489374e-01	k: 26697	n:60000
KALRN   60000 perm   19 sec   (3126 perm/sec)   p_kst 4.449500e-01   p_cons 2.456667e-02   p_joint 3.809500e-01

Joint ci ratio: 1.885031e-02	ci left: 3.782559e-01	ci right 3.854682e-01	k: 26730	n:70000
Cons ci ratio: 9.354583e-02	ci left: 2.332548e-02	ci right 2.562845e-02	k: 1712	n:70000
KS ci ratio: 1.656419e-02	ci left: 4.407713e-01	ci right 4.481476e-01	k: 31112	n:70000
KALRN   70000 perm   23 sec   (3024 perm/sec)   p_kst 4.444571e-01   p_cons 2.445714e-02   p_joint 3.818571e-01

Outputting figure to mutsig2_images.part000000000088/KALRN.3_9357_70000_0.44446_0.024457_0.38186.png
                gene_name: KALRN
               theta_stop: 0.094 
                    nperm: 70000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.024 
      ci_cons_bounds_left: 0.023 
     ci_cons_bounds_right: 0.026 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.39 

Current progress: 33 percent done.
KCNH7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.340863e-02	ci left: 5.694520e-01	ci right 5.889019e-01	k: 5792	n:10000
Cons ci ratio: 3.037421e-02	ci left: 6.152251e-01	ci right 6.343022e-01	k: 6248	n:10000
KS ci ratio: 3.991392e-02	ci left: 4.810557e-01	ci right 5.007496e-01	k: 4909	n:10000
KCNH7   10000 perm   2 sec   (5010 perm/sec)   p_kst 4.909000e-01   p_cons 6.248000e-01   p_joint 5.792000e-01

Outputting figure to mutsig2_images.part000000000088/KCNH7.3_3721_10000_0.4909_0.6248_0.5792.png
                gene_name: KCNH7
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.62 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 50 percent done.
KAT2A
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: 6.540739e-03	ci left: 9.696322e-01	ci right 9.760884e-01	k: 9730	n:10000
KS ci ratio: 1.095686e-02	ci left: 9.223452e-01	ci right 9.326041e-01	k: 9276	n:10000
KAT2A   10000 perm   2 sec   (5950 perm/sec)   p_kst 9.276000e-01   p_cons 9.730000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000088/KAT2A.2_2586_10000_0.9276_0.973_1.png
                gene_name: KAT2A
               theta_stop: 0.011 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   p_cons: 0.97 
      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: 67 percent done.
KCNH8
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: 2.855426e-02	ci left: 6.438786e-01	ci right 6.626321e-01	k: 6533	n:10000
KS ci ratio: 2.729774e-02	ci left: 6.641089e-01	ci right 6.825900e-01	k: 6734	n:10000
KCNH8   10000 perm   2 sec   (5411 perm/sec)   p_kst 6.734000e-01   p_cons 6.533000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000088/KCNH8.2_3388_10000_0.6734_0.6533_1.png
                gene_name: KCNH8
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.68 
                   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: 83 percent done.
KCNJ16
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: 1.766047e-02	ci left: 8.238140e-01	ci right 8.385925e-01	k: 8313	n:10000
KS ci ratio: 1.841078e-02	ci left: 8.116160e-01	ci right 8.267975e-01	k: 8193	n:10000
KCNJ16   10000 perm   2 sec   (4203 perm/sec)   p_kst 8.193000e-01   p_cons 8.313000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000088/KCNJ16.2_1261_10000_0.8193_0.8313_1.png
                gene_name: KCNJ16
               theta_stop: 0.018 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.83 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000088
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 88 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1714>
Subject: Job 1120017: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1714>, 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/181708/iteration1/scatter.0000000089> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:47:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000089.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000089.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 89  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    227.26 sec.
    Max Memory :      1405 MB
    Max Swap   :      3948 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.165.3896/
-whichjob
89
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 89: processing genes 7962 - 8052
Calculating significance of each gene.
Using projection method.
7962	KCNK10	1
7963	KCNK12	1
7964	KCNK13	1
7965	KCNK15	1
7966	KCNK16	1
7967	KCNK17	1
7968	KCNK18	1
7969	KCNK2	2.632588e-02
7970	KCNK3	1
7971	KCNK4	1.261758e-01
7972	KCNK5	1
7973	KCNK6	1
7974	KCNK7	1
7975	KCNK9	1
7976	KCNMA1	1
7977	KCNMB1	1
7978	KCNMB2	1
7979	KCNMB3	1
7980	KCNMB4	1
7981	KCNN1	4.629996e-02
7982	KCNN2	2.599709e-01
7983	KCNN3	1
7984	KCNN4	1
7985	KCNQ1	1
7986	KCNQ2	1
7987	KCNQ3	1
7988	KCNQ4	1
7989	KCNQ5	3.733313e-01
7990	KCNRG	1
7991	KCNS1	1
7992	KCNS2	4.449943e-02
7993	KCNS3	1.652649e-01
7994	KCNT1	3.701923e-01
7995	KCNT2	1
7996	KCNU1	1
7997	KCNV1	1.258977e-01
7998	KCNV2	1
7999	KCTD1	1
8000/18094 8000	KCTD10	1
8001	KCTD11	1
8002	KCTD12	1
8003	KCTD13	1
8004	KCTD14	1
8005	KCTD15	4.186698e-02
8006	KCTD16	1.260771e-01
8007	KCTD17	1
8008	KCTD18	1
8009	KCTD19	1
8010	KCTD2	1
8011	KCTD20	1
8012	KCTD21	1
8013	KCTD3	1
8014	KCTD4	1
8015	KCTD5	1
8016	KCTD6	1
8017	KCTD7	1
8018	KCTD8	1
8019	KCTD9	1
8020	KDELC1	1
8021	KDELC2	1
8022	KDELR1	1
8023	KDELR2	1
8024	KDELR3	1
8025	KDM1A	1
8026	KDM1B	1
8027	KDM2A	9.523376e-02
8028	KDM2B	1
8029	KDM3A	1
8030	KDM3B	3.975118e-02
8031	KDM4A	3.748467e-01
8032	KDM4B	1
8033	KDM4C	1
8034	KDM4D	1.646234e-01
8035	KDM4DL	1
8036	KDM5A	1.232669e-01
8037	KDM5B	2.917390e-02
8038	KDM5C	1
8039	KDM5D	1
8040	KDM6A	4.803472e-06
8041	KDM6B	1
8042	KDR	1.843968e-01
8043	KDSR	1
8044	KEAP1	1.654318e-01
8045	KEL	1
8046	KERA	1
8047	KHDC1	1
8048	KHDC1L	1
8049	KHDRBS1	1
8050	KHDRBS2	5.428460e-02
8051	KHDRBS3	5.485468e-02
8052	KHK	1
Done

Running MutSig 2:
Scatter job 89: processing genes 7962 - 8052
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KDM6A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.477842e-02	ci left: 8.689718e-01	ci right 8.820086e-01	k: 8756	n:10000
Cons ci ratio: 4.969165e-02	ci left: 3.739550e-01	ci right 3.931129e-01	k: 3835	n:10000
KS ci ratio: 1.697625e-02	ci left: 8.348036e-01	ci right 8.491966e-01	k: 8421	n:10000
KDM6A   10000 perm   4 sec   (2447 perm/sec)   p_kst 8.421000e-01   p_cons 3.835000e-01   p_joint 8.756000e-01

Outputting figure to mutsig2_images.part000000000089/KDM6A.6_4322_10000_0.8421_0.3835_0.8756.png
                gene_name: KDM6A
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.88 
     ci_joint_bounds_left: 0.87 
    ci_joint_bounds_right: 0.88 

Current progress: 14 percent done.
KDM3B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.655280e-01	ci left: 4.868974e-02	ci right 5.757286e-02	k: 530	n:10000
Cons ci ratio: 1.565438e-01	ci left: 5.436451e-02	ci right 6.369444e-02	k: 589	n:10000
KS ci ratio: 1.306344e-01	ci left: 7.717981e-02	ci right 8.806479e-02	k: 825	n:10000
KDM3B   10000 perm   3 sec   (3736 perm/sec)   p_kst 8.250000e-02   p_cons 5.890000e-02   p_joint 5.300000e-02

Joint ci ratio: 9.851894e-02	ci left: 6.972516e-02	ci right 7.699946e-02	k: 1466	n:20000
Cons ci ratio: 1.109456e-01	ci left: 5.548160e-02	ci right 6.204742e-02	k: 1174	n:20000
KS ci ratio: 9.311361e-02	ci left: 7.759738e-02	ci right 8.522484e-02	k: 1627	n:20000
KDM3B   20000 perm   5 sec   (3653 perm/sec)   p_kst 8.135000e-02   p_cons 5.870000e-02   p_joint 7.330000e-02

Joint ci ratio: 5.986915e-02	ci left: 1.212774e-01	ci right 1.287954e-01	k: 3750	n:30000
Cons ci ratio: 9.786246e-02	ci left: 4.827697e-02	ci right 5.327714e-02	k: 1522	n:30000
KS ci ratio: 7.579121e-02	ci left: 7.875547e-02	ci right 8.499245e-02	k: 2455	n:30000
KDM3B   30000 perm   8 sec   (3664 perm/sec)   p_kst 8.183333e-02   p_cons 5.073333e-02   p_joint 1.250000e-01

Outputting figure to mutsig2_images.part000000000089/KDM3B.3_5382_30000_0.081833_0.050733_0.125.png
                gene_name: KDM3B
               theta_stop: 0.098 
                    nperm: 30000 
                     p_ks: 0.082 
        ci_ks_bounds_left: 0.079 
       ci_ks_bounds_right: 0.085 
                   p_cons: 0.051 
      ci_cons_bounds_left: 0.048 
     ci_cons_bounds_right: 0.053 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 29 percent done.
KDM5B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.786775e-02	ci left: 8.204583e-01	ci right 8.353502e-01	k: 8280	n:10000
Cons ci ratio: 5.201841e-02	ci left: 3.526716e-01	ci right 3.716088e-01	k: 3621	n:10000
KS ci ratio: 2.493607e-02	ci left: 7.029129e-01	ci right 7.207635e-01	k: 7119	n:10000
KDM5B   10000 perm   3 sec   (3352 perm/sec)   p_kst 7.119000e-01   p_cons 3.621000e-01   p_joint 8.280000e-01

Outputting figure to mutsig2_images.part000000000089/KDM5B.3_4743_10000_0.7119_0.3621_0.828.png
                gene_name: KDM5B
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.71 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.83 
     ci_joint_bounds_left: 0.82 
    ci_joint_bounds_right: 0.84 

Current progress: 43 percent done.
KCNK2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.064274e-01	ci left: 1.363247e-02	ci right 1.865513e-02	k: 160	n:10000
Cons ci ratio: 2.220488e-03	ci left: 9.956027e-01	ci right 9.978928e-01	k: 9969	n:10000
KS ci ratio: 4.668639e-01	ci left: 5.372463e-03	ci right 8.724383e-03	k: 69	n:10000
KCNK2   10000 perm   2 sec   (5133 perm/sec)   p_kst 6.900000e-03   p_cons 9.969000e-01   p_joint 1.600000e-02

Joint ci ratio: 1.094685e-01	ci left: 5.694265e-02	ci right 6.358591e-02	k: 1204	n:20000
Cons ci ratio: 1.468604e-03	ci left: 9.964220e-01	ci right 9.979277e-01	k: 19945	n:20000
KS ci ratio: 3.349842e-01	ci left: 5.662386e-03	ci right 7.984485e-03	k: 135	n:20000
KCNK2   20000 perm   4 sec   (5085 perm/sec)   p_kst 6.750000e-03   p_cons 9.972500e-01   p_joint 6.020000e-02

Joint ci ratio: 2.762558e-01	ci left: 5.746141e-03	ci right 7.617986e-03	k: 199	n:30000
Cons ci ratio: 1.184759e-03	ci left: 9.966452e-01	ci right 9.978552e-01	k: 29919	n:30000
KS ci ratio: 2.762558e-01	ci left: 5.746141e-03	ci right 7.617986e-03	k: 199	n:30000
KCNK2   30000 perm   6 sec   (5084 perm/sec)   p_kst 6.633333e-03   p_cons 9.973000e-01   p_joint 6.633333e-03

Joint ci ratio: 7.693232e-02	ci left: 5.860039e-02	ci right 6.331360e-02	k: 2437	n:40000
Cons ci ratio: 1.019760e-03	ci left: 9.967684e-01	ci right 9.978073e-01	k: 39893	n:40000
KS ci ratio: 2.390951e-01	ci left: 5.876993e-03	ci right 7.495874e-03	k: 266	n:40000
KCNK2   40000 perm   8 sec   (4952 perm/sec)   p_kst 6.650000e-03   p_cons 9.973250e-01   p_joint 6.092500e-02

Joint ci ratio: 6.817548e-02	ci left: 5.990169e-02	ci right 6.414933e-02	k: 3100	n:50000
Cons ci ratio: 9.255635e-04	ci left: 9.967400e-01	ci right 9.976808e-01	k: 49862	n:50000
KS ci ratio: 2.128131e-01	ci left: 6.022641e-03	ci right 7.475515e-03	k: 336	n:50000
KCNK2   50000 perm   10 sec   (4868 perm/sec)   p_kst 6.720000e-03   p_cons 9.972400e-01   p_joint 6.200000e-02

Joint ci ratio: 6.203315e-02	ci left: 6.046103e-02	ci right 6.434810e-02	k: 3743	n:60000
Cons ci ratio: 8.274781e-04	ci left: 9.969053e-01	ci right 9.977455e-01	k: 59841	n:60000
KS ci ratio: 1.936454e-01	ci left: 6.126308e-03	ci right 7.455406e-03	k: 406	n:60000
KCNK2   60000 perm   13 sec   (4794 perm/sec)   p_kst 6.766667e-03   p_cons 9.973500e-01   p_joint 6.238333e-02

Joint ci ratio: 1.538031e-02	ci left: 4.776066e-01	ci right 4.850235e-01	k: 33692	n:70000
Cons ci ratio: 7.564383e-04	ci left: 9.970095e-01	ci right 9.977769e-01	k: 69819	n:70000
KS ci ratio: 1.766470e-01	ci left: 6.368423e-03	ci right 7.615827e-03	k: 488	n:70000
KCNK2   70000 perm   15 sec   (4701 perm/sec)   p_kst 6.971429e-03   p_cons 9.974143e-01   p_joint 4.813143e-01

Joint ci ratio: 1.157616e-02	ci left: 5.856187e-01	ci right 5.924499e-01	k: 47123	n:80000
Cons ci ratio: 7.126843e-04	ci left: 9.969955e-01	ci right 9.977177e-01	k: 79790	n:80000
KS ci ratio: 1.637485e-01	ci left: 6.529866e-03	ci right 7.706304e-03	k: 568	n:80000
KCNK2   80000 perm   17 sec   (4629 perm/sec)   p_kst 7.100000e-03   p_cons 9.973750e-01   p_joint 5.890375e-01

Joint ci ratio: 1.092550e-02	ci left: 5.853100e-01	ci right 5.917510e-01	k: 52968	n:90000
Cons ci ratio: 6.656905e-04	ci left: 9.970688e-01	ci right 9.977429e-01	k: 89768	n:90000
KS ci ratio: 1.555039e-01	ci left: 6.465691e-03	ci right 7.566444e-03	k: 630	n:90000
KCNK2   90000 perm   20 sec   (4403 perm/sec)   p_kst 7.000000e-03   p_cons 9.974222e-01   p_joint 5.885333e-01

Joint ci ratio: 1.034973e-02	ci left: 5.861832e-01	ci right 5.922916e-01	k: 58924	n:100000
Cons ci ratio: 6.461735e-04	ci left: 9.969585e-01	ci right 9.976121e-01	k: 99730	n:100000
KS ci ratio: 1.471137e-01	ci left: 6.531135e-03	ci right 7.577763e-03	k: 704	n:100000
KCNK2   100000 perm   23 sec   (4304 perm/sec)   p_kst 7.040000e-03   p_cons 9.973000e-01   p_joint 5.892400e-01

Joint ci ratio: 9.855570e-03	ci left: 5.869410e-01	ci right 5.927633e-01	k: 64884	n:110000
Cons ci ratio: 6.149628e-04	ci left: 9.969849e-01	ci right 9.976066e-01	k: 109704	n:110000
KS ci ratio: 1.403130e-01	ci left: 6.550890e-03	ci right 7.548094e-03	k: 774	n:110000
KCNK2   110000 perm   27 sec   (4137 perm/sec)   p_kst 7.036364e-03   p_cons 9.973091e-01   p_joint 5.898545e-01

Joint ci ratio: 9.439825e-03	ci left: 5.868689e-01	ci right 5.924434e-01	k: 70759	n:120000
Cons ci ratio: 5.978252e-04	ci left: 9.969108e-01	ci right 9.975147e-01	k: 119667	n:120000
KS ci ratio: 1.342959e-01	ci left: 6.576335e-03	ci right 7.531054e-03	k: 845	n:120000
KCNK2   120000 perm   31 sec   (3866 perm/sec)   p_kst 7.041667e-03   p_cons 9.972250e-01   p_joint 5.896583e-01

Joint ci ratio: 9.063528e-03	ci left: 5.872975e-01	ci right 5.926523e-01	k: 76697	n:130000
Cons ci ratio: 5.705131e-04	ci left: 9.969622e-01	ci right 9.975383e-01	k: 129644	n:130000
KS ci ratio: 1.284989e-01	ci left: 6.650762e-03	ci right 7.571430e-03	k: 923	n:130000
KCNK2   130000 perm   36 sec   (3628 perm/sec)   p_kst 7.100000e-03   p_cons 9.972615e-01   p_joint 5.899769e-01

Joint ci ratio: 8.733165e-03	ci left: 5.874326e-01	ci right 5.925923e-01	k: 82602	n:140000
Cons ci ratio: 5.451089e-04	ci left: 9.970215e-01	ci right 9.975718e-01	k: 139623	n:140000
KS ci ratio: 1.238295e-01	ci left: 6.666851e-03	ci right 7.553748e-03	k: 994	n:140000
KCNK2   140000 perm   41 sec   (3451 perm/sec)   p_kst 7.100000e-03   p_cons 9.973071e-01   p_joint 5.900143e-01

Joint ci ratio: 1.050143e-02	ci left: 4.790418e-01	ci right 4.841056e-01	k: 72236	n:150000
Cons ci ratio: 5.240118e-04	ci left: 9.970592e-01	ci right 9.975880e-01	k: 149600	n:150000
KS ci ratio: 1.204338e-01	ci left: 6.590769e-03	ci right 7.441788e-03	k: 1051	n:150000
KCNK2   150000 perm   44 sec   (3442 perm/sec)   p_kst 7.006667e-03   p_cons 9.973333e-01   p_joint 4.815733e-01

Joint ci ratio: 8.159671e-03	ci left: 5.881608e-01	ci right 5.929859e-01	k: 94492	n:160000
Cons ci ratio: 5.075313e-04	ci left: 9.970661e-01	ci right 9.975781e-01	k: 159573	n:160000
KS ci ratio: 1.167739e-01	ci left: 6.585172e-03	ci right 7.407844e-03	k: 1118	n:160000
KCNK2   160000 perm   47 sec   (3416 perm/sec)   p_kst 6.987500e-03   p_cons 9.973313e-01   p_joint 5.905750e-01

Joint ci ratio: 7.912654e-03	ci left: 5.884406e-01	ci right 5.931210e-01	k: 100433	n:170000
Cons ci ratio: 4.892470e-04	ci left: 9.971094e-01	ci right 9.976028e-01	k: 169552	n:170000
KS ci ratio: 1.127602e-01	ci left: 6.660618e-03	ci right 7.462213e-03	k: 1199	n:170000
KCNK2   170000 perm   51 sec   (3339 perm/sec)   p_kst 7.052941e-03   p_cons 9.973647e-01   p_joint 5.907824e-01

Joint ci ratio: 9.584246e-03	ci left: 4.793781e-01	ci right 4.840002e-01	k: 86704	n:180000
Cons ci ratio: 4.777580e-04	ci left: 9.970899e-01	ci right 9.975716e-01	k: 179521	n:180000
KS ci ratio: 1.096958e-01	ci left: 6.657851e-03	ci right 7.435930e-03	k: 1267	n:180000
KCNK2   180000 perm   54 sec   (3303 perm/sec)   p_kst 7.038889e-03   p_cons 9.973389e-01   p_joint 4.816889e-01

Joint ci ratio: 9.327041e-03	ci left: 4.795246e-01	ci right 4.840233e-01	k: 91537	n:190000
Cons ci ratio: 4.647090e-04	ci left: 9.971002e-01	ci right 9.975686e-01	k: 189495	n:190000
KS ci ratio: 1.071921e-01	ci left: 6.614654e-03	ci right 7.368927e-03	k: 1327	n:190000
KCNK2   190000 perm   58 sec   (3284 perm/sec)   p_kst 6.984211e-03   p_cons 9.973421e-01   p_joint 4.817737e-01

Joint ci ratio: 9.090399e-03	ci left: 4.796079e-01	ci right 4.839926e-01	k: 96360	n:200000
Cons ci ratio: 4.535256e-04	ci left: 9.970992e-01	ci right 9.975562e-01	k: 199467	n:200000
KS ci ratio: 1.043988e-01	ci left: 6.634399e-03	ci right 7.369999e-03	k: 1399	n:200000
KCNK2   200000 perm   61 sec   (3254 perm/sec)   p_kst 6.995000e-03   p_cons 9.973350e-01   p_joint 4.818000e-01

Joint ci ratio: 7.116590e-03	ci left: 5.888602e-01	ci right 5.930706e-01	k: 124103	n:210000
Cons ci ratio: 4.419227e-04	ci left: 9.971133e-01	ci right 9.975585e-01	k: 209442	n:210000
KS ci ratio: 1.021984e-01	ci left: 6.601441e-03	ci right 7.317032e-03	k: 1460	n:210000
KCNK2   210000 perm   66 sec   (3201 perm/sec)   p_kst 6.952381e-03   p_cons 9.973429e-01   p_joint 5.909667e-01

Joint ci ratio: 6.954910e-03	ci left: 5.887738e-01	ci right 5.928874e-01	k: 129983	n:220000
Cons ci ratio: 4.311636e-04	ci left: 9.971262e-01	ci right 9.975605e-01	k: 219417	n:220000
KS ci ratio: 1.001977e-01	ci left: 6.562763e-03	ci right 7.259415e-03	k: 1519	n:220000
KCNK2   220000 perm   69 sec   (3190 perm/sec)   p_kst 6.904545e-03   p_cons 9.973500e-01   p_joint 5.908318e-01

Joint ci ratio: 6.801139e-03	ci left: 5.888830e-01	ci right 5.929060e-01	k: 135906	n:230000
Cons ci ratio: 4.259774e-04	ci left: 9.970748e-01	ci right 9.975038e-01	k: 229378	n:230000
KS ci ratio: 9.821620e-02	ci left: 6.540298e-03	ci right 7.220044e-03	k: 1581	n:230000
KCNK2   230000 perm   72 sec   (3175 perm/sec)   p_kst 6.873913e-03   p_cons 9.972957e-01   p_joint 5.908957e-01

Outputting figure to mutsig2_images.part000000000089/KCNK2.2_1352_230000_0.0068739_0.9973_0.5909.png
                gene_name: KCNK2
               theta_stop: 0.098 
                    nperm: 230000 
                     p_ks: 0.0069 
        ci_ks_bounds_left: 0.0065 
       ci_ks_bounds_right: 0.0072 
                   p_cons: 1.00 
      ci_cons_bounds_left: 1.00 
     ci_cons_bounds_right: 1.00 
                  p_joint: 0.59 
     ci_joint_bounds_left: 0.59 
    ci_joint_bounds_right: 0.59 

Current progress: 57 percent done.
KDM2A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.716754e-02	ci left: 6.662236e-01	ci right 6.846741e-01	k: 6755	n:10000
Cons ci ratio: 1.650160e-02	ci left: 8.423403e-01	ci right 8.564555e-01	k: 8495	n:10000
KS ci ratio: 5.109680e-02	ci left: 3.609240e-01	ci right 3.799515e-01	k: 3704	n:10000
KDM2A   10000 perm   2 sec   (5369 perm/sec)   p_kst 3.704000e-01   p_cons 8.495000e-01   p_joint 6.755000e-01

Outputting figure to mutsig2_images.part000000000089/KDM2A.2_3569_10000_0.3704_0.8495_0.6755.png
                gene_name: KDM2A
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.68 
     ci_joint_bounds_left: 0.67 
    ci_joint_bounds_right: 0.68 

Current progress: 71 percent done.
KDM5A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.909731e-02	ci left: 8.003440e-01	ci right 8.158761e-01	k: 8082	n:10000
Cons ci ratio: 3.493343e-02	ci left: 5.474992e-01	ci right 5.670674e-01	k: 5573	n:10000
KS ci ratio: 6.903667e-02	ci left: 2.353112e-01	ci right 2.522383e-01	k: 2437	n:10000
KDM5A   10000 perm   2 sec   (4989 perm/sec)   p_kst 2.437000e-01   p_cons 5.573000e-01   p_joint 8.082000e-01

Outputting figure to mutsig2_images.part000000000089/KDM5A.2_5185_10000_0.2437_0.5573_0.8082.png
                gene_name: KDM5A
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.57 
                  p_joint: 0.81 
     ci_joint_bounds_left: 0.80 
    ci_joint_bounds_right: 0.82 

Current progress: 86 percent done.
KEAP1
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: 5.290849e-03	ci left: 9.794135e-01	ci right 9.847004e-01	k: 9822	n:10000
KS ci ratio: 7.113958e-03	ci left: 9.645717e-01	ci right 9.715522e-01	k: 9682	n:10000
KEAP1   10000 perm   2 sec   (6228 perm/sec)   p_kst 9.682000e-01   p_cons 9.822000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000089/KEAP1.2_1895_10000_0.9682_0.9822_1.png
                gene_name: KEAP1
               theta_stop: 0.0071 
                    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: 0.98 
     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.165.3896/
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/181708/iteration1/scatter.0000000089
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 89 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120021: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000090> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:50:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000090.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000090.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 90  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    407.87 sec.
    Max Memory :      1480 MB
    Max Swap   :      3858 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.165.3896/
-whichjob
90
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 90: processing genes 8053 - 8142
Calculating significance of each gene.
Using projection method.
8053	KHNYN	1
8054	KHSRP	1
8055	KIAA0020	1
8056	KIAA0090	1
8057	KIAA0100	7.189758e-02
8058	KIAA0101	1
8059	KIAA0141	1
8060	KIAA0146	3.352696e-01
8061	KIAA0174	1
8062	KIAA0182	7.384632e-02
8063	KIAA0195	1
8064	KIAA0196	1
8065	KIAA0226	1.868900e-01
8066	KIAA0232	4.628722e-01
8067	KIAA0240	1
8068	KIAA0247	1
8069	KIAA0284	1
8070	KIAA0317	1
8071	KIAA0319	1
8072	KIAA0319L	1.190606e-01
8073	KIAA0355	1
8074	KIAA0368	7.182624e-02
8075	KIAA0391	1
8076	KIAA0406	1
8077	KIAA0408	1
8078	KIAA0415	1
8079	KIAA0427	1
8080	KIAA0430	1
8081	KIAA0467	1
8082	KIAA0494	1
8083	KIAA0495	1
8084	KIAA0513	1
8085	KIAA0528	1.797818e-01
8086	KIAA0556	3.670684e-01
8087	KIAA0562	1
8088	KIAA0564	1.878301e-02
8089	KIAA0586	1.682593e-01
8090	KIAA0649	1
8091	KIAA0652	1
8092	KIAA0664	1.071502e-02
8093	KIAA0748	1
8094	KIAA0753	1
8095	KIAA0754	3.527710e-01
8096	KIAA0776	1.241341e-01
8097	KIAA0802	1
8098	KIAA0831	1
8099	KIAA0892	1
8100	KIAA0895	1
8101	KIAA0895L	1
8102	KIAA0907	2.396235e-01
8103	KIAA0913	2.558304e-01
8104	KIAA0922	3.799770e-01
8105	KIAA0947	1
8106	KIAA1009	1
8107	KIAA1012	3.834604e-01
8108	KIAA1024	1
8109	KIAA1033	8.930637e-02
8110	KIAA1045	9.321018e-02
8111	KIAA1109	5.975903e-01
8112	KIAA1143	1
8113	KIAA1147	1
8114	KIAA1161	1
8115	KIAA1191	1
8116	KIAA1199	1
8117	KIAA1210	2.969810e-01
8118	KIAA1211	1
8119	KIAA1217	3.171323e-01
8120	KIAA1244	1
8121	KIAA1257	1
8122	KIAA1267	1.851439e-01
8123	KIAA1274	8.663518e-02
8124	KIAA1279	1
8125	KIAA1310	1.059014e-01
8126	KIAA1324	1.438574e-01
8127	KIAA1324L	1
8128	KIAA1328	1
8129	KIAA1370	1
8130	KIAA1377	1
8131	KIAA1383	1
8132	KIAA1407	1
8133	KIAA1409	1
8134	KIAA1429	6.370173e-01
8135	KIAA1430	1
8136	KIAA1432	1
8137	KIAA1462	1
8138	KIAA1467	1
8139	KIAA1468	3.028181e-02
8140	KIAA1486	1
8141	KIAA1522	1
8142	KIAA1524	2.688219e-01
Done

Running MutSig 2:
Scatter job 90: processing genes 8053 - 8142
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KIAA0100
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.689324e-02	ci left: 8.361272e-01	ci right 8.504722e-01	k: 8434	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: 2.447480e-02	ci left: 7.105819e-01	ci right 7.282901e-01	k: 7195	n:10000
KIAA0100   10000 perm   3 sec   (3037 perm/sec)   p_kst 7.195000e-01   p_cons 4.624000e-01   p_joint 8.434000e-01

Outputting figure to mutsig2_images.part000000000090/KIAA0100.3_6864_10000_0.7195_0.4624_0.8434.png
                gene_name: KIAA0100
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.84 
     ci_joint_bounds_left: 0.84 
    ci_joint_bounds_right: 0.85 

Current progress: 11 percent done.
KIAA0564
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: 1.546220e-02	ci left: 8.585543e-01	ci right 8.720322e-01	k: 8654	n:10000
KS ci ratio: 2.767080e-02	ci left: 6.580680e-01	ci right 6.766344e-01	k: 6674	n:10000
KIAA0564   10000 perm   3 sec   (3861 perm/sec)   p_kst 6.674000e-01   p_cons 8.654000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000090/KIAA0564.3_5902_10000_0.6674_0.8654_1.png
                gene_name: KIAA0564
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.68 
                   p_cons: 0.87 
      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: 22 percent done.
KIAA0664
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.211914e-02	ci left: 2.758690e-01	ci right 2.936566e-01	k: 2847	n:10000
Cons ci ratio: 3.555350e-02	ci left: 5.387836e-01	ci right 5.583881e-01	k: 5486	n:10000
KS ci ratio: 7.241845e-02	ci left: 2.183268e-01	ci right 2.348328e-01	k: 2265	n:10000
KIAA0664   10000 perm   2 sec   (4722 perm/sec)   p_kst 2.265000e-01   p_cons 5.486000e-01   p_joint 2.847000e-01

Outputting figure to mutsig2_images.part000000000090/KIAA0664.3_4030_10000_0.2265_0.5486_0.2847.png
                gene_name: KIAA0664
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.55 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.28 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.29 

Current progress: 33 percent done.
KIAA0146
Processing conservation and coverage...
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: 2.540473e-02	ci left: 6.951461e-01	ci right 7.131348e-01	k: 7042	n:10000
KS ci ratio: 6.918207e-01	ci left: 2.107242e-03	ci right 4.397341e-03	k: 31	n:10000
KIAA0146   10000 perm   2 sec   (5719 perm/sec)   p_kst 3.100000e-03   p_cons 7.042000e-01   p_joint 8.700000e-03

Joint ci ratio: 3.076857e-01	ci left: 6.812321e-03	ci right 9.333850e-03	k: 160	n:20000
Cons ci ratio: 1.886796e-02	ci left: 6.768519e-01	ci right 6.897948e-01	k: 13667	n:20000
KS ci ratio: 4.817099e-01	ci left: 2.509150e-03	ci right 4.140543e-03	k: 65	n:20000
KIAA0146   20000 perm   4 sec   (5010 perm/sec)   p_kst 3.250000e-03   p_cons 6.833500e-01   p_joint 8.000000e-03

Joint ci ratio: 1.984924e-01	ci left: 1.155866e-02	ci right 1.413697e-02	k: 384	n:30000
Cons ci ratio: 1.527957e-02	ci left: 6.816176e-01	ci right 6.921461e-01	k: 20607	n:30000
KS ci ratio: 4.196513e-01	ci left: 2.293583e-03	ci right 3.539117e-03	k: 86	n:30000
KIAA0146   30000 perm   6 sec   (4755 perm/sec)   p_kst 2.866667e-03   p_cons 6.869000e-01   p_joint 1.280000e-02

Joint ci ratio: 1.882394e-01	ci left: 9.714880e-03	ci right 1.175708e-02	k: 428	n:40000
Cons ci ratio: 1.326872e-02	ci left: 6.811498e-01	ci right 6.902732e-01	k: 27429	n:40000
KS ci ratio: 3.650115e-01	ci left: 2.351456e-03	ci right 3.422738e-03	k: 114	n:40000
KIAA0146   40000 perm   9 sec   (4577 perm/sec)   p_kst 2.850000e-03   p_cons 6.857250e-01   p_joint 1.070000e-02

Joint ci ratio: 1.773156e-01	ci left: 8.821240e-03	ci right 1.055640e-02	k: 483	n:50000
Cons ci ratio: 1.188295e-02	ci left: 6.810884e-01	ci right 6.892501e-01	k: 34259	n:50000
KS ci ratio: 3.228373e-01	ci left: 2.466107e-03	ci right 3.433034e-03	k: 146	n:50000
KIAA0146   50000 perm   11 sec   (4447 perm/sec)   p_kst 2.920000e-03   p_cons 6.851800e-01   p_joint 9.660000e-03

Joint ci ratio: 1.881388e-01	ci left: 6.507312e-03	ci right 7.874341e-03	k: 430	n:60000
Cons ci ratio: 1.085886e-02	ci left: 6.809984e-01	ci right 6.884503e-01	k: 41084	n:60000
KS ci ratio: 2.893301e-01	ci left: 2.609169e-03	ci right 3.506634e-03	k: 182	n:60000
KIAA0146   60000 perm   14 sec   (4333 perm/sec)   p_kst 3.033333e-03   p_cons 6.847333e-01   p_joint 7.166667e-03

Joint ci ratio: 1.745036e-01	ci left: 6.532365e-03	ci right 7.794720e-03	k: 500	n:70000
Cons ci ratio: 1.004516e-02	ci left: 6.816301e-01	ci right 6.885260e-01	k: 47956	n:70000
KS ci ratio: 2.760963e-01	ci left: 2.475326e-03	ci right 3.281045e-03	k: 200	n:70000
KIAA0146   70000 perm   17 sec   (4234 perm/sec)   p_kst 2.857143e-03   p_cons 6.850857e-01   p_joint 7.142857e-03

Joint ci ratio: 2.047123e-01	ci left: 4.095436e-03	ci right 5.041046e-03	k: 364	n:80000
Cons ci ratio: 9.425494e-03	ci left: 6.805148e-01	ci right 6.869718e-01	k: 54700	n:80000
KS ci ratio: 2.598085e-01	ci left: 2.469094e-03	ci right 3.217683e-03	k: 226	n:80000
KIAA0146   80000 perm   19 sec   (4150 perm/sec)   p_kst 2.825000e-03   p_cons 6.837500e-01   p_joint 4.550000e-03

Joint ci ratio: 1.929163e-01	ci left: 4.126079e-03	ci right 5.017427e-03	k: 410	n:90000
Cons ci ratio: 8.884509e-03	ci left: 6.807952e-01	ci right 6.868818e-01	k: 61546	n:90000
KS ci ratio: 2.436971e-01	ci left: 2.517490e-03	ci right 3.226266e-03	k: 257	n:90000
KIAA0146   90000 perm   22 sec   (4066 perm/sec)   p_kst 2.855556e-03   p_cons 6.838444e-01   p_joint 4.555556e-03

Joint ci ratio: 1.272533e-01	ci left: 8.801496e-03	ci right 1.000722e-02	k: 939	n:100000
Cons ci ratio: 8.433356e-03	ci left: 6.807072e-01	ci right 6.864821e-01	k: 68360	n:100000
KS ci ratio: 2.314616e-01	ci left: 2.529085e-03	ci right 3.200266e-03	k: 285	n:100000
KIAA0146   100000 perm   25 sec   (3945 perm/sec)   p_kst 2.850000e-03   p_cons 6.836000e-01   p_joint 9.390000e-03

Joint ci ratio: 1.138432e-01	ci left: 1.005620e-02	ci right 1.127890e-02	k: 1172	n:110000
Cons ci ratio: 8.039881e-03	ci left: 6.808970e-01	ci right 6.864024e-01	k: 75202	n:110000
KS ci ratio: 2.171200e-01	ci left: 2.633828e-03	ci right 3.283727e-03	k: 324	n:110000
KIAA0146   110000 perm   28 sec   (3877 perm/sec)   p_kst 2.945455e-03   p_cons 6.836545e-01   p_joint 1.065455e-02

Joint ci ratio: 1.092834e-01	ci left: 1.002826e-02	ci right 1.119557e-02	k: 1272	n:120000
Cons ci ratio: 7.705100e-03	ci left: 6.805926e-01	ci right 6.858652e-01	k: 81988	n:120000
KS ci ratio: 2.051511e-01	ci left: 2.722182e-03	ci right 3.352214e-03	k: 363	n:120000
KIAA0146   120000 perm   31 sec   (3812 perm/sec)   p_kst 3.025000e-03   p_cons 6.832333e-01   p_joint 1.060000e-02

Joint ci ratio: 1.050378e-01	ci left: 1.004291e-02	ci right 1.116370e-02	k: 1377	n:130000
Cons ci ratio: 7.405499e-03	ci left: 6.805398e-01	ci right 6.856059e-01	k: 88800	n:130000
KS ci ratio: 1.974380e-01	ci left: 2.724620e-03	ci right 3.328655e-03	k: 392	n:130000
KIAA0146   130000 perm   35 sec   (3705 perm/sec)   p_kst 3.015385e-03   p_cons 6.830769e-01   p_joint 1.059231e-02

Joint ci ratio: 1.014245e-01	ci left: 1.002140e-02	ci right 1.109902e-02	k: 1477	n:140000
Cons ci ratio: 7.133150e-03	ci left: 6.808129e-01	ci right 6.856938e-01	k: 95656	n:140000
KS ci ratio: 1.891898e-01	ci left: 2.767915e-03	ci right 3.352968e-03	k: 427	n:140000
KIAA0146   140000 perm   39 sec   (3589 perm/sec)   p_kst 3.050000e-03   p_cons 6.832571e-01   p_joint 1.055000e-02

Joint ci ratio: 9.784717e-02	ci left: 1.006837e-02	ci right 1.111067e-02	k: 1587	n:150000
Cons ci ratio: 6.889642e-03	ci left: 6.809991e-01	ci right 6.857138e-01	k: 102504	n:150000
KS ci ratio: 1.826892e-01	ci left: 2.780437e-03	ci right 3.345708e-03	k: 458	n:150000
KIAA0146   150000 perm   43 sec   (3512 perm/sec)   p_kst 3.053333e-03   p_cons 6.833600e-01   p_joint 1.058000e-02

Joint ci ratio: 9.490639e-02	ci left: 1.004903e-02	ci right 1.105632e-02	k: 1687	n:160000
Cons ci ratio: 6.668904e-03	ci left: 6.812020e-01	ci right 6.857663e-01	k: 109358	n:160000
KS ci ratio: 1.760961e-01	ci left: 2.815594e-03	ci right 3.365156e-03	k: 493	n:160000
KIAA0146   160000 perm   46 sec   (3462 perm/sec)   p_kst 3.081250e-03   p_cons 6.834875e-01   p_joint 1.054375e-02

Joint ci ratio: 9.159648e-02	ci left: 1.017034e-02	ci right 1.115233e-02	k: 1811	n:170000
Cons ci ratio: 6.473648e-03	ci left: 6.810119e-01	ci right 6.854407e-01	k: 116149	n:170000
KS ci ratio: 1.682651e-01	ci left: 2.914544e-03	ci right 3.455559e-03	k: 540	n:170000
KIAA0146   170000 perm   50 sec   (3407 perm/sec)   p_kst 3.176471e-03   p_cons 6.832294e-01   p_joint 1.065294e-02

Joint ci ratio: 8.910004e-02	ci left: 1.016462e-02	ci right 1.111791e-02	k: 1914	n:180000
Cons ci ratio: 6.280624e-03	ci left: 6.818076e-01	ci right 6.861087e-01	k: 123113	n:180000
KS ci ratio: 1.632135e-01	ci left: 2.933683e-03	ci right 3.460297e-03	k: 574	n:180000
KIAA0146   180000 perm   54 sec   (3355 perm/sec)   p_kst 3.188889e-03   p_cons 6.839611e-01   p_joint 1.063333e-02

Joint ci ratio: 8.610976e-02	ci left: 1.032463e-02	ci right 1.125880e-02	k: 2049	n:190000
Cons ci ratio: 6.112785e-03	ci left: 6.818883e-01	ci right 6.860745e-01	k: 129957	n:190000
KS ci ratio: 1.576846e-01	ci left: 2.986411e-03	ci right 3.502613e-03	k: 615	n:190000
KIAA0146   190000 perm   57 sec   (3306 perm/sec)   p_kst 3.236842e-03   p_cons 6.839842e-01   p_joint 1.078421e-02

Joint ci ratio: 8.382924e-02	ci left: 1.036141e-02	ci right 1.127286e-02	k: 2162	n:200000
Cons ci ratio: 5.959443e-03	ci left: 6.818371e-01	ci right 6.859176e-01	k: 136776	n:200000
KS ci ratio: 1.525655e-01	ci left: 3.038947e-03	ci right 3.545619e-03	k: 657	n:200000
KIAA0146   200000 perm   61 sec   (3254 perm/sec)   p_kst 3.285000e-03   p_cons 6.838800e-01   p_joint 1.081000e-02

Joint ci ratio: 8.186638e-02	ci left: 1.035764e-02	ci right 1.124641e-02	k: 2267	n:210000
Cons ci ratio: 5.817026e-03	ci left: 6.817968e-01	ci right 6.857791e-01	k: 143596	n:210000
KS ci ratio: 1.484475e-01	ci left: 3.063794e-03	ci right 3.559597e-03	k: 694	n:210000
KIAA0146   210000 perm   66 sec   (3199 perm/sec)   p_kst 3.304762e-03   p_cons 6.837905e-01   p_joint 1.079524e-02

Joint ci ratio: 7.979763e-02	ci left: 1.041683e-02	ci right 1.128704e-02	k: 2386	n:220000
Cons ci ratio: 5.680292e-03	ci left: 6.820708e-01	ci right 6.859607e-01	k: 150484	n:220000
KS ci ratio: 1.449441e-01	ci left: 3.073405e-03	ci right 3.558009e-03	k: 728	n:220000
KIAA0146   220000 perm   70 sec   (3154 perm/sec)   p_kst 3.309091e-03   p_cons 6.840182e-01   p_joint 1.084545e-02

Joint ci ratio: 7.794107e-02	ci left: 1.045407e-02	ci right 1.130615e-02	k: 2501	n:230000
Cons ci ratio: 5.554049e-03	ci left: 6.822218e-01	ci right 6.860257e-01	k: 157349	n:230000
KS ci ratio: 1.419579e-01	ci left: 3.069723e-03	ci right 3.542931e-03	k: 759	n:230000
KIAA0146   230000 perm   74 sec   (3109 perm/sec)   p_kst 3.300000e-03   p_cons 6.841261e-01   p_joint 1.087391e-02

Joint ci ratio: 7.648956e-02	ci left: 1.041075e-02	ci right 1.124279e-02	k: 2597	n:240000
Cons ci ratio: 5.438853e-03	ci left: 6.821232e-01	ci right 6.858474e-01	k: 164157	n:240000
KS ci ratio: 1.391490e-01	ci left: 3.066442e-03	ci right 3.529015e-03	k: 790	n:240000
KIAA0146   240000 perm   78 sec   (3064 perm/sec)   p_kst 3.291667e-03   p_cons 6.839875e-01   p_joint 1.082083e-02

Joint ci ratio: 7.486380e-02	ci left: 1.044170e-02	ci right 1.125770e-02	k: 2711	n:250000
Cons ci ratio: 5.331327e-03	ci left: 6.819691e-01	ci right 6.856186e-01	k: 170949	n:250000
KS ci ratio: 1.361685e-01	ci left: 3.078964e-03	ci right 3.532671e-03	k: 825	n:250000
KIAA0146   250000 perm   83 sec   (3021 perm/sec)   p_kst 3.300000e-03   p_cons 6.837960e-01   p_joint 1.084400e-02

Joint ci ratio: 4.987509e-02	ci left: 2.262856e-02	ci right 2.378980e-02	k: 6033	n:260000
Cons ci ratio: 5.228865e-03	ci left: 6.819162e-01	ci right 6.854950e-01	k: 177764	n:260000
KS ci ratio: 1.332940e-01	ci left: 3.094339e-03	ci right 3.539923e-03	k: 861	n:260000
KIAA0146   260000 perm   87 sec   (2982 perm/sec)   p_kst 3.311538e-03   p_cons 6.837077e-01   p_joint 2.320385e-02

Joint ci ratio: 4.898311e-02	ci left: 2.260251e-02	ci right 2.374109e-02	k: 6255	n:270000
Cons ci ratio: 5.129894e-03	ci left: 6.820534e-01	ci right 6.855649e-01	k: 184629	n:270000
KS ci ratio: 1.312557e-01	ci left: 3.076423e-03	ci right 3.512125e-03	k: 888	n:270000
KIAA0146   270000 perm   92 sec   (2946 perm/sec)   p_kst 3.288889e-03   p_cons 6.838111e-01   p_joint 2.316667e-02

Joint ci ratio: 7.080379e-02	ci left: 1.044500e-02	ci right 1.121517e-02	k: 3031	n:280000
Cons ci ratio: 5.037669e-03	ci left: 6.820668e-01	ci right 6.855151e-01	k: 191462	n:280000
KS ci ratio: 1.288854e-01	ci left: 3.080573e-03	ci right 3.508381e-03	k: 921	n:280000
KIAA0146   280000 perm   96 sec   (2906 perm/sec)   p_kst 3.289286e-03   p_cons 6.837929e-01   p_joint 1.082500e-02

Joint ci ratio: 6.950842e-02	ci left: 1.047104e-02	ci right 1.122844e-02	k: 3145	n:290000
Cons ci ratio: 4.952180e-03	ci left: 6.819107e-01	ci right 6.852994e-01	k: 198246	n:290000
KS ci ratio: 1.270400e-01	ci left: 3.064468e-03	ci right 3.483487e-03	k: 948	n:290000
KIAA0146   290000 perm   101 sec   (2869 perm/sec)   p_kst 3.268966e-03   p_cons 6.836069e-01   p_joint 1.084483e-02

Joint ci ratio: 6.813389e-02	ci left: 1.054134e-02	ci right 1.128815e-02	k: 3273	n:300000
Cons ci ratio: 4.869172e-03	ci left: 6.819190e-01	ci right 6.852508e-01	k: 205076	n:300000
KS ci ratio: 1.241285e-01	ci left: 3.107611e-03	ci right 3.522075e-03	k: 993	n:300000
KIAA0146   300000 perm   106 sec   (2826 perm/sec)   p_kst 3.310000e-03   p_cons 6.835867e-01   p_joint 1.091000e-02

Joint ci ratio: 6.704733e-02	ci left: 1.054063e-02	ci right 1.127501e-02	k: 3380	n:310000
Cons ci ratio: 4.789096e-03	ci left: 6.820274e-01	ci right 6.853047e-01	k: 211937	n:310000
KS ci ratio: 1.219988e-01	ci left: 3.116794e-03	ci right 3.524836e-03	k: 1028	n:310000
KIAA0146   310000 perm   111 sec   (2789 perm/sec)   p_kst 3.316129e-03   p_cons 6.836677e-01   p_joint 1.090323e-02

Joint ci ratio: 6.608781e-02	ci left: 1.051545e-02	ci right 1.123720e-02	k: 3479	n:320000
Cons ci ratio: 4.712538e-03	ci left: 6.821575e-01	ci right 6.853829e-01	k: 218807	n:320000
KS ci ratio: 1.203731e-01	ci left: 3.104241e-03	ci right 3.504838e-03	k: 1056	n:320000
KIAA0146   320000 perm   116 sec   (2751 perm/sec)   p_kst 3.300000e-03   p_cons 6.837719e-01   p_joint 1.087187e-02

Joint ci ratio: 6.513155e-02	ci left: 1.050380e-02	ci right 1.121392e-02	k: 3582	n:330000
Cons ci ratio: 4.639342e-03	ci left: 6.822984e-01	ci right 6.854741e-01	k: 225683	n:330000
KS ci ratio: 1.188656e-01	ci left: 3.089541e-03	ci right 3.482897e-03	k: 1083	n:330000
KIAA0146   330000 perm   122 sec   (2715 perm/sec)   p_kst 3.281818e-03   p_cons 6.838879e-01   p_joint 1.085455e-02

Joint ci ratio: 6.426854e-02	ci left: 1.047554e-02	ci right 1.117401e-02	k: 3679	n:340000
Cons ci ratio: 4.573122e-03	ci left: 6.820838e-01	ci right 6.852131e-01	k: 232441	n:340000
KS ci ratio: 1.173604e-01	ci left: 3.078591e-03	ci right 3.465246e-03	k: 1111	n:340000
KIAA0146   340000 perm   127 sec   (2684 perm/sec)   p_kst 3.267647e-03   p_cons 6.836500e-01   p_joint 1.082059e-02

Joint ci ratio: 6.338806e-02	ci left: 1.046582e-02	ci right 1.115374e-02	k: 3782	n:350000
Cons ci ratio: 4.507899e-03	ci left: 6.820506e-01	ci right 6.851350e-01	k: 239258	n:350000
KS ci ratio: 1.157075e-01	ci left: 3.079395e-03	ci right 3.460331e-03	k: 1143	n:350000
KIAA0146   350000 perm   132 sec   (2652 perm/sec)   p_kst 3.265714e-03   p_cons 6.835943e-01   p_joint 1.080571e-02

Joint ci ratio: 6.253467e-02	ci left: 1.045945e-02	ci right 1.113735e-02	k: 3886	n:360000
Cons ci ratio: 4.444191e-03	ci left: 6.821363e-01	ci right 6.851774e-01	k: 246117	n:360000
KS ci ratio: 1.143177e-01	ci left: 3.069396e-03	ci right 3.444226e-03	k: 1171	n:360000
KIAA0146   360000 perm   138 sec   (2614 perm/sec)   p_kst 3.252778e-03   p_cons 6.836583e-01   p_joint 1.079444e-02

Joint ci ratio: 6.169141e-02	ci left: 1.046146e-02	ci right 1.113002e-02	k: 3993	n:370000
Cons ci ratio: 4.382561e-03	ci left: 6.822719e-01	ci right 6.852712e-01	k: 252996	n:370000
KS ci ratio: 1.128825e-01	ci left: 3.065216e-03	ci right 3.434524e-03	k: 1201	n:370000
KIAA0146   370000 perm   144 sec   (2575 perm/sec)   p_kst 3.245946e-03   p_cons 6.837730e-01   p_joint 1.079189e-02

Joint ci ratio: 6.084388e-02	ci left: 1.047638e-02	ci right 1.113638e-02	k: 4105	n:380000
Cons ci ratio: 4.327083e-03	ci left: 6.820343e-01	ci right 6.849945e-01	k: 259736	n:380000
KS ci ratio: 1.109592e-01	ci left: 3.091987e-03	ci right 3.457758e-03	k: 1243	n:380000
KIAA0146   380000 perm   150 sec   (2539 perm/sec)   p_kst 3.271053e-03   p_cons 6.835158e-01   p_joint 1.080263e-02

Joint ci ratio: 6.005195e-02	ci left: 1.048302e-02	ci right 1.113454e-02	k: 4214	n:390000
Cons ci ratio: 4.271024e-03	ci left: 6.820761e-01	ci right 6.849981e-01	k: 266580	n:390000
KS ci ratio: 1.096886e-01	ci left: 3.085012e-03	ci right 3.445508e-03	k: 1272	n:390000
KIAA0146   390000 perm   156 sec   (2504 perm/sec)   p_kst 3.261538e-03   p_cons 6.835385e-01   p_joint 1.080513e-02

Joint ci ratio: 5.926937e-02	ci left: 1.049677e-02	ci right 1.114035e-02	k: 4326	n:400000
Cons ci ratio: 4.215870e-03	ci left: 6.822413e-01	ci right 6.851261e-01	k: 273474	n:400000
KS ci ratio: 1.084606e-01	ci left: 3.078408e-03	ci right 3.433848e-03	k: 1301	n:400000
KIAA0146   400000 perm   162 sec   (2474 perm/sec)   p_kst 3.252500e-03   p_cons 6.836850e-01   p_joint 1.081500e-02

Joint ci ratio: 5.863021e-02	ci left: 1.046903e-02	ci right 1.110376e-02	k: 4421	n:410000
Cons ci ratio: 4.164371e-03	ci left: 6.822350e-01	ci right 6.850844e-01	k: 280301	n:410000
KS ci ratio: 1.074757e-01	ci left: 3.060279e-03	ci right 3.410215e-03	k: 1325	n:410000
KIAA0146   410000 perm   168 sec   (2439 perm/sec)   p_kst 3.231707e-03   p_cons 6.836610e-01   p_joint 1.078293e-02

Joint ci ratio: 5.790770e-02	ci left: 1.048021e-02	ci right 1.110752e-02	k: 4532	n:420000
Cons ci ratio: 4.114307e-03	ci left: 6.822721e-01	ci right 6.850873e-01	k: 287146	n:420000
KS ci ratio: 1.058895e-01	ci left: 3.080114e-03	ci right 3.426795e-03	k: 1365	n:420000
KIAA0146   420000 perm   174 sec   (2414 perm/sec)   p_kst 3.250000e-03   p_cons 6.836810e-01   p_joint 1.079048e-02

Joint ci ratio: 5.721126e-02	ci left: 1.049091e-02	ci right 1.111106e-02	k: 4643	n:430000
Cons ci ratio: 4.066596e-03	ci left: 6.822448e-01	ci right 6.850271e-01	k: 293964	n:430000
KS ci ratio: 1.045956e-01	ci left: 3.085472e-03	ci right 3.428252e-03	k: 1399	n:430000
KIAA0146   430000 perm   180 sec   (2389 perm/sec)   p_kst 3.253488e-03   p_cons 6.836372e-01   p_joint 1.079767e-02

Joint ci ratio: 5.655138e-02	ci left: 1.049668e-02	ci right 1.110978e-02	k: 4752	n:440000
Cons ci ratio: 4.017381e-03	ci left: 6.825557e-01	ci right 6.853055e-01	k: 300930	n:440000
KS ci ratio: 1.034929e-01	ci left: 3.081755e-03	ci right 3.420293e-03	k: 1429	n:440000
KIAA0146   440000 perm   186 sec   (2364 perm/sec)   p_kst 3.247727e-03   p_cons 6.839318e-01   p_joint 1.080000e-02

Joint ci ratio: 5.590801e-02	ci left: 1.050443e-02	ci right 1.111078e-02	k: 4862	n:450000
Cons ci ratio: 3.971438e-03	ci left: 6.826861e-01	ci right 6.854049e-01	k: 307821	n:450000
KS ci ratio: 1.024244e-01	ci left: 3.078221e-03	ci right 3.412670e-03	k: 1459	n:450000
KIAA0146   450000 perm   192 sec   (2341 perm/sec)   p_kst 3.242222e-03   p_cons 6.840467e-01   p_joint 1.080444e-02

Joint ci ratio: 5.528611e-02	ci left: 1.051188e-02	ci right 1.111169e-02	k: 4972	n:460000
Cons ci ratio: 3.927134e-03	ci left: 6.828001e-01	ci right 6.854889e-01	k: 314707	n:460000
KS ci ratio: 1.011164e-01	ci left: 3.091810e-03	ci right 3.423191e-03	k: 1497	n:460000
KIAA0146   460000 perm   199 sec   (2315 perm/sec)   p_kst 3.254348e-03   p_cons 6.841457e-01   p_joint 1.080870e-02

Joint ci ratio: 5.480454e-02	ci left: 1.047288e-02	ci right 1.106509e-02	k: 5060	n:470000
Cons ci ratio: 3.884566e-03	ci left: 6.828774e-01	ci right 6.855373e-01	k: 321578	n:470000
KS ci ratio: 1.000862e-01	ci left: 3.090325e-03	ci right 3.417974e-03	k: 1528	n:470000
KIAA0146   470000 perm   205 sec   (2293 perm/sec)   p_kst 3.251064e-03   p_cons 6.842085e-01   p_joint 1.076596e-02

Joint ci ratio: 5.420247e-02	ci left: 1.048690e-02	ci right 1.107319e-02	k: 5173	n:480000
Cons ci ratio: 3.843835e-03	ci left: 6.828975e-01	ci right 6.855295e-01	k: 328423	n:480000
KS ci ratio: 9.911882e-02	ci left: 3.086886e-03	ci right 3.410823e-03	k: 1558	n:480000
KIAA0146   480000 perm   212 sec   (2268 perm/sec)   p_kst 3.245833e-03   p_cons 6.842146e-01   p_joint 1.077708e-02

Outputting figure to mutsig2_images.part000000000090/KIAA0146.2_2828_480000_0.0032458_0.68421_0.010777.png
                gene_name: KIAA0146
               theta_stop: 0.099 
                    nperm: 480000 
                     p_ks: 0.0032 
        ci_ks_bounds_left: 0.0031 
       ci_ks_bounds_right: 0.0034 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.011 
     ci_joint_bounds_left: 0.010 
    ci_joint_bounds_right: 0.011 

Current progress: 44 percent done.
KIAA0182
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.429577e-03	ci left: 9.906076e-01	ci right 9.940963e-01	k: 9925	n:10000
Cons ci ratio: 6.285915e-02	ci left: 2.711159e-01	ci right 2.888125e-01	k: 2799	n:10000
KS ci ratio: 1.682287e-02	ci left: 8.372473e-01	ci right 8.515515e-01	k: 8445	n:10000
KIAA0182   10000 perm   2 sec   (4912 perm/sec)   p_kst 8.445000e-01   p_cons 2.799000e-01   p_joint 9.925000e-01

Outputting figure to mutsig2_images.part000000000090/KIAA0182.2_3718_10000_0.8445_0.2799_0.9925.png
                gene_name: KIAA0182
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.29 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 56 percent done.
KIAA0368
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.647465e-02	ci left: 5.260662e-01	ci right 5.457129e-01	k: 5359	n:10000
Cons ci ratio: 8.114669e-02	ci left: 1.814664e-01	ci right 1.969151e-01	k: 1891	n:10000
KS ci ratio: 5.125049e-02	ci left: 3.595318e-01	ci right 3.785446e-01	k: 3690	n:10000
KIAA0368   10000 perm   3 sec   (3394 perm/sec)   p_kst 3.690000e-01   p_cons 1.891000e-01   p_joint 5.359000e-01

Outputting figure to mutsig2_images.part000000000090/KIAA0368.2_6258_10000_0.369_0.1891_0.5359.png
                gene_name: KIAA0368
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 67 percent done.
KIAA1033
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: 5.181638e-02	ci left: 3.544610e-01	ci right 3.734183e-01	k: 3639	n:10000
KS ci ratio: 2.758361e-02	ci left: 6.594774e-01	ci right 6.780242e-01	k: 6688	n:10000
KIAA1033   10000 perm   2 sec   (4274 perm/sec)   p_kst 6.688000e-01   p_cons 3.639000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000090/KIAA1033.2_3654_10000_0.6688_0.3639_1.png
                gene_name: KIAA1033
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.68 
                   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: 78 percent done.
KIAA1109
Processing conservation and coverage...
65% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.739775e-03	ci left: 9.761027e-01	ci right 9.818135e-01	k: 9791	n:10000
Cons ci ratio: 5.012518e-02	ci left: 3.698758e-01	ci right 3.889945e-01	k: 3794	n:10000
KS ci ratio: 4.000985e-02	ci left: 4.798565e-01	ci right 4.995495e-01	k: 4897	n:10000
KIAA1109   10000 perm   4 sec   (2255 perm/sec)   p_kst 4.897000e-01   p_cons 3.794000e-01   p_joint 9.791000e-01

Outputting figure to mutsig2_images.part000000000090/KIAA1109.2_15354_10000_0.4897_0.3794_0.9791.png
                gene_name: KIAA1109
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 89 percent done.
KIAA1468
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.822146e-02	ci left: 3.881880e-01	ci right 4.074716e-01	k: 3978	n:10000
Cons ci ratio: 1.687404e-01	ci left: 4.686539e-02	ci right 5.559839e-02	k: 511	n:10000
KS ci ratio: 7.113958e-03	ci left: 9.645717e-01	ci right 9.715522e-01	k: 9682	n:10000
KIAA1468   10000 perm   2 sec   (4932 perm/sec)   p_kst 9.682000e-01   p_cons 5.110000e-02   p_joint 3.978000e-01

Joint ci ratio: 7.492109e-03	ci left: 9.283716e-01	ci right 9.354022e-01	k: 18639	n:20000
Cons ci ratio: 1.222419e-01	ci left: 4.590339e-02	ci right 5.192862e-02	k: 977	n:20000
KS ci ratio: 5.026891e-03	ci left: 9.656741e-01	ci right 9.705885e-01	k: 19364	n:20000
KIAA1468   20000 perm   5 sec   (4423 perm/sec)   p_kst 9.682000e-01   p_cons 4.885000e-02   p_joint 9.319500e-01

Joint ci ratio: 5.003155e-03	ci left: 9.509880e-01	ci right 9.557903e-01	k: 28603	n:30000
Cons ci ratio: 9.966803e-02	ci left: 4.658437e-02	ci right 5.150343e-02	k: 1470	n:30000
KS ci ratio: 4.103503e-03	ci left: 9.661519e-01	ci right 9.701568e-01	k: 29046	n:30000
KIAA1468   30000 perm   7 sec   (4219 perm/sec)   p_kst 9.682000e-01   p_cons 4.900000e-02   p_joint 9.534333e-01

Outputting figure to mutsig2_images.part000000000090/KIAA1468.2_3767_30000_0.9682_0.049_0.95343.png
                gene_name: KIAA1468
               theta_stop: 0.100 
                    nperm: 30000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.049 
      ci_cons_bounds_left: 0.047 
     ci_cons_bounds_right: 0.052 
                  p_joint: 0.95 
     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.165.3896/
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/181708/iteration1/scatter.0000000090
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 90 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120024: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000091> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:46:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000091.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000091.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 91  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    181.31 sec.
    Max Memory :      1530 MB
    Max Swap   :      3944 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.165.3896/
-whichjob
91
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 91: processing genes 8143 - 8233
Calculating significance of each gene.
Using projection method.
8143	KIAA1529	3.739043e-01
8144	KIAA1530	3.004199e-01
8145	KIAA1539	1
8146	KIAA1543	3.334409e-01
8147	KIAA1549	1
8148	KIAA1586	1
8149	KIAA1598	1
8150	KIAA1609	1
8151	KIAA1614	3.500457e-01
8152	KIAA1632	2.533492e-01
8153	KIAA1644	1
8154	KIAA1683	1
8155	KIAA1704	5.254614e-02
8156	KIAA1712	1
8157	KIAA1715	1
8158	KIAA1737	1
8159	KIAA1751	1
8160	KIAA1755	1
8161	KIAA1797	5.364104e-01
8162	KIAA1804	1
8163	KIAA1826	3.860514e-03
8164	KIAA1841	8.224603e-02
8165	KIAA1919	1
8166	KIAA1949	4.535090e-02
8167	KIAA1958	1
8168	KIAA1967	1
8169	KIAA1984	1
8170	KIAA2013	1
8171	KIAA2018	2.846015e-01
8172	KIAA2022	1.330297e-02
8173	KIAA2026	4.455540e-01
8174	KIDINS220	3.053814e-01
8175	KIF11	4.272337e-01
8176	KIF12	1
8177	KIF13A	6.352792e-02
8178	KIF13B	1
8179	KIF14	3.586003e-01
8180	KIF15	1.823748e-01
8181	KIF16B	1
8182	KIF17	1
8183	KIF18A	2.971032e-02
8184	KIF18B	1
8185	KIF19	1
8186	KIF1A	3.419081e-01
8187	KIF1B	1
8188	KIF1C	2.663167e-01
8189	KIF20A	1
8190	KIF20B	1
8191	KIF21A	1.572754e-01
8192	KIF21B	2.304677e-01
8193	KIF22	1
8194	KIF23	1
8195	KIF24	1
8196	KIF25	1
8197	KIF26B	1
8198	KIF27	4.183450e-01
8199	KIF2A	1
8200	KIF2B	1
8201	KIF2C	2.300132e-01
8202	KIF3A	1
8203	KIF3B	1
8204	KIF3C	3.454039e-01
8205	KIF4A	1
8206	KIF4B	1
8207	KIF5A	1
8208	KIF5B	1
8209	KIF5C	1
8210	KIF6	1.582557e-01
8211	KIF7	2.792488e-01
8212	KIF9	1
8213	KIFAP3	2.928493e-01
8214	KIFC1	1
8215	KIFC2	9.515996e-02
8216	KIFC3	1
8217	KIN	1
8218	KIR2DL1	1
8219	KIR2DL3	1
8220	KIR2DL4	1
8221	KIR2DS4	1
8222	KIR3DL1	9.082933e-02
8223	KIR3DL2	1
8224	KIR3DL3	1
8225	KIR3DP1	1
8226	KIRREL	1
8227	KIRREL2	3.027219e-01
8228	KIRREL3	1
8229	KISS1	1
8230	KIT	1
8231	KITLG	1
8232	KL	1
8233	KLB	1
Done

Running MutSig 2:
Scatter job 91: processing genes 8143 - 8233
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KIAA2022
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.866778e-02	ci left: 6.420678e-01	ci right 6.608439e-01	k: 6515	n:10000
Cons ci ratio: 4.560629e-02	ci left: 4.150847e-01	ci right 4.345591e-01	k: 4248	n:10000
KS ci ratio: 3.466525e-02	ci left: 5.513070e-01	ci right 5.708574e-01	k: 5611	n:10000
KIAA2022   10000 perm   4 sec   (2824 perm/sec)   p_kst 5.611000e-01   p_cons 4.248000e-01   p_joint 6.515000e-01

Outputting figure to mutsig2_images.part000000000091/KIAA2022.3_4563_10000_0.5611_0.4248_0.6515.png
                gene_name: KIAA2022
               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: 0.42 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.65 
     ci_joint_bounds_left: 0.64 
    ci_joint_bounds_right: 0.66 

Current progress: 10 percent done.
KIAA1543
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.520741e-01	ci left: 5.754436e-02	ci right 6.711256e-02	k: 622	n:10000
Cons ci ratio: 1.025873e-01	ci left: 1.208265e-01	ci right 1.339914e-01	k: 1273	n:10000
KS ci ratio: 1.824960e-01	ci left: 4.006355e-02	ci right 4.820470e-02	k: 440	n:10000
KIAA1543   10000 perm   2 sec   (4736 perm/sec)   p_kst 4.400000e-02   p_cons 1.273000e-01   p_joint 6.220000e-02

Joint ci ratio: 1.022936e-01	ci left: 6.489067e-02	ci right 7.193544e-02	k: 1367	n:20000
Cons ci ratio: 7.280364e-02	ci left: 1.219718e-01	ci right 1.312370e-01	k: 2531	n:20000
KS ci ratio: 1.301312e-01	ci left: 4.056926e-02	ci right 4.626445e-02	k: 867	n:20000
KIAA1543   20000 perm   6 sec   (3332 perm/sec)   p_kst 4.335000e-02   p_cons 1.265500e-01   p_joint 6.835000e-02

Joint ci ratio: 8.590647e-02	ci left: 6.210525e-02	ci right 6.771271e-02	k: 1946	n:30000
Cons ci ratio: 5.639746e-02	ci left: 1.347744e-01	ci right 1.426291e-01	k: 4160	n:30000
KS ci ratio: 1.075985e-01	ci left: 4.008265e-02	ci right 4.467317e-02	k: 1270	n:30000
KIAA1543   30000 perm   10 sec   (3028 perm/sec)   p_kst 4.233333e-02   p_cons 1.386667e-01   p_joint 6.486667e-02

Joint ci ratio: 5.766866e-02	ci left: 1.005559e-01	ci right 1.065518e-01	k: 4141	n:40000
Cons ci ratio: 4.910412e-02	ci left: 1.340401e-01	ci right 1.408126e-01	k: 5496	n:40000
KS ci ratio: 9.323129e-02	ci left: 4.034835e-02	ci right 4.431844e-02	k: 1692	n:40000
KIAA1543   40000 perm   12 sec   (3218 perm/sec)   p_kst 4.230000e-02   p_cons 1.374000e-01   p_joint 1.035250e-01

Outputting figure to mutsig2_images.part000000000091/KIAA1543.2_3907_40000_0.0423_0.1374_0.10353.png
                gene_name: KIAA1543
               theta_stop: 0.093 
                    nperm: 40000 
                     p_ks: 0.042 
        ci_ks_bounds_left: 0.040 
       ci_ks_bounds_right: 0.044 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.10 
     ci_joint_bounds_left: 0.10 
    ci_joint_bounds_right: 0.11 

Current progress: 20 percent done.
KIAA1632
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.086125e-02	ci left: 7.710409e-01	ci right 7.873961e-01	k: 7793	n:10000
Cons ci ratio: 2.617518e-02	ci left: 6.824434e-01	ci right 7.006449e-01	k: 6916	n:10000
KS ci ratio: 3.624069e-02	ci left: 5.292700e-01	ci right 5.489072e-01	k: 5391	n:10000
KIAA1632   10000 perm   3 sec   (3892 perm/sec)   p_kst 5.391000e-01   p_cons 6.916000e-01   p_joint 7.793000e-01

Outputting figure to mutsig2_images.part000000000091/KIAA1632.2_7916_10000_0.5391_0.6916_0.7793.png
                gene_name: KIAA1632
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.69 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.70 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.79 

Current progress: 30 percent done.
KIAA1826
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: 1.068561e-02	ci left: 9.257524e-01	ci right 9.357949e-01	k: 9309	n:10000
KS ci ratio: 6.429240e-02	ci left: 2.622072e-01	ci right 2.797264e-01	k: 2709	n:10000
KIAA1826   10000 perm   2 sec   (5325 perm/sec)   p_kst 2.709000e-01   p_cons 9.309000e-01   p_joint 8.675000e-01

Outputting figure to mutsig2_images.part000000000091/KIAA1826.2_1046_10000_0.2709_0.9309_0.8675.png
                gene_name: KIAA1826
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

Current progress: 40 percent done.
KIAA2018
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: 5.274675e-02	ci left: 3.463103e-01	ci right 3.651738e-01	k: 3557	n:10000
KS ci ratio: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
KIAA2018   10000 perm   2 sec   (4339 perm/sec)   p_kst 1   p_cons 3.557000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000091/KIAA2018.2_6758_10000_1_0.3557_1.png
                gene_name: KIAA2018
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 1 
        ci_ks_bounds_left: 1.00 
       ci_ks_bounds_right: 1 
                   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: 50 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: 7.662992e-02	ci left: 1.993910e-01	ci right 2.153799e-01	k: 2073	n:10000
KS ci ratio: 1.038389e-02	ci left: 9.294731e-01	ci right 9.392720e-01	k: 9345	n:10000
KIF13A   10000 perm   2 sec   (4743 perm/sec)   p_kst 9.345000e-01   p_cons 2.073000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000091/KIF13A.2_5599_10000_0.9345_0.2073_1.png
                gene_name: KIF13A
               theta_stop: 0.077 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.22 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
KIF15
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: 7.852670e-03	ci left: 9.575422e-01	ci right 9.651860e-01	k: 9615	n:10000
KS ci ratio: 2.234819e-02	ci left: 7.461435e-01	ci right 7.631079e-01	k: 7547	n:10000
KIF15   10000 perm   2 sec   (5149 perm/sec)   p_kst 7.547000e-01   p_cons 9.615000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000091/KIF15.2_4307_10000_0.7547_0.9615_1.png
                gene_name: KIF15
               theta_stop: 0.022 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.96 
     ci_cons_bounds_right: 0.97 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 70 percent done.
KIF18A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.127142e-02	ci left: 9.183224e-01	ci right 9.288293e-01	k: 9237	n:10000
Cons ci ratio: 1.092424e-02	ci left: 9.227580e-01	ci right 9.329911e-01	k: 9280	n:10000
KS ci ratio: 2.988391e-02	ci left: 6.228625e-01	ci right 6.418603e-01	k: 6324	n:10000
KIF18A   10000 perm   2 sec   (5308 perm/sec)   p_kst 6.324000e-01   p_cons 9.280000e-01   p_joint 9.237000e-01

Outputting figure to mutsig2_images.part000000000091/KIF18A.2_2761_10000_0.6324_0.928_0.9237.png
                gene_name: KIF18A
               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: 0.92 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

Current progress: 80 percent done.
KIF21A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.755249e-02	ci left: 6.599808e-01	ci right 6.785206e-01	k: 6693	n:10000
Cons ci ratio: 3.801281e-02	ci left: 5.054515e-01	ci right 5.251396e-01	k: 5153	n:10000
KS ci ratio: 4.152849e-02	ci left: 4.612762e-01	ci right 4.809407e-01	k: 4711	n:10000
KIF21A   10000 perm   3 sec   (3709 perm/sec)   p_kst 4.711000e-01   p_cons 5.153000e-01   p_joint 6.693000e-01

Outputting figure to mutsig2_images.part000000000091/KIF21A.2_5177_10000_0.4711_0.5153_0.6693.png
                gene_name: KIF21A
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.67 
     ci_joint_bounds_left: 0.66 
    ci_joint_bounds_right: 0.68 

Current progress: 90 percent done.
KIRREL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.546038e-01	ci left: 5.571306e-02	ci right 6.514503e-02	k: 603	n:10000
Cons ci ratio: 1.220526e-01	ci left: 8.776567e-02	ci right 9.927239e-02	k: 934	n:10000
KS ci ratio: 1.121871e-01	ci left: 1.026640e-01	ci right 1.149650e-01	k: 1087	n:10000
KIRREL2   10000 perm   2 sec   (5902 perm/sec)   p_kst 1.087000e-01   p_cons 9.340000e-02   p_joint 6.030000e-02

Joint ci ratio: 1.826955e-01	ci left: 2.044155e-02	ci right 2.459888e-02	k: 449	n:20000
Cons ci ratio: 8.452258e-02	ci left: 9.298115e-02	ci right 1.012364e-01	k: 1941	n:20000
KS ci ratio: 8.068851e-02	ci left: 1.012751e-01	ci right 1.098399e-01	k: 2110	n:20000
KIRREL2   20000 perm   4 sec   (5278 perm/sec)   p_kst 1.055000e-01   p_cons 9.705000e-02   p_joint 2.245000e-02

Joint ci ratio: 8.913233e-02	ci left: 5.786080e-02	ci right 6.329135e-02	k: 1816	n:30000
Cons ci ratio: 6.862217e-02	ci left: 9.472364e-02	ci right 1.014877e-01	k: 2942	n:30000
KS ci ratio: 6.600472e-02	ci left: 1.017170e-01	ci right 1.086930e-01	k: 3155	n:30000
KIRREL2   30000 perm   6 sec   (5085 perm/sec)   p_kst 1.051667e-01   p_cons 9.806667e-02   p_joint 6.053333e-02

Outputting figure to mutsig2_images.part000000000091/KIRREL2.2_2231_30000_0.10517_0.098067_0.060533.png
                gene_name: KIRREL2
               theta_stop: 0.089 
                    nperm: 30000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.098 
      ci_cons_bounds_left: 0.095 
     ci_cons_bounds_right: 0.10 
                  p_joint: 0.061 
     ci_joint_bounds_left: 0.058 
    ci_joint_bounds_right: 0.063 

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.165.3896/
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/181708/iteration1/scatter.0000000091
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 91 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120027: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000092> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:45:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000092.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000092.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 92  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    104.65 sec.
    Max Memory :      1120 MB
    Max Swap   :      3793 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.165.3896/
-whichjob
92
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 92: processing genes 8234 - 8323
Calculating significance of each gene.
Using projection method.
8234	KLC1	1.593376e-01
8235	KLC2	1
8236	KLC3	1
8237	KLC4	1
8238	KLF1	1
8239	KLF10	1
8240	KLF11	1
8241	KLF12	1
8242	KLF13	1
8243	KLF14	1
8244	KLF15	1
8245	KLF16	1
8246	KLF17	1
8247	KLF3	1
8248	KLF4	1
8249	KLF5	4.780156e-03
8250	KLF6	1
8251	KLF7	1
8252	KLF8	1
8253	KLF9	1
8254	KLHDC1	1
8255	KLHDC10	1
8256	KLHDC2	1.486155e-01
8257	KLHDC3	1
8258	KLHDC4	8.906399e-02
8259	KLHDC5	1
8260	KLHDC7A	1
8261	KLHDC7B	6.079946e-02
8262	KLHDC8A	1.222005e-01
8263	KLHDC8B	1
8264	KLHDC9	1
8265	KLHL1	1
8266	KLHL10	1
8267	KLHL11	2.633662e-01
8268	KLHL12	1
8269	KLHL13	9.396765e-02
8270	KLHL14	1
8271	KLHL15	1
8272	KLHL17	5.087320e-02
8273	KLHL18	1
8274	KLHL2	4.955242e-02
8275	KLHL20	1
8276	KLHL21	1
8277	KLHL22	1
8278	KLHL23	8.530059e-02
8279	KLHL24	1
8280	KLHL25	1
8281	KLHL26	1
8282	KLHL28	1
8283	KLHL3	1
8284	KLHL30	1
8285	KLHL31	1
8286	KLHL32	1
8287	KLHL34	7.858983e-02
8288	KLHL35	1
8289	KLHL36	1
8290	KLHL38	1
8291	KLHL4	1
8292	KLHL5	1
8293	KLHL6	2.464144e-01
8294	KLHL7	2.136993e-01
8295	KLHL8	1
8296	KLHL9	1
8297	KLK1	4.628343e-02
8298	KLK10	1
8299	KLK11	1
8300	KLK12	3.856627e-02
8301	KLK13	1
8302	KLK14	1
8303	KLK15	1
8304	KLK2	1
8305	KLK3	1
8306	KLK4	1
8307	KLK5	6.399549e-02
8308	KLK6	1
8309	KLK7	1
8310	KLK8	1
8311	KLK9	1
8312	KLKB1	1
8313	KLRAQ1	1
8314	KLRB1	1
8315	KLRC1	1
8316	KLRC2	1
8317	KLRC3	1
8318	KLRC4	1
8319	KLRD1	1
8320	KLRF1	1
8321	KLRG1	1
8322	KLRG2	1
8323	KLRK1	1
Done

Running MutSig 2:
Scatter job 92: processing genes 8234 - 8323
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KLF5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.163782e-02	ci left: 3.560517e-01	ci right 3.750267e-01	k: 3655	n:10000
Cons ci ratio: 5.637744e-02	ci left: 3.166160e-01	ci right 3.350856e-01	k: 3258	n:10000
KS ci ratio: 1.377594e-01	ci left: 6.971834e-02	ci right 8.013090e-02	k: 748	n:10000
KLF5   10000 perm   2 sec   (5784 perm/sec)   p_kst 7.480000e-02   p_cons 3.258000e-01   p_joint 3.655000e-01

Joint ci ratio: 5.449296e-02	ci left: 1.999181e-01	ci right 2.111676e-01	k: 4110	n:20000
Cons ci ratio: 3.996036e-02	ci left: 3.183107e-01	ci right 3.313403e-01	k: 6496	n:20000
KS ci ratio: 9.958521e-02	ci left: 6.830848e-02	ci right 7.551658e-02	k: 1437	n:20000
KLF5   20000 perm   6 sec   (3298 perm/sec)   p_kst 7.185000e-02   p_cons 3.248000e-01   p_joint 2.055000e-01

Outputting figure to mutsig2_images.part000000000092/KLF5.2_1390_20000_0.07185_0.3248_0.2055.png
                gene_name: KLF5
               theta_stop: 0.100 
                    nperm: 20000 
                     p_ks: 0.072 
        ci_ks_bounds_left: 0.068 
       ci_ks_bounds_right: 0.076 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.21 

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.165.3896/
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/181708/iteration1/scatter.0000000092
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 92 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1417>
Subject: Job 1120029: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1417>, 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/181708/iteration1/scatter.0000000093> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:46:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000093.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000093.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 93  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    153.92 sec.
    Max Memory :      1341 MB
    Max Swap   :      3863 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.165.3896/
-whichjob
93
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 93: processing genes 8324 - 8414
Calculating significance of each gene.
Using projection method.
8324	KMO	1
8325	KNCN	1
8326	KNDC1	1
8327	KNG1	1.846057e-01
8328	KNTC1	1.064616e-01
8329	KPNA1	1.239981e-02
8330	KPNA2	1.281905e-01
8331	KPNA3	1.816400e-02
8332	KPNA4	1
8333	KPNA5	9.903680e-02
8334	KPNA6	1
8335	KPNB1	1.583333e-01
8336	KPRP	1.106120e-01
8337	KPTN	1
8338	KRAS	1
8339	KRBA1	1
8340	KRBA2	1
8341	KRCC1	1
8342	KREMEN1	1
8343	KREMEN2	1
8344	KRI1	1
8345	KRIT1	1
8346	KRR1	1
8347	KRT1	1
8348	KRT10	1
8349	KRT12	1
8350	KRT13	1
8351	KRT14	1
8352	KRT15	1
8353	KRT16	1
8354	KRT17	1
8355	KRT18	1
8356	KRT19	1
8357	KRT2	1
8358	KRT20	1
8359	KRT222	1
8360	KRT23	1
8361	KRT24	2.165119e-01
8362	KRT25	1
8363	KRT26	1
8364	KRT27	1
8365	KRT28	1
8366	KRT3	1
8367	KRT31	2.104731e-01
8368	KRT32	3.927466e-02
8369	KRT33A	1
8370	KRT33B	1
8371	KRT34	1
8372	KRT35	1
8373	KRT36	1
8374	KRT37	1
8375	KRT38	1
8376	KRT39	1
8377	KRT4	1
8378	KRT40	1
8379	KRT5	1
8380	KRT6A	1
8381	KRT6B	1
8382	KRT6C	1
8383	KRT7	1
8384	KRT71	2.050118e-01
8385	KRT72	1
8386	KRT73	1
8387	KRT74	2.030451e-01
8388	KRT75	1
8389	KRT76	1.916333e-01
8390	KRT77	1
8391	KRT78	4.022207e-02
8392	KRT79	1.243122e-01
8393	KRT8	1
8394	KRT80	1
8395	KRT81	1
8396	KRT82	1
8397	KRT83	1
8398	KRT84	1
8399	KRT85	1
8400	KRT86	1
8401	KRT9	1
8402	KRTAP1-1	1
8403	KRTAP1-3	1
8404	KRTAP1-5	1
8405	KRTAP10-1	1
8406	KRTAP10-10	1
8407	KRTAP10-11	1
8408	KRTAP10-12	1
8409	KRTAP10-2	1
8410	KRTAP10-3	1
8411	KRTAP10-4	1
8412	KRTAP10-5	1
8413	KRTAP10-6	1
8414	KRTAP10-7	1
Done

Running MutSig 2:
Scatter job 93: processing genes 8324 - 8414
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KPNA3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.543425e-02	ci left: 2.553802e-01	ci right 2.727574e-01	k: 2640	n:10000
Cons ci ratio: 4.906704e-02	ci left: 3.799258e-01	ci right 3.991386e-01	k: 3895	n:10000
KS ci ratio: 9.008395e-02	ci left: 1.519811e-01	ci right 1.664180e-01	k: 1591	n:10000
KPNA3   10000 perm   2 sec   (5400 perm/sec)   p_kst 1.591000e-01   p_cons 3.895000e-01   p_joint 2.640000e-01

Outputting figure to mutsig2_images.part000000000093/KPNA3.4_1634_10000_0.1591_0.3895_0.264.png
                gene_name: KPNA3
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.26 
     ci_joint_bounds_left: 0.26 
    ci_joint_bounds_right: 0.27 

Current progress: 25 percent done.
KNTC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.078422e-01	ci left: 1.103719e-01	ci right 1.230523e-01	k: 1166	n:10000
Cons ci ratio: 3.944572e-02	ci left: 4.869525e-01	ci right 5.066494e-01	k: 4968	n:10000
KS ci ratio: 1.658582e-01	ci left: 4.849762e-02	ci right 5.736510e-02	k: 528	n:10000
KNTC1   10000 perm   3 sec   (3517 perm/sec)   p_kst 5.280000e-02   p_cons 4.968000e-01   p_joint 1.166000e-01

Joint ci ratio: 4.656878e-02	ci left: 2.554693e-01	ci right 2.677001e-01	k: 5231	n:20000
Cons ci ratio: 2.786100e-02	ci left: 4.904464e-01	ci right 5.043544e-01	k: 9948	n:20000
KS ci ratio: 1.137492e-01	ci left: 5.285323e-02	ci right 5.927660e-02	k: 1120	n:20000
KNTC1   20000 perm   6 sec   (3268 perm/sec)   p_kst 5.600000e-02   p_cons 4.974000e-01   p_joint 2.615500e-01

Joint ci ratio: 5.765029e-02	ci left: 1.296703e-01	ci right 1.374009e-01	k: 4005	n:30000
Cons ci ratio: 2.289962e-02	ci left: 4.884266e-01	ci right 4.997745e-01	k: 14823	n:30000
KS ci ratio: 9.259969e-02	ci left: 5.375070e-02	ci right 5.900230e-02	k: 1690	n:30000
KNTC1   30000 perm   10 sec   (3158 perm/sec)   p_kst 5.633333e-02   p_cons 4.941000e-01   p_joint 1.335000e-01

Outputting figure to mutsig2_images.part000000000093/KNTC1.3_6882_30000_0.056333_0.4941_0.1335.png
                gene_name: KNTC1
               theta_stop: 0.093 
                    nperm: 30000 
                     p_ks: 0.056 
        ci_ks_bounds_left: 0.054 
       ci_ks_bounds_right: 0.059 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 50 percent done.
KPNA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.083508e-02	ci left: 4.696656e-01	ci right 4.893464e-01	k: 4795	n:10000
Cons ci ratio: 1.740181e-02	ci left: 8.279846e-01	ci right 8.426195e-01	k: 8354	n:10000
KS ci ratio: 4.332111e-02	ci left: 4.403148e-01	ci right 4.599142e-01	k: 4501	n:10000
KPNA1   10000 perm   2 sec   (6344 perm/sec)   p_kst 4.501000e-01   p_cons 8.354000e-01   p_joint 4.795000e-01

Outputting figure to mutsig2_images.part000000000093/KPNA1.3_1669_10000_0.4501_0.8354_0.4795.png
                gene_name: KPNA1
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.84 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 75 percent done.
KPNA2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.306040e-02	ci left: 5.745671e-01	ci right 5.939838e-01	k: 5843	n:10000
Cons ci ratio: 3.470045e-02	ci left: 5.508059e-01	ci right 5.703587e-01	k: 5606	n:10000
KS ci ratio: 2.583643e-01	ci left: 1.958938e-02	ci right 2.549330e-02	k: 224	n:10000
KPNA2   10000 perm   2 sec   (6119 perm/sec)   p_kst 2.240000e-02   p_cons 5.606000e-01   p_joint 5.843000e-01

Joint ci ratio: 1.327921e-01	ci left: 3.897135e-02	ci right 4.456287e-02	k: 834	n:20000
Cons ci ratio: 2.549655e-02	ci left: 5.347139e-01	ci right 5.485740e-01	k: 10833	n:20000
KS ci ratio: 1.904138e-01	ci left: 1.877169e-02	ci right 2.276934e-02	k: 414	n:20000
KPNA2   20000 perm   4 sec   (5271 perm/sec)   p_kst 2.070000e-02   p_cons 5.416500e-01   p_joint 4.170000e-02

Joint ci ratio: 1.275258e-01	ci left: 2.858305e-02	ci right 3.250857e-02	k: 915	n:30000
Cons ci ratio: 2.009027e-02	ci left: 5.536264e-01	ci right 5.648954e-01	k: 16778	n:30000
KS ci ratio: 1.550290e-01	ci left: 1.924700e-02	ci right 2.251338e-02	k: 625	n:30000
KPNA2   30000 perm   6 sec   (5000 perm/sec)   p_kst 2.083333e-02   p_cons 5.592667e-01   p_joint 3.050000e-02

Joint ci ratio: 1.105968e-01	ci left: 2.876350e-02	ci right 3.215512e-02	k: 1217	n:40000
Cons ci ratio: 1.735098e-02	ci left: 5.557445e-01	ci right 5.654967e-01	k: 22425	n:40000
KS ci ratio: 1.354803e-01	ci left: 1.910956e-02	ci right 2.191066e-02	k: 819	n:40000
KPNA2   40000 perm   8 sec   (4809 perm/sec)   p_kst 2.047500e-02   p_cons 5.606250e-01   p_joint 3.042500e-02

Joint ci ratio: 9.867060e-02	ci left: 2.908813e-02	ci right 3.212669e-02	k: 1529	n:50000
Cons ci ratio: 1.549866e-02	ci left: 5.569170e-01	ci right 5.656359e-01	k: 28064	n:50000
KS ci ratio: 1.204004e-01	ci left: 1.950873e-02	ci right 2.202734e-02	k: 1037	n:50000
KPNA2   50000 perm   11 sec   (4660 perm/sec)   p_kst 2.074000e-02   p_cons 5.612800e-01   p_joint 3.058000e-02

Joint ci ratio: 9.009898e-02	ci left: 2.920369e-02	ci right 3.197529e-02	k: 1834	n:60000
Cons ci ratio: 1.415686e-02	ci left: 5.570012e-01	ci right 5.649595e-01	k: 33659	n:60000
KS ci ratio: 1.102541e-01	ci left: 1.949457e-02	ci right 2.178546e-02	k: 1237	n:60000
KPNA2   60000 perm   13 sec   (4539 perm/sec)   p_kst 2.061667e-02   p_cons 5.609833e-01   p_joint 3.056667e-02

Joint ci ratio: 8.375582e-02	ci left: 2.907054e-02	ci right 3.162573e-02	k: 2123	n:70000
Cons ci ratio: 1.311124e-02	ci left: 5.571282e-01	ci right 5.644953e-01	k: 39257	n:70000
KS ci ratio: 1.024869e-01	ci left: 1.942126e-02	ci right 2.153304e-02	k: 1432	n:70000
KPNA2   70000 perm   16 sec   (4435 perm/sec)   p_kst 2.045714e-02   p_cons 5.608143e-01   p_joint 3.032857e-02

Joint ci ratio: 7.823732e-02	ci left: 2.923337e-02	ci right 3.162584e-02	k: 2433	n:80000
Cons ci ratio: 1.226234e-02	ci left: 5.574526e-01	ci right 5.643430e-01	k: 44872	n:80000
KS ci ratio: 9.585931e-02	ci left: 1.949261e-02	ci right 2.146738e-02	k: 1637	n:80000
KPNA2   80000 perm   18 sec   (4346 perm/sec)   p_kst 2.046250e-02   p_cons 5.609000e-01   p_joint 3.041250e-02

Outputting figure to mutsig2_images.part000000000093/KPNA2.2_1630_80000_0.020463_0.5609_0.030412.png
                gene_name: KPNA2
               theta_stop: 0.096 
                    nperm: 80000 
                     p_ks: 0.020 
        ci_ks_bounds_left: 0.019 
       ci_ks_bounds_right: 0.021 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.030 
     ci_joint_bounds_left: 0.029 
    ci_joint_bounds_right: 0.032 

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.165.3896/
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/181708/iteration1/scatter.0000000093
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 93 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1550>
Subject: Job 1120033: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1550>, 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/181708/iteration1/scatter.0000000094> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:45:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000094.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000094.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 94  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    119.64 sec.
    Max Memory :       855 MB
    Max Swap   :      3636 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.165.3896/
-whichjob
94
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 94: processing genes 8415 - 8504
Calculating significance of each gene.
Using projection method.
8415	KRTAP10-8	1
8416	KRTAP10-9	1
8417	KRTAP11-1	1
8418	KRTAP12-1	1
8419	KRTAP12-2	1
8420	KRTAP12-3	1
8421	KRTAP12-4	1
8422	KRTAP13-1	7.129200e-02
8423	KRTAP13-2	9.485370e-02
8424	KRTAP13-3	1
8425	KRTAP13-4	1
8426	KRTAP15-1	1
8427	KRTAP17-1	1
8428	KRTAP19-1	1
8429	KRTAP19-2	1
8430	KRTAP19-3	1
8431	KRTAP19-4	3.657163e-02
8432	KRTAP19-5	1
8433	KRTAP19-6	1
8434	KRTAP19-7	1
8435	KRTAP19-8	1
8436	KRTAP20-1	1
8437	KRTAP20-2	1
8438	KRTAP21-1	6.365555e-03
8439	KRTAP21-2	1
8440	KRTAP22-1	1.825196e-02
8441	KRTAP23-1	1
8442	KRTAP24-1	3.858298e-03
8443	KRTAP26-1	1
8444	KRTAP27-1	1
8445	KRTAP3-1	1
8446	KRTAP3-2	1
8447	KRTAP3-3	1
8448	KRTAP4-1	1
8449	KRTAP4-11	1
8450	KRTAP4-12	1
8451	KRTAP4-2	1
8452	KRTAP4-3	1
8453	KRTAP4-4	1
8454	KRTAP4-5	1
8455	KRTAP4-7	6.427511e-03
8456	KRTAP4-8	1
8457	KRTAP4-9	4.589749e-04
8458	KRTAP5-1	1
8459	KRTAP5-10	1
8460	KRTAP5-11	1
8461	KRTAP5-2	1
8462	KRTAP5-3	1
8463	KRTAP5-4	1
8464	KRTAP5-5	1.606647e-02
8465	KRTAP5-6	1
8466	KRTAP5-7	1
8467	KRTAP5-8	1
8468	KRTAP5-9	1
8469	KRTAP6-1	1
8470	KRTAP6-2	1
8471	KRTAP6-3	1
8472	KRTAP8-1	1
8473	KRTAP9-2	1
8474	KRTAP9-3	1
8475	KRTAP9-4	1
8476	KRTAP9-8	1
8477	KRTAP9-9	1
8478	KRTCAP2	1
8479	KRTCAP3	1
8480	KRTDAP	1
8481	KSR1	9.950484e-02
8482	KSR2	3.446720e-01
8483	KTELC1	1
8484	KTI12	9.749813e-02
8485	KTN1	1
8486	KY	1
8487	KYNU	1
8488	L1CAM	1
8489	L1TD1	1
8490	L2HGDH	1
8491	L3MBTL	1
8492	L3MBTL2	3.292412e-01
8493	L3MBTL3	1.539585e-01
8494	L3MBTL4	9.568988e-02
8495	LACE1	1
8496	LACRT	1
8497	LACTB	1
8498	LACTB2	1
8499	LAD1	1
8500	LAG3	1
8501	LAGE3	1
8502	LAIR1	1
8503	LAIR2	1
8504	LALBA	1
Done

Running MutSig 2:
Scatter job 94: processing genes 8415 - 8504
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
KRTAP24-1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.887686e-03	ci left: 9.930731e-01	ci right 9.960275e-01	k: 9947	n:10000
Cons ci ratio: 6.772759e-03	ci left: 9.676262e-01	ci right 9.742956e-01	k: 9711	n:10000
KS ci ratio: 3.078365e-02	ci left: 6.088960e-01	ci right 6.280350e-01	k: 6185	n:10000
KRTAP24-1   10000 perm   2 sec   (5783 perm/sec)   p_kst 6.185000e-01   p_cons 9.711000e-01   p_joint 9.947000e-01

Outputting figure to mutsig2_images.part000000000094/KRTAP24-1.2_769_10000_0.6185_0.9711_0.9947.png
                gene_name: KRTAP24-1
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 1.00 

Current progress: 50 percent done.
KRTAP4-9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.424497e-02	ci left: 5.573205e-01	ci right 5.768404e-01	k: 5671	n:10000
Cons ci ratio: 4.535527e-02	ci left: 4.177760e-01	ci right 4.372662e-01	k: 4275	n:10000
KS ci ratio: 5.445811e-02	ci left: 3.319049e-01	ci right 3.505876e-01	k: 3412	n:10000
KRTAP4-9   10000 perm   2 sec   (6017 perm/sec)   p_kst 3.412000e-01   p_cons 4.275000e-01   p_joint 5.671000e-01

Outputting figure to mutsig2_images.part000000000094/KRTAP4-9.2_637_10000_0.3412_0.4275_0.5671.png
                gene_name: KRTAP4-9
               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: 0.57 
     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.165.3896/
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/181708/iteration1/scatter.0000000094
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 94 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1706>
Subject: Job 1120038: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1706>, 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/181708/iteration1/scatter.0000000095> was used as the working directory.
Started at Wed Oct 10 10:43:29 2012
Results reported at Wed Oct 10 10:46:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000095.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000095.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 95  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    174.87 sec.
    Max Memory :      1489 MB
    Max Swap   :      3906 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.165.3896/
-whichjob
95
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 95: processing genes 8505 - 8595
Calculating significance of each gene.
Using projection method.
8505	LAMA1	1
8506	LAMA2	1.900529e-01
8507	LAMA3	1.762389e-02
8508	LAMA4	1
8509	LAMA5	4.077336e-01
8510	LAMB1	1
8511	LAMB2	1.247678e-01
8512	LAMB3	4.048077e-01
8513	LAMB4	1
8514	LAMC1	1
8515	LAMC2	1
8516	LAMC3	1
8517	LAMP1	1
8518	LAMP2	5.044739e-02
8519	LAMP3	1
8520	LANCL1	1
8521	LANCL2	9.695782e-02
8522	LANCL3	1
8523	LAP3	3.296874e-02
8524	LAPTM4A	1
8525	LAPTM4B	1
8526	LAPTM5	1
8527	LARGE	1.405624e-01
8528	LARP1	1
8529	LARP1B	1
8530	LARP4	1.983755e-01
8531	LARP4B	1
8532	LARP6	1
8533	LARP7	1
8534	LARS	1
8535	LARS2	1
8536	LAS1L	2.591122e-01
8537	LASP1	3.512830e-03
8538	LASS1	1
8539	LASS2	1
8540	LASS3	5.262875e-02
8541	LASS4	1
8542	LASS5	1
8543	LASS6	1.199085e-01
8544	LAT	7.561057e-02
8545	LAT2	1
8546	LATS1	3.853696e-01
8547	LATS2	5.310705e-02
8548	LAX1	1.088106e-02
8549	LAYN	1
8550	LBH	1
8551	LBP	1
8552	LBR	1
8553	LBX1	1
8554	LBX2	1
8555	LBXCOR1	1.353538e-01
8556	LCA5	1
8557	LCA5L	1
8558	LCAT	1
8559	LCE1A	1
8560	LCE1B	1
8561	LCE1C	1
8562	LCE1D	1
8563	LCE1E	1
8564	LCE1F	1.567967e-02
8565	LCE2A	1
8566	LCE2B	1
8567	LCE2C	1
8568	LCE2D	1
8569	LCE3A	1
8570	LCE3D	1
8571	LCE3E	1
8572	LCE4A	1
8573	LCE5A	1
8574	LCK	1.018294e-01
8575	LCLAT1	1
8576	LCMT1	1
8577	LCMT2	2.311204e-01
8578	LCN1	1
8579	LCN10	1
8580	LCN12	1
8581	LCN15	1
8582	LCN2	1.094820e-01
8583	LCN6	1
8584	LCN8	1
8585	LCN9	1.559125e-02
8586	LCNL1	1
8587	LCOR	2.137858e-01
8588	LCORL	1
8589	LCP1	1
8590	LCP2	1
8591	LCT	3.036911e-02
8592	LCTL	2.352706e-01
8593	LDB1	1
8594	LDB2	1.305518e-01
8595	LDB3	1
Done

Running MutSig 2:
Scatter job 95: processing genes 8505 - 8595
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
LAMA3
Processing conservation and coverage...
95% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.541019e-02	ci left: 5.407869e-01	ci right 5.603836e-01	k: 5506	n:10000
Cons ci ratio: 1.573306e-02	ci left: 8.543705e-01	ci right 8.680184e-01	k: 8613	n:10000
KS ci ratio: 6.587477e-02	ci left: 2.528084e-01	ci right 2.701307e-01	k: 2614	n:10000
LAMA3   10000 perm   3 sec   (3291 perm/sec)   p_kst 2.614000e-01   p_cons 8.613000e-01   p_joint 5.506000e-01

Outputting figure to mutsig2_images.part000000000095/LAMA3.5_10477_10000_0.2614_0.8613_0.5506.png
                gene_name: LAMA3
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.87 
                  p_joint: 0.55 
     ci_joint_bounds_left: 0.54 
    ci_joint_bounds_right: 0.56 

Current progress: 11 percent done.
LCT
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.160559e-02	ci left: 7.585873e-01	ci right 7.752569e-01	k: 7670	n:10000
Cons ci ratio: 5.637744e-02	ci left: 3.166160e-01	ci right 3.350856e-01	k: 3258	n:10000
KS ci ratio: 1.293953e-02	ci left: 8.957999e-01	ci right 9.075649e-01	k: 9018	n:10000
LCT   10000 perm   3 sec   (3187 perm/sec)   p_kst 9.018000e-01   p_cons 3.258000e-01   p_joint 7.670000e-01

Outputting figure to mutsig2_images.part000000000095/LCT.4_5852_10000_0.9018_0.3258_0.767.png
                gene_name: LCT
               theta_stop: 0.056 
                    nperm: 10000 
                     p_ks: 0.90 
        ci_ks_bounds_left: 0.90 
       ci_ks_bounds_right: 0.91 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.34 
                  p_joint: 0.77 
     ci_joint_bounds_left: 0.76 
    ci_joint_bounds_right: 0.78 

Current progress: 22 percent done.
LAMA2
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: 3.135385e-02	ci left: 6.001585e-01	ci right 6.193775e-01	k: 6098	n:10000
LAMA2   10000 perm   3 sec   (3551 perm/sec)   p_kst 6.098000e-01   p_cons 6.332000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000095/LAMA2.2_9629_10000_0.6098_0.6332_1.png
                gene_name: LAMA2
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.63 
      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: 33 percent done.
LAMA5
Processing conservation and coverage...
87% 
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: 1.586443e-02	ci left: 8.523304e-01	ci right 8.660597e-01	k: 8593	n:10000
KS ci ratio: 1.857837e-02	ci left: 8.088732e-01	ci right 8.241419e-01	k: 8166	n:10000
LAMA5   10000 perm   5 sec   (2011 perm/sec)   p_kst 8.166000e-01   p_cons 8.593000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000095/LAMA5.2_11408_10000_0.8166_0.8593_1.png
                gene_name: LAMA5
               theta_stop: 0.019 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.87 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 44 percent done.
LAMB2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.292739e-02	ci left: 7.364378e-01	ci right 7.536193e-01	k: 7451	n:10000
Cons ci ratio: 5.045670e-02	ci left: 3.667920e-01	ci right 3.858801e-01	k: 3763	n:10000
KS ci ratio: 4.090877e-02	ci left: 4.687666e-01	ci right 4.884459e-01	k: 4786	n:10000
LAMB2   10000 perm   2 sec   (4494 perm/sec)   p_kst 4.786000e-01   p_cons 3.763000e-01   p_joint 7.451000e-01

Outputting figure to mutsig2_images.part000000000095/LAMB2.2_5525_10000_0.4786_0.3763_0.7451.png
                gene_name: LAMB2
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.75 
     ci_joint_bounds_left: 0.74 
    ci_joint_bounds_right: 0.75 

Current progress: 56 percent done.
LASP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.799618e-03	ci left: 9.580656e-01	ci right 9.656623e-01	k: 9620	n:10000
Cons ci ratio: 3.213668e-02	ci left: 5.883129e-01	ci right 6.076300e-01	k: 5980	n:10000
KS ci ratio: 3.755887e-02	ci left: 5.114541e-01	ci right 5.311335e-01	k: 5213	n:10000
LASP1   10000 perm   2 sec   (5917 perm/sec)   p_kst 5.213000e-01   p_cons 5.980000e-01   p_joint 9.620000e-01

Outputting figure to mutsig2_images.part000000000095/LASP1.2_814_10000_0.5213_0.598_0.962.png
                gene_name: LASP1
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.96 
    ci_joint_bounds_right: 0.97 

Current progress: 67 percent done.
LATS1
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: 5.076116e-03	ci left: 9.809150e-01	ci right 9.859977e-01	k: 9836	n:10000
KS ci ratio: 8.516918e-02	ci left: 1.673034e-01	ci right 1.822866e-01	k: 1747	n:10000
LATS1   10000 perm   2 sec   (5400 perm/sec)   p_kst 1.747000e-01   p_cons 9.836000e-01   p_joint 6.340000e-01

Outputting figure to mutsig2_images.part000000000095/LATS1.2_3421_10000_0.1747_0.9836_0.634.png
                gene_name: LATS1
               theta_stop: 0.085 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.64 

Current progress: 78 percent done.
LATS2
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: 2.143635e-02	ci left: 7.614214e-01	ci right 7.780212e-01	k: 7698	n:10000
KS ci ratio: 1.495306e-01	ci left: 5.947341e-02	ci right 6.918228e-02	k: 642	n:10000
LATS2   10000 perm   2 sec   (5611 perm/sec)   p_kst 6.420000e-02   p_cons 7.698000e-01   p_joint 1

Joint ci ratio: 3.704259e-02	ci left: 3.522480e-01	ci right 3.655930e-01	k: 7178	n:20000
Cons ci ratio: 1.559565e-02	ci left: 7.535648e-01	ci right 7.654597e-01	k: 15191	n:20000
KS ci ratio: 1.057364e-01	ci left: 6.089032e-02	ci right 6.773701e-02	k: 1285	n:20000
LATS2   20000 perm   4 sec   (4830 perm/sec)   p_kst 6.425000e-02   p_cons 7.595500e-01   p_joint 3.589000e-01

Joint ci ratio: 3.306510e-02	ci left: 3.137269e-01	ci right 3.243082e-01	k: 9570	n:30000
Cons ci ratio: 1.265305e-02	ci left: 7.570049e-01	ci right 7.666777e-01	k: 22856	n:30000
KS ci ratio: 8.640586e-02	ci left: 6.141936e-02	ci right 6.699874e-02	k: 1925	n:30000
LATS2   30000 perm   7 sec   (4287 perm/sec)   p_kst 6.416667e-02   p_cons 7.618667e-01   p_joint 3.190000e-01

Outputting figure to mutsig2_images.part000000000095/LATS2.2_3295_30000_0.064167_0.76187_0.319.png
                gene_name: LATS2
               theta_stop: 0.086 
                    nperm: 30000 
                     p_ks: 0.064 
        ci_ks_bounds_left: 0.061 
       ci_ks_bounds_right: 0.067 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.32 

Current progress: 89 percent done.
LAX1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.075815e-01	ci left: 1.108601e-01	ci right 1.235638e-01	k: 1171	n:10000
Cons ci ratio: 3.560377e-02	ci left: 5.380825e-01	ci right 5.576896e-01	k: 5479	n:10000
KS ci ratio: 1.670282e-01	ci left: 4.782537e-02	ci right 5.663779e-02	k: 521	n:10000
LAX1   10000 perm   2 sec   (6007 perm/sec)   p_kst 5.210000e-02   p_cons 5.479000e-01   p_joint 1.171000e-01

Joint ci ratio: 5.927148e-02	ci left: 1.741044e-01	ci right 1.847890e-01	k: 3588	n:20000
Cons ci ratio: 2.472076e-02	ci left: 5.500327e-01	ci right 5.638507e-01	k: 11139	n:20000
KS ci ratio: 1.189533e-01	ci left: 4.842873e-02	ci right 5.460248e-02	k: 1029	n:20000
LAX1   20000 perm   4 sec   (5542 perm/sec)   p_kst 5.145000e-02   p_cons 5.569500e-01   p_joint 1.794000e-01

Joint ci ratio: 5.003712e-02	ci left: 1.655668e-01	ci right 1.740972e-01	k: 5094	n:30000
Cons ci ratio: 1.986978e-02	ci left: 5.590669e-01	ci right 5.703205e-01	k: 16941	n:30000
KS ci ratio: 9.709255e-02	ci left: 4.902588e-02	ci right 5.406141e-02	k: 1545	n:30000
LAX1   30000 perm   6 sec   (5356 perm/sec)   p_kst 5.150000e-02   p_cons 5.647000e-01   p_joint 1.698000e-01

Outputting figure to mutsig2_images.part000000000095/LAX1.2_1262_30000_0.0515_0.5647_0.1698.png
                gene_name: LAX1
               theta_stop: 0.097 
                    nperm: 30000 
                     p_ks: 0.051 
        ci_ks_bounds_left: 0.049 
       ci_ks_bounds_right: 0.054 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.57 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.17 
    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.165.3896/
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/181708/iteration1/scatter.0000000095
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 95 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120041: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000096> was used as the working directory.
Started at Wed Oct 10 10:43:33 2012
Results reported at Wed Oct 10 10:45:02 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000096.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000096.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 96  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    102.97 sec.
    Max Memory :       613 MB
    Max Swap   :      3377 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.165.3896/
-whichjob
96
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 96: processing genes 8596 - 8685
Calculating significance of each gene.
Using projection method.
8596	LDHA	1
8597	LDHAL6A	7.334902e-02
8598	LDHAL6B	1
8599	LDHB	1
8600	LDHC	1
8601	LDHD	1
8602	LDLR	2.050207e-01
8603	LDLRAD1	1
8604	LDLRAD2	1
8605	LDLRAD3	1
8606	LDLRAP1	7.839038e-02
8607	LDOC1	1
8608	LDOC1L	1
8609	LEAP2	1
8610	LECT1	1.177831e-01
8611	LECT2	1
8612	LEF1	1
8613	LEFTY1	1
8614	LEFTY2	1
8615	LEKR1	1
8616	LELP1	1
8617	LEMD1	1
8618	LEMD2	1
8619	LEMD3	1
8620	LENEP	1
8621	LENG1	1
8622	LENG8	1
8623	LENG9	1
8624	LEO1	1
8625	LEP	1
8626	LEPR	1
8627	LEPRE1	1.641315e-01
8628	LEPREL1	1
8629	LEPREL2	1
8630	LEPROT	1
8631	LEPROTL1	1
8632	LETM1	1.093739e-01
8633	LETM2	1
8634	LETMD1	5.964783e-04
8635	LFNG	1.820209e-01
8636	LGALS1	1
8637	LGALS12	1
8638	LGALS13	5.345474e-02
8639	LGALS14	1
8640	LGALS2	1
8641	LGALS3	1
8642	LGALS3BP	1
8643	LGALS4	1
8644	LGALS7	1
8645	LGALS7B	1
8646	LGALS8	1
8647	LGALS9	1
8648	LGALS9B	1.756694e-02
8649	LGALS9C	1
8650	LGI1	1
8651	LGI2	1
8652	LGI3	1
8653	LGI4	1
8654	LGMN	1
8655	LGR4	1
8656	LGR5	1
8657	LGR6	1
8658	LGSN	1
8659	LGTN	1
8660	LHB	1
8661	LHCGR	1
8662	LHFP	1
8663	LHFPL1	1
8664	LHFPL2	1
8665	LHFPL3	1
8666	LHFPL4	1
8667	LHFPL5	1
8668	LHPP	1
8669	LHX1	1
8670	LHX2	1
8671	LHX3	1
8672	LHX4	1
8673	LHX5	1
8674	LHX6	1
8675	LHX8	5.505548e-02
8676	LHX9	4.795169e-02
8677	LIAS	1
8678	LIF	1
8679	LIFR	2.486228e-01
8680	LIG1	1
8681	LIG3	1
8682	LIG4	2.914247e-01
8683	LILRA1	1
8684	LILRA2	7.389912e-03
8685	LILRA3	1.641223e-01
Done

Running MutSig 2:
Scatter job 96: processing genes 8596 - 8685
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
LETMD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.623483e-02	ci left: 2.507315e-01	ci right 2.680089e-01	k: 2593	n:10000
Cons ci ratio: 1.159911e-01	ci left: 9.652432e-02	ci right 1.085084e-01	k: 1024	n:10000
KS ci ratio: 1.815547e-02	ci left: 8.157822e-01	ci right 8.308289e-01	k: 8234	n:10000
LETMD1   10000 perm   2 sec   (6236 perm/sec)   p_kst 8.234000e-01   p_cons 1.024000e-01   p_joint 2.593000e-01

Joint ci ratio: 4.936573e-02	ci left: 2.337472e-01	ci right 2.456286e-01	k: 4793	n:20000
Cons ci ratio: 8.447442e-02	ci left: 9.307925e-02	ci right 1.013383e-01	k: 1943	n:20000
KS ci ratio: 1.272250e-02	ci left: 8.206736e-01	ci right 8.312314e-01	k: 16520	n:20000
LETMD1   20000 perm   6 sec   (3527 perm/sec)   p_kst 8.260000e-01   p_cons 9.715000e-02   p_joint 2.396500e-01

Outputting figure to mutsig2_images.part000000000096/LETMD1.3_1119_20000_0.826_0.09715_0.23965.png
                gene_name: LETMD1
               theta_stop: 0.084 
                    nperm: 20000 
                     p_ks: 0.83 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.097 
      ci_cons_bounds_left: 0.093 
     ci_cons_bounds_right: 0.10 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.25 

Current progress: 50 percent done.
LILRA2
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: 5.465244e-02	ci left: 3.303159e-01	ci right 3.489775e-01	k: 3396	n:10000
KS ci ratio: 1.248719e-01	ci left: 8.407230e-02	ci right 9.536803e-02	k: 896	n:10000
LILRA2   10000 perm   2 sec   (6521 perm/sec)   p_kst 8.960000e-02   p_cons 3.396000e-01   p_joint 8.131000e-01

Joint ci ratio: 3.156802e-02	ci left: 4.284136e-01	ci right 4.422053e-01	k: 8706	n:20000
Cons ci ratio: 3.877465e-02	ci left: 3.315925e-01	ci right 3.447546e-01	k: 6763	n:20000
KS ci ratio: 8.912054e-02	ci left: 8.425585e-02	ci right 9.216434e-02	k: 1763	n:20000
LILRA2   20000 perm   3 sec   (5752 perm/sec)   p_kst 8.815000e-02   p_cons 3.381500e-01   p_joint 4.353000e-01

Outputting figure to mutsig2_images.part000000000096/LILRA2.2_1484_20000_0.08815_0.33815_0.4353.png
                gene_name: LILRA2
               theta_stop: 0.089 
                    nperm: 20000 
                     p_ks: 0.088 
        ci_ks_bounds_left: 0.084 
       ci_ks_bounds_right: 0.092 
                   p_cons: 0.34 
      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: 0.44 

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.165.3896/
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/181708/iteration1/scatter.0000000096
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 96 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120044: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000097> was used as the working directory.
Started at Wed Oct 10 10:43:33 2012
Results reported at Wed Oct 10 13:44:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000097.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000097.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 97  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :  11031.69 sec.
    Max Memory :      1196 MB
    Max Swap   :      3900 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.165.3896/
-whichjob
97
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 97: processing genes 8686 - 8776
Calculating significance of each gene.
Using projection method.
8686	LILRA4	1
8687	LILRA5	1
8688	LILRA6	1.473468e-01
8689	LILRB1	1
8690	LILRB2	1
8691	LILRB3	1.992373e-01
8692	LILRB4	1
8693	LILRB5	1
8694	LIM2	1
8695	LIMA1	1
8696	LIMCH1	1
8697	LIMD1	1
8698	LIMD2	1
8699	LIME1	1
8700	LIMK1	1
8701	LIMK2	1
8702	LIMS1	1
8703	LIMS2	1
8704	LIN28A	1
8705	LIN28B	1
8706	LIN37	1
8707	LIN52	1
8708	LIN54	1
8709	LIN7A	1
8710	LIN7B	1
8711	LIN7C	1
8712	LIN9	1
8713	LINGO1	1
8714	LINGO2	1
8715	LINGO3	1
8716	LINGO4	1
8717	LINS1	1
8718	LIPA	1
8719	LIPC	4.144675e-02
8720	LIPE	2.325596e-01
8721	LIPF	1
8722	LIPG	1
8723	LIPH	1
8724	LIPI	1
8725	LIPJ	1
8726	LIPK	1
8727	LIPN	1
8728	LIPT1	1
8729	LITAF	1
8730	LIX1	1
8731	LIX1L	1
8732	LLGL1	1
8733	LLGL2	1.778293e-02
8734	LLPH	1
8735	LMAN1	1
8736	LMAN1L	1.719172e-01
8737	LMAN2	1
8738	LMAN2L	1.286666e-01
8739	LMBR1	1
8740	LMBR1L	1
8741	LMBRD1	1
8742	LMBRD2	1
8743	LMCD1	1
8744	LMF1	1.420321e-01
8745	LMF2	1
8746	LMLN	1
8747	LMNA	1
8748	LMNB1	1
8749	LMNB2	1
8750	LMO1	1
8751	LMO2	1.147784e-02
8752	LMO3	1
8753	LMO4	1
8754	LMO7	3.098473e-01
8755	LMOD1	1
8756	LMOD2	9.204230e-03
8757	LMOD3	1
8758	LMTK2	1
8759	LMTK3	1
8760	LMX1A	1
8761	LMX1B	1
8762	LNP1	1
8763	LNPEP	1
8764	LNX1	1
8765	LNX2	1
8766	LOC100130932	1
8767	LOC100302652	1
8768	LOC150786	1
8769	LOC153328	1
8770	LOC200726	1
8771	LOC285033	1
8772	LOC286238	1
8773	LOC401052	1
8774	LOC402644	1
8775	LOC440563	1.153784e-01
8776	LOC55908	1
Done

Running MutSig 2:
Scatter job 97: processing genes 8686 - 8776
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
LLGL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.046878e+00	ci left: 6.923711e-04	ci right 2.222014e-03	k: 13	n:10000
Cons ci ratio: 7.627750e-03	ci left: 9.597417e-01	ci right 9.671851e-01	k: 9636	n:10000
KS ci ratio: 1.959510e+00	ci left: 6.187149e-05	ci right 8.764745e-04	k: 3	n:10000
LLGL2   10000 perm   2 sec   (5606 perm/sec)   p_kst 3.000000e-04   p_cons 9.636000e-01   p_joint 1.300000e-03

Joint ci ratio: 1.959755e+00	ci left: 3.093467e-05	ci right 4.383005e-04	k: 3	n:20000
Cons ci ratio: 5.328788e-03	ci left: 9.617386e-01	ci right 9.669253e-01	k: 19288	n:20000
KS ci ratio: 1.959755e+00	ci left: 3.093467e-05	ci right 4.383005e-04	k: 3	n:20000
LLGL2   20000 perm   6 sec   (3355 perm/sec)   p_kst 1.500000e-04   p_cons 9.644000e-01   p_joint 1.500000e-04

Joint ci ratio: 1.752902e+00	ci left: 3.633000e-05	ci right 3.413508e-04	k: 4	n:30000
Cons ci ratio: 4.373221e-03	ci left: 9.618641e-01	ci right 9.661121e-01	k: 28921	n:30000
KS ci ratio: 1.752902e+00	ci left: 3.633000e-05	ci right 3.413508e-04	k: 4	n:30000
LLGL2   30000 perm   8 sec   (3631 perm/sec)   p_kst 1.333333e-04   p_cons 9.640333e-01   p_joint 1.333333e-04

Joint ci ratio: 1.600193e+00	ci left: 4.058837e-05	ci right 2.916840e-04	k: 5	n:40000
Cons ci ratio: 3.809174e-03	ci left: 9.617438e-01	ci right 9.654385e-01	k: 38545	n:40000
KS ci ratio: 1.600193e+00	ci left: 4.058837e-05	ci right 2.916840e-04	k: 5	n:40000
LLGL2   40000 perm   12 sec   (3363 perm/sec)   p_kst 1.250000e-04   p_cons 9.636250e-01   p_joint 1.250000e-04

Joint ci ratio: 1.481502e+00	ci left: 4.403912e-05	ci right 2.611710e-04	k: 6	n:50000
Cons ci ratio: 3.213907e-03	ci left: 9.659083e-01	ci right 9.690371e-01	k: 48375	n:50000
KS ci ratio: 1.481502e+00	ci left: 4.403912e-05	ci right 2.611710e-04	k: 6	n:50000
LLGL2   50000 perm   15 sec   (3400 perm/sec)   p_kst 1.200000e-04   p_cons 9.675000e-01   p_joint 1.200000e-04

Joint ci ratio: 1.385825e+00	ci left: 4.690730e-05	ci right 2.403631e-04	k: 7	n:60000
Cons ci ratio: 2.960843e-03	ci left: 9.654545e-01	ci right 9.683335e-01	k: 58015	n:60000
KS ci ratio: 1.385825e+00	ci left: 4.690730e-05	ci right 2.403631e-04	k: 7	n:60000
LLGL2   60000 perm   18 sec   (3270 perm/sec)   p_kst 1.166667e-04   p_cons 9.669167e-01   p_joint 1.166667e-04

Joint ci ratio: 1.239515e+00	ci left: 5.879268e-05	ci right 2.440545e-04	k: 9	n:70000
Cons ci ratio: 2.735713e-03	ci left: 9.656937e-01	ci right 9.683531e-01	k: 67693	n:70000
KS ci ratio: 1.239515e+00	ci left: 5.879268e-05	ci right 2.440545e-04	k: 9	n:70000
LLGL2   70000 perm   21 sec   (3324 perm/sec)   p_kst 1.285714e-04   p_cons 9.670429e-01   p_joint 1.285714e-04

Joint ci ratio: 1.012038e+00	ci left: 9.567733e-05	ci right 2.936028e-04	k: 14	n:80000
Cons ci ratio: 2.553155e-03	ci left: 9.659297e-01	ci right 9.684112e-01	k: 77375	n:80000
KS ci ratio: 1.012038e+00	ci left: 9.567733e-05	ci right 2.936028e-04	k: 14	n:80000
LLGL2   80000 perm   24 sec   (3283 perm/sec)   p_kst 1.750000e-04   p_cons 9.671875e-01   p_joint 1.750000e-04

Joint ci ratio: 9.506446e-01	ci left: 1.016187e-04	ci right 2.886840e-04	k: 16	n:90000
Cons ci ratio: 2.412091e-03	ci left: 9.658687e-01	ci right 9.682122e-01	k: 87035	n:90000
KS ci ratio: 9.506446e-01	ci left: 1.016187e-04	ci right 2.886840e-04	k: 16	n:90000
LLGL2   90000 perm   27 sec   (3327 perm/sec)   p_kst 1.777778e-04   p_cons 9.670556e-01   p_joint 1.777778e-04

Joint ci ratio: 8.764466e-01	ci left: 1.143962e-04	ci right 2.966927e-04	k: 19	n:100000
Cons ci ratio: 2.288117e-03	ci left: 9.659352e-01	ci right 9.681576e-01	k: 96706	n:100000
KS ci ratio: 8.764466e-01	ci left: 1.143962e-04	ci right 2.966927e-04	k: 19	n:100000
LLGL2   100000 perm   30 sec   (3347 perm/sec)   p_kst 1.900000e-04   p_cons 9.670600e-01   p_joint 1.900000e-04

Joint ci ratio: 7.839073e-01	ci left: 1.397981e-04	ci right 3.246200e-04	k: 24	n:110000
Cons ci ratio: 2.171817e-03	ci left: 9.662782e-01	ci right 9.683880e-01	k: 106408	n:110000
KS ci ratio: 7.839073e-01	ci left: 1.397981e-04	ci right 3.246200e-04	k: 24	n:110000
LLGL2   110000 perm   33 sec   (3342 perm/sec)   p_kst 2.181818e-04   p_cons 9.673455e-01   p_joint 2.181818e-04

Joint ci ratio: 7.686888e-01	ci left: 1.348267e-04	ci right 3.075258e-04	k: 25	n:120000
Cons ci ratio: 2.072595e-03	ci left: 9.665319e-01	ci right 9.685454e-01	k: 116106	n:120000
KS ci ratio: 7.686888e-01	ci left: 1.348267e-04	ci right 3.075258e-04	k: 25	n:120000
LLGL2   120000 perm   36 sec   (3351 perm/sec)   p_kst 2.083333e-04   p_cons 9.675500e-01   p_joint 2.083333e-04

Joint ci ratio: 7.278417e-01	ci left: 1.431261e-04	ci right 3.112758e-04	k: 28	n:130000
Cons ci ratio: 1.990902e-03	ci left: 9.665842e-01	ci right 9.685180e-01	k: 125783	n:130000
KS ci ratio: 7.278417e-01	ci left: 1.431261e-04	ci right 3.112758e-04	k: 28	n:130000
LLGL2   130000 perm   39 sec   (3341 perm/sec)   p_kst 2.153846e-04   p_cons 9.675615e-01   p_joint 2.153846e-04

Joint ci ratio: 7.039723e-01	ci left: 1.445822e-04	ci right 3.058922e-04	k: 30	n:140000
Cons ci ratio: 1.916855e-03	ci left: 9.666737e-01	ci right 9.685354e-01	k: 135466	n:140000
KS ci ratio: 7.039723e-01	ci left: 1.445822e-04	ci right 3.058922e-04	k: 30	n:140000
LLGL2   140000 perm   42 sec   (3341 perm/sec)   p_kst 2.142857e-04   p_cons 9.676143e-01   p_joint 2.142857e-04

Joint ci ratio: 6.928884e-01	ci left: 1.404242e-04	ci right 2.933341e-04	k: 31	n:150000
Cons ci ratio: 1.849510e-03	ci left: 9.667861e-01	ci right 9.685824e-01	k: 145154	n:150000
KS ci ratio: 6.928884e-01	ci left: 1.404242e-04	ci right 2.933341e-04	k: 31	n:150000
LLGL2   150000 perm   45 sec   (3336 perm/sec)   p_kst 2.066667e-04   p_cons 9.676933e-01   p_joint 2.066667e-04

Joint ci ratio: 6.443675e-01	ci left: 1.575921e-04	ci right 3.114814e-04	k: 36	n:160000
Cons ci ratio: 1.796120e-03	ci left: 9.666258e-01	ci right 9.683697e-01	k: 154801	n:160000
KS ci ratio: 6.443675e-01	ci left: 1.575921e-04	ci right 3.114814e-04	k: 36	n:160000
LLGL2   160000 perm   48 sec   (3310 perm/sec)   p_kst 2.250000e-04   p_cons 9.675063e-01   p_joint 2.250000e-04

Joint ci ratio: 6.047926e-01	ci left: 1.730778e-04	ci right 3.271690e-04	k: 41	n:170000
Cons ci ratio: 1.742820e-03	ci left: 9.666402e-01	ci right 9.683321e-01	k: 164474	n:170000
KS ci ratio: 6.047926e-01	ci left: 1.730778e-04	ci right 3.271690e-04	k: 41	n:170000
LLGL2   170000 perm   52 sec   (3297 perm/sec)   p_kst 2.411765e-04   p_cons 9.674941e-01   p_joint 2.411765e-04

Joint ci ratio: 6.047969e-01	ci left: 1.634621e-04	ci right 3.089937e-04	k: 41	n:180000
Cons ci ratio: 1.697586e-03	ci left: 9.665187e-01	ci right 9.681662e-01	k: 174123	n:180000
KS ci ratio: 6.047969e-01	ci left: 1.634621e-04	ci right 3.089937e-04	k: 41	n:180000
LLGL2   180000 perm   55 sec   (3252 perm/sec)   p_kst 2.277778e-04   p_cons 9.673500e-01   p_joint 2.277778e-04

Joint ci ratio: 5.908922e-01	ci left: 1.637905e-04	ci right 3.048339e-04	k: 43	n:190000
Cons ci ratio: 1.725175e-03	ci left: 9.636689e-01	ci right 9.653380e-01	k: 183257	n:190000
KS ci ratio: 5.908922e-01	ci left: 1.637905e-04	ci right 3.048339e-04	k: 43	n:190000
LLGL2   190000 perm   59 sec   (3234 perm/sec)   p_kst 2.263158e-04   p_cons 9.645105e-01   p_joint 2.263158e-04

Joint ci ratio: 5.657339e-01	ci left: 1.726741e-04	ci right 3.124881e-04	k: 47	n:200000
Cons ci ratio: 1.680640e-03	ci left: 9.637253e-01	ci right 9.653512e-01	k: 192909	n:200000
KS ci ratio: 5.657339e-01	ci left: 1.726741e-04	ci right 3.124881e-04	k: 47	n:200000
LLGL2   200000 perm   62 sec   (3215 perm/sec)   p_kst 2.350000e-04   p_cons 9.645450e-01   p_joint 2.350000e-04

Joint ci ratio: 5.285022e-01	ci left: 1.931793e-04	ci right 3.355025e-04	k: 54	n:210000
Cons ci ratio: 1.642352e-03	ci left: 9.636516e-01	ci right 9.652403e-01	k: 202535	n:210000
KS ci ratio: 5.285022e-01	ci left: 1.931793e-04	ci right 3.355025e-04	k: 54	n:210000
LLGL2   210000 perm   66 sec   (3193 perm/sec)   p_kst 2.571429e-04   p_cons 9.644524e-01   p_joint 2.571429e-04

Joint ci ratio: 5.102709e-01	ci left: 2.001960e-04	ci right 3.407980e-04	k: 58	n:220000
Cons ci ratio: 1.600810e-03	ci left: 9.638332e-01	ci right 9.653818e-01	k: 212215	n:220000
KS ci ratio: 5.102709e-01	ci left: 2.001960e-04	ci right 3.407980e-04	k: 58	n:220000
LLGL2   220000 perm   69 sec   (3170 perm/sec)   p_kst 2.636364e-04   p_cons 9.646136e-01   p_joint 2.636364e-04

Joint ci ratio: 4.938049e-01	ci left: 2.066802e-04	ci right 3.455573e-04	k: 62	n:230000
Cons ci ratio: 1.562940e-03	ci left: 9.639685e-01	ci right 9.654806e-01	k: 221888	n:230000
KS ci ratio: 4.938049e-01	ci left: 2.066802e-04	ci right 3.455573e-04	k: 62	n:230000
LLGL2   230000 perm   73 sec   (3145 perm/sec)   p_kst 2.695652e-04   p_cons 9.647304e-01   p_joint 2.695652e-04

Joint ci ratio: 4.718437e-01	ci left: 2.200259e-04	ci right 3.591789e-04	k: 68	n:240000
Cons ci ratio: 1.530900e-03	ci left: 9.639456e-01	ci right 9.654265e-01	k: 231526	n:240000
KS ci ratio: 4.718437e-01	ci left: 2.200259e-04	ci right 3.591789e-04	k: 68	n:240000
LLGL2   240000 perm   77 sec   (3118 perm/sec)   p_kst 2.833333e-04   p_cons 9.646917e-01   p_joint 2.833333e-04

Joint ci ratio: 4.587334e-01	ci left: 2.253489e-04	ci right 3.626748e-04	k: 72	n:250000
Cons ci ratio: 1.496168e-03	ci left: 9.641348e-01	ci right 9.655824e-01	k: 241216	n:250000
KS ci ratio: 4.587334e-01	ci left: 2.253489e-04	ci right 3.626748e-04	k: 72	n:250000
LLGL2   250000 perm   81 sec   (3077 perm/sec)   p_kst 2.880000e-04   p_cons 9.648640e-01   p_joint 2.880000e-04

Joint ci ratio: 4.495883e-01	ci left: 2.268998e-04	ci right 3.615758e-04	k: 75	n:260000
Cons ci ratio: 1.468661e-03	ci left: 9.640768e-01	ci right 9.654975e-01	k: 250846	n:260000
KS ci ratio: 4.495883e-01	ci left: 2.268998e-04	ci right 3.615758e-04	k: 75	n:260000
LLGL2   260000 perm   85 sec   (3053 perm/sec)   p_kst 2.884615e-04   p_cons 9.647923e-01   p_joint 2.884615e-04

Joint ci ratio: 4.382036e-01	ci left: 2.316549e-04	ci right 3.646445e-04	k: 79	n:270000
Cons ci ratio: 1.444103e-03	ci left: 9.639522e-01	ci right 9.653489e-01	k: 260457	n:270000
KS ci ratio: 4.382036e-01	ci left: 2.316549e-04	ci right 3.646445e-04	k: 79	n:270000
LLGL2   270000 perm   89 sec   (3018 perm/sec)   p_kst 2.925926e-04   p_cons 9.646556e-01   p_joint 2.925926e-04

Joint ci ratio: 4.328274e-01	ci left: 2.297410e-04	ci right 3.595431e-04	k: 81	n:280000
Cons ci ratio: 1.419011e-03	ci left: 9.639197e-01	ci right 9.652920e-01	k: 270091	n:280000
KS ci ratio: 4.328274e-01	ci left: 2.297410e-04	ci right 3.595431e-04	k: 81	n:280000
LLGL2   280000 perm   94 sec   (2990 perm/sec)   p_kst 2.892857e-04   p_cons 9.646107e-01   p_joint 2.892857e-04

Joint ci ratio: 4.251206e-01	ci left: 2.310467e-04	ci right 3.586004e-04	k: 84	n:290000
Cons ci ratio: 1.393420e-03	ci left: 9.639767e-01	ci right 9.653243e-01	k: 279750	n:290000
KS ci ratio: 4.251206e-01	ci left: 2.310467e-04	ci right 3.586004e-04	k: 84	n:290000
LLGL2   290000 perm   98 sec   (2964 perm/sec)   p_kst 2.896552e-04   p_cons 9.646552e-01   p_joint 2.896552e-04

Joint ci ratio: 4.178114e-01	ci left: 2.322844e-04	ci right 3.577018e-04	k: 87	n:300000
Cons ci ratio: 1.371240e-03	ci left: 9.639259e-01	ci right 9.652518e-01	k: 289378	n:300000
KS ci ratio: 4.178114e-01	ci left: 2.322844e-04	ci right 3.577018e-04	k: 87	n:300000
LLGL2   300000 perm   103 sec   (2925 perm/sec)   p_kst 2.900000e-04   p_cons 9.645933e-01   p_joint 2.900000e-04

Joint ci ratio: 4.064234e-01	ci left: 2.392484e-04	ci right 3.639550e-04	k: 92	n:310000
Cons ci ratio: 1.348044e-03	ci left: 9.639826e-01	ci right 9.652861e-01	k: 299038	n:310000
KS ci ratio: 4.064234e-01	ci left: 2.392484e-04	ci right 3.639550e-04	k: 92	n:310000
LLGL2   310000 perm   108 sec   (2883 perm/sec)   p_kst 2.967742e-04   p_cons 9.646387e-01   p_joint 2.967742e-04

Joint ci ratio: 4.021232e-01	ci left: 2.373862e-04	ci right 3.594638e-04	k: 94	n:320000
Cons ci ratio: 1.327017e-03	ci left: 9.639823e-01	ci right 9.652655e-01	k: 308681	n:320000
KS ci ratio: 4.021232e-01	ci left: 2.373862e-04	ci right 3.594638e-04	k: 94	n:320000
LLGL2   320000 perm   112 sec   (2855 perm/sec)   p_kst 2.937500e-04   p_cons 9.646281e-01   p_joint 2.937500e-04

Joint ci ratio: 3.959204e-01	ci left: 2.383713e-04	ci right 3.585695e-04	k: 97	n:330000
Cons ci ratio: 1.304913e-03	ci left: 9.640892e-01	ci right 9.653511e-01	k: 318359	n:330000
KS ci ratio: 3.959204e-01	ci left: 2.383713e-04	ci right 3.585695e-04	k: 97	n:330000
LLGL2   330000 perm   117 sec   (2823 perm/sec)   p_kst 2.939394e-04   p_cons 9.647242e-01   p_joint 2.939394e-04

Joint ci ratio: 3.919418e-01	ci left: 2.366600e-04	ci right 3.544857e-04	k: 99	n:340000
Cons ci ratio: 1.284537e-03	ci left: 9.641544e-01	ci right 9.653965e-01	k: 328025	n:340000
KS ci ratio: 3.919418e-01	ci left: 2.366600e-04	ci right 3.544857e-04	k: 99	n:340000
LLGL2   340000 perm   121 sec   (2802 perm/sec)   p_kst 2.911765e-04   p_cons 9.647794e-01   p_joint 2.911765e-04

Joint ci ratio: 3.861917e-01	ci left: 2.376312e-04	ci right 3.537634e-04	k: 102	n:350000
Cons ci ratio: 1.267371e-03	ci left: 9.640920e-01	ci right 9.653174e-01	k: 337648	n:350000
KS ci ratio: 3.861917e-01	ci left: 2.376312e-04	ci right 3.537634e-04	k: 102	n:350000
LLGL2   350000 perm   126 sec   (2781 perm/sec)   p_kst 2.914286e-04   p_cons 9.647086e-01   p_joint 2.914286e-04

Joint ci ratio: 3.824965e-01	ci left: 2.360491e-04	ci right 3.500265e-04	k: 104	n:360000
Cons ci ratio: 1.246228e-03	ci left: 9.642881e-01	ci right 9.654933e-01	k: 347362	n:360000
KS ci ratio: 3.824965e-01	ci left: 2.360491e-04	ci right 3.500265e-04	k: 104	n:360000
LLGL2   360000 perm   130 sec   (2760 perm/sec)   p_kst 2.888889e-04   p_cons 9.648944e-01   p_joint 2.888889e-04

Joint ci ratio: 3.754121e-01	ci left: 2.394505e-04	ci right 3.524021e-04	k: 108	n:370000
Cons ci ratio: 1.228140e-03	ci left: 9.643592e-01	ci right 9.655470e-01	k: 357034	n:370000
KS ci ratio: 3.754121e-01	ci left: 2.394505e-04	ci right 3.524021e-04	k: 108	n:370000
LLGL2   370000 perm   135 sec   (2734 perm/sec)   p_kst 2.918919e-04   p_cons 9.649568e-01   p_joint 2.918919e-04

Joint ci ratio: 3.703501e-01	ci left: 2.403041e-04	ci right 3.517596e-04	k: 111	n:380000
Cons ci ratio: 1.212888e-03	ci left: 9.643100e-01	ci right 9.654829e-01	k: 366662	n:380000
KS ci ratio: 3.703501e-01	ci left: 2.403041e-04	ci right 3.517596e-04	k: 111	n:380000
LLGL2   380000 perm   140 sec   (2713 perm/sec)   p_kst 2.921053e-04   p_cons 9.649000e-01   p_joint 2.921053e-04

Joint ci ratio: 3.670875e-01	ci left: 2.387955e-04	ci right 3.483415e-04	k: 113	n:390000
Cons ci ratio: 1.197644e-03	ci left: 9.642944e-01	ci right 9.654525e-01	k: 376302	n:390000
KS ci ratio: 3.670875e-01	ci left: 2.387955e-04	ci right 3.483415e-04	k: 113	n:390000
LLGL2   390000 perm   145 sec   (2692 perm/sec)   p_kst 2.897436e-04   p_cons 9.648769e-01   p_joint 2.897436e-04

Joint ci ratio: 3.639096e-01	ci left: 2.373664e-04	ci right 3.450903e-04	k: 115	n:400000
Cons ci ratio: 1.182960e-03	ci left: 9.642797e-01	ci right 9.654235e-01	k: 385942	n:400000
KS ci ratio: 3.639096e-01	ci left: 2.373664e-04	ci right 3.450903e-04	k: 115	n:400000
LLGL2   400000 perm   150 sec   (2671 perm/sec)   p_kst 2.875000e-04   p_cons 9.648550e-01   p_joint 2.875000e-04

Joint ci ratio: 3.608129e-01	ci left: 2.360109e-04	ci right 3.419938e-04	k: 117	n:410000
Cons ci ratio: 1.169475e-03	ci left: 9.642265e-01	ci right 9.653572e-01	k: 395566	n:410000
KS ci ratio: 3.608129e-01	ci left: 2.360109e-04	ci right 3.419938e-04	k: 117	n:410000
LLGL2   410000 perm   155 sec   (2650 perm/sec)   p_kst 2.853659e-04   p_cons 9.647951e-01   p_joint 2.853659e-04

Joint ci ratio: 3.505629e-01	ci left: 2.455696e-04	ci right 3.520003e-04	k: 124	n:420000
Cons ci ratio: 1.155709e-03	ci left: 9.642191e-01	ci right 9.653364e-01	k: 405208	n:420000
KS ci ratio: 3.505629e-01	ci left: 2.455696e-04	ci right 3.520003e-04	k: 124	n:420000
LLGL2   420000 perm   160 sec   (2629 perm/sec)   p_kst 2.952381e-04   p_cons 9.647810e-01   p_joint 2.952381e-04

Joint ci ratio: 3.477920e-01	ci left: 2.441019e-04	ci right 3.488718e-04	k: 126	n:430000
Cons ci ratio: 1.143472e-03	ci left: 9.641488e-01	ci right 9.652542e-01	k: 414823	n:430000
KS ci ratio: 3.477920e-01	ci left: 2.441019e-04	ci right 3.488718e-04	k: 126	n:430000
LLGL2   430000 perm   165 sec   (2604 perm/sec)   p_kst 2.930233e-04   p_cons 9.647047e-01   p_joint 2.930233e-04

Joint ci ratio: 3.437556e-01	ci left: 2.447803e-04	ci right 3.483508e-04	k: 129	n:440000
Cons ci ratio: 1.131800e-03	ci left: 9.640704e-01	ci right 9.651644e-01	k: 424433	n:440000
KS ci ratio: 3.437556e-01	ci left: 2.447803e-04	ci right 3.483508e-04	k: 129	n:440000
LLGL2   440000 perm   172 sec   (2559 perm/sec)   p_kst 2.931818e-04   p_cons 9.646205e-01   p_joint 2.931818e-04

Joint ci ratio: 3.411418e-01	ci left: 2.434029e-04	ci right 3.454350e-04	k: 131	n:450000
Cons ci ratio: 1.119306e-03	ci left: 9.640672e-01	ci right 9.651491e-01	k: 434075	n:450000
KS ci ratio: 3.411418e-01	ci left: 2.434029e-04	ci right 3.454350e-04	k: 131	n:450000
LLGL2   450000 perm   178 sec   (2527 perm/sec)   p_kst 2.911111e-04   p_cons 9.646111e-01   p_joint 2.911111e-04

Joint ci ratio: 3.373300e-01	ci left: 2.440778e-04	ci right 3.450007e-04	k: 134	n:460000
Cons ci ratio: 1.106195e-03	ci left: 9.641277e-01	ci right 9.651969e-01	k: 443746	n:460000
KS ci ratio: 3.373300e-01	ci left: 2.440778e-04	ci right 3.450007e-04	k: 134	n:460000
LLGL2   460000 perm   184 sec   (2504 perm/sec)   p_kst 2.913043e-04   p_cons 9.646652e-01   p_joint 2.913043e-04

Joint ci ratio: 3.336432e-01	ci left: 2.447300e-04	ci right 3.445789e-04	k: 137	n:470000
Cons ci ratio: 1.095034e-03	ci left: 9.640913e-01	ci right 9.651497e-01	k: 453373	n:470000
KS ci ratio: 3.336432e-01	ci left: 2.447300e-04	ci right 3.445789e-04	k: 137	n:470000
LLGL2   470000 perm   189 sec   (2484 perm/sec)   p_kst 2.914894e-04   p_cons 9.646234e-01   p_joint 2.914894e-04

Joint ci ratio: 3.312518e-01	ci left: 2.434503e-04	ci right 3.419135e-04	k: 139	n:480000
Cons ci ratio: 1.084235e-03	ci left: 9.640545e-01	ci right 9.651024e-01	k: 462999	n:480000
KS ci ratio: 3.312518e-01	ci left: 2.434503e-04	ci right 3.419135e-04	k: 139	n:480000
LLGL2   480000 perm   195 sec   (2464 perm/sec)   p_kst 2.895833e-04   p_cons 9.645812e-01   p_joint 2.895833e-04

Joint ci ratio: 3.300757e-01	ci left: 2.403533e-04	ci right 3.371454e-04	k: 140	n:490000
Cons ci ratio: 1.073461e-03	ci left: 9.640377e-01	ci right 9.650751e-01	k: 472634	n:490000
KS ci ratio: 3.300757e-01	ci left: 2.403533e-04	ci right 3.371454e-04	k: 140	n:490000
LLGL2   490000 perm   200 sec   (2445 perm/sec)   p_kst 2.857143e-04   p_cons 9.645592e-01   p_joint 2.857143e-04

Joint ci ratio: 3.254907e-01	ci left: 2.428881e-04	ci right 3.390584e-04	k: 144	n:500000
Cons ci ratio: 1.063001e-03	ci left: 9.640217e-01	ci right 9.650489e-01	k: 482269	n:500000
KS ci ratio: 3.254907e-01	ci left: 2.428881e-04	ci right 3.390584e-04	k: 144	n:500000
LLGL2   500000 perm   206 sec   (2426 perm/sec)   p_kst 2.880000e-04   p_cons 9.645380e-01   p_joint 2.880000e-04

Joint ci ratio: 3.243748e-01	ci left: 2.399264e-04	ci right 3.345304e-04	k: 145	n:510000
Cons ci ratio: 1.051784e-03	ci left: 9.640754e-01	ci right 9.650919e-01	k: 491939	n:510000
KS ci ratio: 3.243748e-01	ci left: 2.399264e-04	ci right 3.345304e-04	k: 145	n:510000
LLGL2   510000 perm   212 sec   (2405 perm/sec)   p_kst 2.843137e-04   p_cons 9.645863e-01   p_joint 2.843137e-04

Joint ci ratio: 3.200202e-01	ci left: 2.423827e-04	ci right 3.364094e-04	k: 149	n:520000
Cons ci ratio: 1.041089e-03	ci left: 9.641155e-01	ci right 9.651216e-01	k: 501603	n:520000
KS ci ratio: 3.200202e-01	ci left: 2.423827e-04	ci right 3.364094e-04	k: 149	n:520000
LLGL2   520000 perm   218 sec   (2386 perm/sec)   p_kst 2.865385e-04   p_cons 9.646212e-01   p_joint 2.865385e-04

Joint ci ratio: 3.189593e-01	ci left: 2.395449e-04	ci right 3.320997e-04	k: 150	n:530000
Cons ci ratio: 1.031169e-03	ci left: 9.641237e-01	ci right 9.651203e-01	k: 511251	n:530000
KS ci ratio: 3.189593e-01	ci left: 2.395449e-04	ci right 3.320997e-04	k: 150	n:530000
LLGL2   530000 perm   224 sec   (2365 perm/sec)   p_kst 2.830189e-04   p_cons 9.646245e-01   p_joint 2.830189e-04

Joint ci ratio: 3.138056e-01	ci left: 2.436331e-04	ci right 3.359416e-04	k: 155	n:540000
Cons ci ratio: 1.020585e-03	ci left: 9.641951e-01	ci right 9.651814e-01	k: 520933	n:540000
KS ci ratio: 3.138056e-01	ci left: 2.436331e-04	ci right 3.359416e-04	k: 155	n:540000
LLGL2   540000 perm   230 sec   (2345 perm/sec)   p_kst 2.870370e-04   p_cons 9.646907e-01   p_joint 2.870370e-04

Joint ci ratio: 3.118134e-01	ci left: 2.425543e-04	ci right 3.337545e-04	k: 157	n:550000
Cons ci ratio: 1.011154e-03	ci left: 9.642071e-01	ci right 9.651844e-01	k: 530584	n:550000
KS ci ratio: 3.118134e-01	ci left: 2.425543e-04	ci right 3.337545e-04	k: 157	n:550000
LLGL2   550000 perm   236 sec   (2326 perm/sec)   p_kst 2.854545e-04   p_cons 9.646982e-01   p_joint 2.854545e-04

Joint ci ratio: 3.079395e-01	ci left: 2.448106e-04	ci right 3.354911e-04	k: 161	n:560000
Cons ci ratio: 1.001874e-03	ci left: 9.642260e-01	ci right 9.651942e-01	k: 540239	n:560000
KS ci ratio: 3.079395e-01	ci left: 2.448106e-04	ci right 3.354911e-04	k: 161	n:560000
LLGL2   560000 perm   243 sec   (2308 perm/sec)   p_kst 2.875000e-04   p_cons 9.647125e-01   p_joint 2.875000e-04

Joint ci ratio: 3.051271e-01	ci left: 2.453740e-04	ci right 3.352720e-04	k: 164	n:570000
Cons ci ratio: 9.936632e-04	ci left: 9.641877e-01	ci right 9.651479e-01	k: 549862	n:570000
KS ci ratio: 3.051271e-01	ci left: 2.453740e-04	ci right 3.352720e-04	k: 164	n:570000
LLGL2   570000 perm   249 sec   (2289 perm/sec)   p_kst 2.877193e-04   p_cons 9.646702e-01   p_joint 2.877193e-04

Joint ci ratio: 3.032948e-01	ci left: 2.443285e-04	ci right 3.332021e-04	k: 166	n:580000
Cons ci ratio: 9.851517e-04	ci left: 9.641855e-01	ci right 9.651375e-01	k: 559505	n:580000
KS ci ratio: 3.032948e-01	ci left: 2.443285e-04	ci right 3.332021e-04	k: 166	n:580000
LLGL2   580000 perm   255 sec   (2271 perm/sec)   p_kst 2.862069e-04   p_cons 9.646638e-01   p_joint 2.862069e-04

Joint ci ratio: 3.023912e-01	ci left: 2.417535e-04	ci right 3.293780e-04	k: 167	n:590000
Cons ci ratio: 9.770010e-04	ci left: 9.641731e-01	ci right 9.651172e-01	k: 569142	n:590000
KS ci ratio: 3.023912e-01	ci left: 2.417535e-04	ci right 3.293780e-04	k: 167	n:590000
LLGL2   590000 perm   262 sec   (2253 perm/sec)   p_kst 2.830508e-04   p_cons 9.646475e-01   p_joint 2.830508e-04

Joint ci ratio: 3.014957e-01	ci left: 2.392646e-04	ci right 3.256810e-04	k: 168	n:600000
Cons ci ratio: 9.692384e-04	ci left: 9.641478e-01	ci right 9.650844e-01	k: 578771	n:600000
KS ci ratio: 3.014957e-01	ci left: 2.392646e-04	ci right 3.256810e-04	k: 168	n:600000
LLGL2   600000 perm   268 sec   (2235 perm/sec)   p_kst 2.800000e-04   p_cons 9.646183e-01   p_joint 2.800000e-04

Joint ci ratio: 2.988548e-01	ci left: 2.398900e-04	ci right 3.256293e-04	k: 171	n:610000
Cons ci ratio: 9.615880e-04	ci left: 9.641283e-01	ci right 9.650574e-01	k: 588403	n:610000
KS ci ratio: 2.988548e-01	ci left: 2.398900e-04	ci right 3.256293e-04	k: 171	n:610000
LLGL2   610000 perm   275 sec   (2218 perm/sec)   p_kst 2.803279e-04   p_cons 9.645951e-01   p_joint 2.803279e-04

Joint ci ratio: 2.954389e-01	ci left: 2.419916e-04	ci right 3.273082e-04	k: 175	n:620000
Cons ci ratio: 9.528991e-04	ci left: 9.641971e-01	ci right 9.651179e-01	k: 598089	n:620000
KS ci ratio: 2.954389e-01	ci left: 2.419916e-04	ci right 3.273082e-04	k: 175	n:620000
LLGL2   620000 perm   282 sec   (2201 perm/sec)   p_kst 2.822581e-04   p_cons 9.646597e-01   p_joint 2.822581e-04

Joint ci ratio: 2.946036e-01	ci left: 2.396202e-04	ci right 3.238174e-04	k: 176	n:630000
Cons ci ratio: 9.447907e-04	ci left: 9.642382e-01	ci right 9.651512e-01	k: 607759	n:630000
KS ci ratio: 2.946036e-01	ci left: 2.396202e-04	ci right 3.238174e-04	k: 176	n:630000
LLGL2   630000 perm   289 sec   (2184 perm/sec)   p_kst 2.793651e-04   p_cons 9.646968e-01   p_joint 2.793651e-04

Joint ci ratio: 2.913299e-01	ci left: 2.416669e-04	ci right 3.254657e-04	k: 180	n:640000
Cons ci ratio: 9.380029e-04	ci left: 9.641963e-01	ci right 9.651026e-01	k: 617377	n:640000
KS ci ratio: 2.913299e-01	ci left: 2.416669e-04	ci right 3.254657e-04	k: 180	n:640000
LLGL2   640000 perm   295 sec   (2166 perm/sec)   p_kst 2.812500e-04   p_cons 9.646516e-01   p_joint 2.812500e-04

Joint ci ratio: 2.897337e-01	ci left: 2.408017e-04	ci right 3.237590e-04	k: 182	n:650000
Cons ci ratio: 9.303711e-04	ci left: 9.642284e-01	ci right 9.651274e-01	k: 627042	n:650000
KS ci ratio: 2.897337e-01	ci left: 2.408017e-04	ci right 3.237590e-04	k: 182	n:650000
LLGL2   650000 perm   302 sec   (2149 perm/sec)   p_kst 2.800000e-04   p_cons 9.646800e-01   p_joint 2.800000e-04

Joint ci ratio: 2.873876e-01	ci left: 2.413697e-04	ci right 3.237271e-04	k: 185	n:660000
Cons ci ratio: 9.238867e-04	ci left: 9.641880e-01	ci right 9.650807e-01	k: 636660	n:660000
KS ci ratio: 2.873876e-01	ci left: 2.413697e-04	ci right 3.237271e-04	k: 185	n:660000
LLGL2   660000 perm   310 sec   (2131 perm/sec)   p_kst 2.803030e-04   p_cons 9.646364e-01   p_joint 2.803030e-04

Joint ci ratio: 2.858551e-01	ci left: 2.405377e-04	ci right 3.220945e-04	k: 187	n:670000
Cons ci ratio: 9.170333e-04	ci left: 9.641863e-01	ci right 9.650724e-01	k: 646303	n:670000
KS ci ratio: 2.858551e-01	ci left: 2.405377e-04	ci right 3.220945e-04	k: 187	n:670000
LLGL2   670000 perm   317 sec   (2114 perm/sec)   p_kst 2.791045e-04   p_cons 9.646313e-01   p_joint 2.791045e-04

Joint ci ratio: 2.821275e-01	ci left: 2.438297e-04	ci right 3.252329e-04	k: 192	n:680000
Cons ci ratio: 9.101537e-04	ci left: 9.641980e-01	ci right 9.650774e-01	k: 655955	n:680000
KS ci ratio: 2.821275e-01	ci left: 2.438297e-04	ci right 3.252329e-04	k: 192	n:680000
LLGL2   680000 perm   324 sec   (2098 perm/sec)   p_kst 2.823529e-04   p_cons 9.646397e-01   p_joint 2.823529e-04

Joint ci ratio: 2.806772e-01	ci left: 2.429900e-04	ci right 3.236220e-04	k: 194	n:690000
Cons ci ratio: 9.037912e-04	ci left: 9.641817e-01	ci right 9.650550e-01	k: 665588	n:690000
KS ci ratio: 2.806772e-01	ci left: 2.429900e-04	ci right 3.236220e-04	k: 194	n:690000
LLGL2   690000 perm   332 sec   (2080 perm/sec)   p_kst 2.811594e-04   p_cons 9.646203e-01   p_joint 2.811594e-04

Joint ci ratio: 2.806777e-01	ci left: 2.395186e-04	ci right 3.189989e-04	k: 194	n:700000
Cons ci ratio: 8.977852e-04	ci left: 9.641487e-01	ci right 9.650161e-01	k: 675209	n:700000
KS ci ratio: 2.806777e-01	ci left: 2.395186e-04	ci right 3.189989e-04	k: 194	n:700000
LLGL2   700000 perm   339 sec   (2063 perm/sec)   p_kst 2.771429e-04   p_cons 9.645843e-01   p_joint 2.771429e-04

Joint ci ratio: 2.778423e-01	ci left: 2.413845e-04	ci right 3.205332e-04	k: 198	n:710000
Cons ci ratio: 8.918415e-04	ci left: 9.641208e-01	ci right 9.649824e-01	k: 684833	n:710000
KS ci ratio: 2.778423e-01	ci left: 2.413845e-04	ci right 3.205332e-04	k: 198	n:710000
LLGL2   710000 perm   347 sec   (2047 perm/sec)   p_kst 2.788732e-04   p_cons 9.645535e-01   p_joint 2.788732e-04

Joint ci ratio: 2.771472e-01	ci left: 2.393241e-04	ci right 3.175667e-04	k: 199	n:720000
Cons ci ratio: 8.861754e-04	ci left: 9.640812e-01	ci right 9.649373e-01	k: 694448	n:720000
KS ci ratio: 2.771472e-01	ci left: 2.393241e-04	ci right 3.175667e-04	k: 199	n:720000
LLGL2   720000 perm   355 sec   (2031 perm/sec)   p_kst 2.763889e-04   p_cons 9.645111e-01   p_joint 2.763889e-04

Joint ci ratio: 2.737460e-01	ci left: 2.424221e-04	ci right 3.205376e-04	k: 204	n:730000
Cons ci ratio: 8.806851e-04	ci left: 9.640372e-01	ci right 9.648879e-01	k: 704059	n:730000
KS ci ratio: 2.737460e-01	ci left: 2.424221e-04	ci right 3.205376e-04	k: 204	n:730000
LLGL2   730000 perm   362 sec   (2015 perm/sec)   p_kst 2.794521e-04   p_cons 9.644644e-01   p_joint 2.794521e-04

Joint ci ratio: 2.724205e-01	ci left: 2.416638e-04	ci right 3.190933e-04	k: 206	n:740000
Cons ci ratio: 8.750010e-04	ci left: 9.640175e-01	ci right 9.648627e-01	k: 713687	n:740000
KS ci ratio: 2.724205e-01	ci left: 2.416638e-04	ci right 3.190933e-04	k: 206	n:740000
LLGL2   740000 perm   370 sec   (2000 perm/sec)   p_kst 2.783784e-04   p_cons 9.644419e-01   p_joint 2.783784e-04

Joint ci ratio: 2.685557e-01	ci left: 2.458992e-04	ci right 3.233798e-04	k: 212	n:750000
Cons ci ratio: 8.690705e-04	ci left: 9.640265e-01	ci right 9.648659e-01	k: 723336	n:750000
KS ci ratio: 2.685557e-01	ci left: 2.458992e-04	ci right 3.233798e-04	k: 212	n:750000
LLGL2   750000 perm   378 sec   (1985 perm/sec)   p_kst 2.826667e-04   p_cons 9.644480e-01   p_joint 2.826667e-04

Joint ci ratio: 2.654576e-01	ci left: 2.488023e-04	ci right 3.261430e-04	k: 217	n:760000
Cons ci ratio: 8.636730e-04	ci left: 9.640022e-01	ci right 9.648364e-01	k: 732960	n:760000
KS ci ratio: 2.654576e-01	ci left: 2.488023e-04	ci right 3.261430e-04	k: 217	n:760000
LLGL2   760000 perm   386 sec   (1970 perm/sec)   p_kst 2.855263e-04   p_cons 9.644211e-01   p_joint 2.855263e-04

Joint ci ratio: 2.642484e-01	ci left: 2.479961e-04	ci right 3.246769e-04	k: 219	n:770000
Cons ci ratio: 8.578386e-04	ci left: 9.640216e-01	ci right 9.648502e-01	k: 742617	n:770000
KS ci ratio: 2.642484e-01	ci left: 2.479961e-04	ci right 3.246769e-04	k: 219	n:770000
LLGL2   770000 perm   394 sec   (1956 perm/sec)   p_kst 2.844156e-04   p_cons 9.644377e-01   p_joint 2.844156e-04

Joint ci ratio: 2.630556e-01	ci left: 2.472113e-04	ci right 3.232475e-04	k: 221	n:780000
Cons ci ratio: 8.521047e-04	ci left: 9.640419e-01	ci right 9.648649e-01	k: 752275	n:780000
KS ci ratio: 2.630556e-01	ci left: 2.472113e-04	ci right 3.232475e-04	k: 221	n:780000
LLGL2   780000 perm   402 sec   (1941 perm/sec)   p_kst 2.833333e-04   p_cons 9.644551e-01   p_joint 2.833333e-04

Joint ci ratio: 2.624654e-01	ci left: 2.452644e-04	ci right 3.205049e-04	k: 222	n:790000
Cons ci ratio: 8.469529e-04	ci left: 9.640234e-01	ci right 9.648415e-01	k: 761903	n:790000
KS ci ratio: 2.624654e-01	ci left: 2.452644e-04	ci right 3.205049e-04	k: 222	n:790000
LLGL2   790000 perm   410 sec   (1926 perm/sec)   p_kst 2.810127e-04   p_cons 9.644342e-01   p_joint 2.810127e-04

Joint ci ratio: 2.607175e-01	ci left: 2.457028e-04	ci right 3.204939e-04	k: 225	n:800000
Cons ci ratio: 8.416632e-04	ci left: 9.640243e-01	ci right 9.648373e-01	k: 771546	n:800000
KS ci ratio: 2.607175e-01	ci left: 2.457028e-04	ci right 3.204939e-04	k: 225	n:800000
LLGL2   800000 perm   419 sec   (1911 perm/sec)   p_kst 2.812500e-04   p_cons 9.644325e-01   p_joint 2.812500e-04

Joint ci ratio: 2.590041e-01	ci left: 2.461319e-04	ci right 3.204816e-04	k: 228	n:810000
Cons ci ratio: 8.362908e-04	ci left: 9.640401e-01	ci right 9.648479e-01	k: 781201	n:810000
KS ci ratio: 2.590041e-01	ci left: 2.461319e-04	ci right 3.204816e-04	k: 228	n:810000
LLGL2   810000 perm   427 sec   (1897 perm/sec)   p_kst 2.814815e-04   p_cons 9.644457e-01   p_joint 2.814815e-04

Joint ci ratio: 2.556758e-01	ci left: 2.499755e-04	ci right 3.243612e-04	k: 234	n:820000
Cons ci ratio: 8.314041e-04	ci left: 9.640237e-01	ci right 9.648267e-01	k: 790830	n:820000
KS ci ratio: 2.556758e-01	ci left: 2.499755e-04	ci right 3.243612e-04	k: 234	n:820000
LLGL2   820000 perm   435 sec   (1883 perm/sec)   p_kst 2.853659e-04   p_cons 9.644268e-01   p_joint 2.853659e-04

Joint ci ratio: 2.540593e-01	ci left: 2.503473e-04	ci right 3.242980e-04	k: 237	n:830000
Cons ci ratio: 8.268049e-04	ci left: 9.639907e-01	ci right 9.647892e-01	k: 800445	n:830000
KS ci ratio: 2.540593e-01	ci left: 2.503473e-04	ci right 3.242980e-04	k: 237	n:830000
LLGL2   830000 perm   444 sec   (1869 perm/sec)   p_kst 2.855422e-04   p_cons 9.643916e-01   p_joint 2.855422e-04

Joint ci ratio: 2.519507e-01	ci left: 2.518270e-04	ci right 3.255005e-04	k: 241	n:840000
Cons ci ratio: 8.221522e-04	ci left: 9.639692e-01	ci right 9.647633e-01	k: 810069	n:840000
KS ci ratio: 2.519507e-01	ci left: 2.518270e-04	ci right 3.255005e-04	k: 241	n:840000
LLGL2   840000 perm   453 sec   (1855 perm/sec)   p_kst 2.869048e-04   p_cons 9.643679e-01   p_joint 2.869048e-04

Joint ci ratio: 2.498938e-01	ci left: 2.532744e-04	ci right 3.266723e-04	k: 245	n:850000
Cons ci ratio: 8.170452e-04	ci left: 9.639933e-01	ci right 9.647824e-01	k: 819731	n:850000
KS ci ratio: 2.498938e-01	ci left: 2.532744e-04	ci right 3.266723e-04	k: 245	n:850000
LLGL2   850000 perm   462 sec   (1841 perm/sec)   p_kst 2.882353e-04   p_cons 9.643894e-01   p_joint 2.882353e-04

Joint ci ratio: 2.493877e-01	ci left: 2.514193e-04	ci right 3.241092e-04	k: 246	n:860000
Cons ci ratio: 8.125132e-04	ci left: 9.639758e-01	ci right 9.647606e-01	k: 829358	n:860000
KS ci ratio: 2.493877e-01	ci left: 2.514193e-04	ci right 3.241092e-04	k: 246	n:860000
LLGL2   860000 perm   470 sec   (1828 perm/sec)   p_kst 2.860465e-04   p_cons 9.643698e-01   p_joint 2.860465e-04

Joint ci ratio: 2.488846e-01	ci left: 2.496071e-04	ci right 3.216049e-04	k: 247	n:870000
Cons ci ratio: 8.080150e-04	ci left: 9.639623e-01	ci right 9.647426e-01	k: 838988	n:870000
KS ci ratio: 2.488846e-01	ci left: 2.496071e-04	ci right 3.216049e-04	k: 247	n:870000
LLGL2   870000 perm   480 sec   (1813 perm/sec)   p_kst 2.839080e-04   p_cons 9.643540e-01   p_joint 2.839080e-04

Joint ci ratio: 2.469013e-01	ci left: 2.510338e-04	ci right 3.227775e-04	k: 251	n:880000
Cons ci ratio: 8.036702e-04	ci left: 9.639422e-01	ci right 9.647183e-01	k: 848612	n:880000
KS ci ratio: 2.469013e-01	ci left: 2.510338e-04	ci right 3.227775e-04	k: 251	n:880000
LLGL2   880000 perm   489 sec   (1801 perm/sec)   p_kst 2.852273e-04   p_cons 9.643318e-01   p_joint 2.852273e-04

Joint ci ratio: 2.454446e-01	ci left: 2.513760e-04	ci right 3.227291e-04	k: 254	n:890000
Cons ci ratio: 7.989246e-04	ci left: 9.639633e-01	ci right 9.647348e-01	k: 858272	n:890000
KS ci ratio: 2.454446e-01	ci left: 2.513760e-04	ci right 3.227291e-04	k: 254	n:890000
LLGL2   890000 perm   498 sec   (1787 perm/sec)   p_kst 2.853933e-04   p_cons 9.643506e-01   p_joint 2.853933e-04

Joint ci ratio: 2.444878e-01	ci left: 2.506688e-04	ci right 3.215016e-04	k: 256	n:900000
Cons ci ratio: 7.944801e-04	ci left: 9.639649e-01	ci right 9.647321e-01	k: 867915	n:900000
KS ci ratio: 2.444878e-01	ci left: 2.506688e-04	ci right 3.215016e-04	k: 256	n:900000
LLGL2   900000 perm   507 sec   (1774 perm/sec)   p_kst 2.844444e-04   p_cons 9.643500e-01   p_joint 2.844444e-04

Joint ci ratio: 2.430732e-01	ci left: 2.510095e-04	ci right 3.214663e-04	k: 259	n:910000
Cons ci ratio: 7.901974e-04	ci left: 9.639587e-01	ci right 9.647218e-01	k: 877551	n:910000
KS ci ratio: 2.430732e-01	ci left: 2.510095e-04	ci right 3.214663e-04	k: 259	n:910000
LLGL2   910000 perm   517 sec   (1761 perm/sec)   p_kst 2.846154e-04   p_cons 9.643418e-01   p_joint 2.846154e-04

Joint ci ratio: 2.416829e-01	ci left: 2.513440e-04	ci right 3.214306e-04	k: 262	n:920000
Cons ci ratio: 7.859583e-04	ci left: 9.639549e-01	ci right 9.647139e-01	k: 887189	n:920000
KS ci ratio: 2.416829e-01	ci left: 2.513440e-04	ci right 3.214306e-04	k: 262	n:920000
LLGL2   920000 perm   526 sec   (1748 perm/sec)   p_kst 2.847826e-04   p_cons 9.643359e-01   p_joint 2.847826e-04

Joint ci ratio: 2.398655e-01	ci left: 2.526830e-04	ci right 3.225344e-04	k: 266	n:930000
Cons ci ratio: 7.815911e-04	ci left: 9.639685e-01	ci right 9.647233e-01	k: 896843	n:930000
KS ci ratio: 2.398655e-01	ci left: 2.526830e-04	ci right 3.225344e-04	k: 266	n:930000
LLGL2   930000 perm   537 sec   (1733 perm/sec)   p_kst 2.860215e-04   p_cons 9.643473e-01   p_joint 2.860215e-04

Joint ci ratio: 2.380886e-01	ci left: 2.539954e-04	ci right 3.236128e-04	k: 270	n:940000
Cons ci ratio: 7.774522e-04	ci left: 9.639679e-01	ci right 9.647186e-01	k: 906484	n:940000
KS ci ratio: 2.380886e-01	ci left: 2.539954e-04	ci right 3.236128e-04	k: 270	n:940000
LLGL2   940000 perm   547 sec   (1720 perm/sec)   p_kst 2.872340e-04   p_cons 9.643447e-01   p_joint 2.872340e-04

Joint ci ratio: 2.372150e-01	ci left: 2.533017e-04	ci right 3.224367e-04	k: 272	n:950000
Cons ci ratio: 7.731771e-04	ci left: 9.639853e-01	ci right 9.647319e-01	k: 916142	n:950000
KS ci ratio: 2.372150e-01	ci left: 2.533017e-04	ci right 3.224367e-04	k: 272	n:950000
LLGL2   950000 perm   556 sec   (1708 perm/sec)   p_kst 2.863158e-04   p_cons 9.643600e-01   p_joint 2.863158e-04

Joint ci ratio: 2.359222e-01	ci left: 2.536029e-04	ci right 3.223879e-04	k: 275	n:960000
Cons ci ratio: 7.691116e-04	ci left: 9.639897e-01	ci right 9.647325e-01	k: 925788	n:960000
KS ci ratio: 2.359222e-01	ci left: 2.536029e-04	ci right 3.223879e-04	k: 275	n:960000
LLGL2   960000 perm   566 sec   (1696 perm/sec)   p_kst 2.864583e-04   p_cons 9.643625e-01   p_joint 2.864583e-04

Joint ci ratio: 2.350722e-01	ci left: 2.529287e-04	ci right 3.212476e-04	k: 277	n:970000
Cons ci ratio: 7.649488e-04	ci left: 9.640086e-01	ci right 9.647473e-01	k: 935448	n:970000
KS ci ratio: 2.350722e-01	ci left: 2.529287e-04	ci right 3.212476e-04	k: 277	n:970000
LLGL2   970000 perm   576 sec   (1684 perm/sec)   p_kst 2.855670e-04   p_cons 9.643794e-01   p_joint 2.855670e-04

Joint ci ratio: 2.338139e-01	ci left: 2.532292e-04	ci right 3.212103e-04	k: 280	n:980000
Cons ci ratio: 7.612596e-04	ci left: 9.639902e-01	ci right 9.647254e-01	k: 945072	n:980000
KS ci ratio: 2.338139e-01	ci left: 2.532292e-04	ci right 3.212103e-04	k: 280	n:980000
LLGL2   980000 perm   586 sec   (1672 perm/sec)   p_kst 2.857143e-04   p_cons 9.643592e-01   p_joint 2.857143e-04

Joint ci ratio: 2.329864e-01	ci left: 2.525734e-04	ci right 3.201038e-04	k: 282	n:990000
Cons ci ratio: 7.574227e-04	ci left: 9.639905e-01	ci right 9.647219e-01	k: 954714	n:990000
KS ci ratio: 2.329864e-01	ci left: 2.525734e-04	ci right 3.201038e-04	k: 282	n:990000
LLGL2   990000 perm   597 sec   (1659 perm/sec)   p_kst 2.848485e-04   p_cons 9.643576e-01   p_joint 2.848485e-04

Joint ci ratio: 2.321676e-01	ci left: 2.519311e-04	ci right 3.190191e-04	k: 284	n:1000000
Cons ci ratio: 7.537638e-04	ci left: 9.639797e-01	ci right 9.647076e-01	k: 964345	n:1000000
KS ci ratio: 2.321676e-01	ci left: 2.519311e-04	ci right 3.190191e-04	k: 284	n:1000000
LLGL2   1000000 perm   607 sec   (1648 perm/sec)   p_kst 2.840000e-04   p_cons 9.643450e-01   p_joint 2.840000e-04

Joint ci ratio: 2.293674e-01	ci left: 2.559669e-04	ci right 3.231911e-04	k: 291	n:1010000
Cons ci ratio: 7.503085e-04	ci left: 9.639552e-01	ci right 9.646797e-01	k: 973962	n:1010000
KS ci ratio: 2.293674e-01	ci left: 2.559669e-04	ci right 3.231911e-04	k: 291	n:1010000
LLGL2   1010000 perm   617 sec   (1638 perm/sec)   p_kst 2.881188e-04   p_cons 9.643188e-01   p_joint 2.881188e-04

Joint ci ratio: 2.285860e-01	ci left: 2.553057e-04	ci right 3.220956e-04	k: 293	n:1020000
Cons ci ratio: 7.463255e-04	ci left: 9.639844e-01	ci right 9.647051e-01	k: 983633	n:1020000
KS ci ratio: 2.285860e-01	ci left: 2.553057e-04	ci right 3.220956e-04	k: 293	n:1020000
LLGL2   1020000 perm   628 sec   (1624 perm/sec)   p_kst 2.872549e-04   p_cons 9.643461e-01   p_joint 2.872549e-04

Joint ci ratio: 2.270465e-01	ci left: 2.564889e-04	ci right 3.230732e-04	k: 297	n:1030000
Cons ci ratio: 7.425936e-04	ci left: 9.639955e-01	ci right 9.647126e-01	k: 993286	n:1030000
KS ci ratio: 2.270465e-01	ci left: 2.564889e-04	ci right 3.230732e-04	k: 297	n:1030000
LLGL2   1030000 perm   638 sec   (1613 perm/sec)   p_kst 2.883495e-04   p_cons 9.643553e-01   p_joint 2.883495e-04

Joint ci ratio: 2.251652e-01	ci left: 2.585581e-04	ci right 3.250462e-04	k: 302	n:1040000
Cons ci ratio: 7.389585e-04	ci left: 9.640025e-01	ci right 9.647161e-01	k: 1002935	n:1040000
KS ci ratio: 2.251652e-01	ci left: 2.585581e-04	ci right 3.250462e-04	k: 302	n:1040000
LLGL2   1040000 perm   649 sec   (1602 perm/sec)   p_kst 2.903846e-04   p_cons 9.643606e-01   p_joint 2.903846e-04

Joint ci ratio: 2.236934e-01	ci left: 2.596910e-04	ci right 3.259739e-04	k: 306	n:1050000
Cons ci ratio: 7.352539e-04	ci left: 9.640209e-01	ci right 9.647309e-01	k: 1012596	n:1050000
KS ci ratio: 2.236934e-01	ci left: 2.596910e-04	ci right 3.259739e-04	k: 306	n:1050000
LLGL2   1050000 perm   660 sec   (1591 perm/sec)   p_kst 2.914286e-04   p_cons 9.643771e-01   p_joint 2.914286e-04

Joint ci ratio: 2.229684e-01	ci left: 2.590224e-04	ci right 3.248908e-04	k: 308	n:1060000
Cons ci ratio: 7.315540e-04	ci left: 9.640436e-01	ci right 9.647501e-01	k: 1022262	n:1060000
KS ci ratio: 2.229684e-01	ci left: 2.590224e-04	ci right 3.248908e-04	k: 308	n:1060000
LLGL2   1060000 perm   671 sec   (1580 perm/sec)   p_kst 2.905660e-04   p_cons 9.643981e-01   p_joint 2.905660e-04

Joint ci ratio: 2.222504e-01	ci left: 2.583665e-04	ci right 3.238277e-04	k: 310	n:1070000
Cons ci ratio: 7.283749e-04	ci left: 9.640218e-01	ci right 9.647252e-01	k: 1031881	n:1070000
KS ci ratio: 2.222504e-01	ci left: 2.583665e-04	ci right 3.238277e-04	k: 310	n:1070000
LLGL2   1070000 perm   682 sec   (1570 perm/sec)   p_kst 2.897196e-04   p_cons 9.643748e-01   p_joint 2.897196e-04

Joint ci ratio: 2.222507e-01	ci left: 2.559742e-04	ci right 3.208293e-04	k: 310	n:1080000
Cons ci ratio: 7.249827e-04	ci left: 9.640246e-01	ci right 9.647247e-01	k: 1041526	n:1080000
KS ci ratio: 2.222507e-01	ci left: 2.559742e-04	ci right 3.208293e-04	k: 310	n:1080000
LLGL2   1080000 perm   692 sec   (1561 perm/sec)   p_kst 2.870370e-04   p_cons 9.643759e-01   p_joint 2.870370e-04

Joint ci ratio: 2.215396e-01	ci left: 2.553587e-04	ci right 3.198226e-04	k: 312	n:1090000
Cons ci ratio: 7.217241e-04	ci left: 9.640191e-01	ci right 9.647160e-01	k: 1051162	n:1090000
KS ci ratio: 2.215396e-01	ci left: 2.553587e-04	ci right 3.198226e-04	k: 312	n:1090000
LLGL2   1090000 perm   703 sec   (1552 perm/sec)   p_kst 2.862385e-04   p_cons 9.643688e-01   p_joint 2.862385e-04

Joint ci ratio: 2.211867e-01	ci left: 2.538959e-04	ci right 3.178746e-04	k: 313	n:1100000
Cons ci ratio: 7.187656e-04	ci left: 9.639890e-01	ci right 9.646831e-01	k: 1060771	n:1100000
KS ci ratio: 2.211867e-01	ci left: 2.538959e-04	ci right 3.178746e-04	k: 313	n:1100000
LLGL2   1100000 perm   714 sec   (1542 perm/sec)   p_kst 2.845455e-04   p_cons 9.643373e-01   p_joint 2.845455e-04

Joint ci ratio: 2.187613e-01	ci left: 2.575675e-04	ci right 3.216640e-04	k: 320	n:1110000
Cons ci ratio: 7.152240e-04	ci left: 9.640192e-01	ci right 9.647099e-01	k: 1070446	n:1110000
KS ci ratio: 2.187613e-01	ci left: 2.575675e-04	ci right 3.216640e-04	k: 320	n:1110000
LLGL2   1110000 perm   725 sec   (1531 perm/sec)   p_kst 2.882883e-04   p_cons 9.643658e-01   p_joint 2.882883e-04

Joint ci ratio: 2.180831e-01	ci left: 2.569558e-04	ci right 3.206753e-04	k: 322	n:1120000
Cons ci ratio: 7.122519e-04	ci left: 9.639987e-01	ci right 9.646864e-01	k: 1080065	n:1120000
KS ci ratio: 2.180831e-01	ci left: 2.569558e-04	ci right 3.206753e-04	k: 322	n:1120000
LLGL2   1120000 perm   737 sec   (1521 perm/sec)   p_kst 2.875000e-04   p_cons 9.643438e-01   p_joint 2.875000e-04

Joint ci ratio: 2.174111e-01	ci left: 2.563552e-04	ci right 3.197037e-04	k: 324	n:1130000
Cons ci ratio: 7.094166e-04	ci left: 9.639687e-01	ci right 9.646537e-01	k: 1089673	n:1130000
KS ci ratio: 2.174111e-01	ci left: 2.563552e-04	ci right 3.197037e-04	k: 324	n:1130000
LLGL2   1130000 perm   748 sec   (1512 perm/sec)   p_kst 2.867257e-04   p_cons 9.643124e-01   p_joint 2.867257e-04

Joint ci ratio: 2.157576e-01	ci left: 2.582546e-04	ci right 3.215228e-04	k: 329	n:1140000
Cons ci ratio: 7.061822e-04	ci left: 9.639816e-01	ci right 9.646634e-01	k: 1099329	n:1140000
KS ci ratio: 2.157576e-01	ci left: 2.582546e-04	ci right 3.215228e-04	k: 329	n:1140000
LLGL2   1140000 perm   759 sec   (1502 perm/sec)   p_kst 2.885965e-04   p_cons 9.643237e-01   p_joint 2.885965e-04

Joint ci ratio: 2.147835e-01	ci left: 2.584770e-04	ci right 3.214760e-04	k: 332	n:1150000
Cons ci ratio: 7.031428e-04	ci left: 9.639794e-01	ci right 9.646583e-01	k: 1108968	n:1150000
KS ci ratio: 2.147835e-01	ci left: 2.584770e-04	ci right 3.214760e-04	k: 332	n:1150000
LLGL2   1150000 perm   770 sec   (1493 perm/sec)   p_kst 2.886957e-04   p_cons 9.643200e-01   p_joint 2.886957e-04

Joint ci ratio: 2.135049e-01	ci left: 2.595121e-04	ci right 3.223376e-04	k: 336	n:1160000
Cons ci ratio: 6.999668e-04	ci left: 9.639945e-01	ci right 9.646704e-01	k: 1118627	n:1160000
KS ci ratio: 2.135049e-01	ci left: 2.595121e-04	ci right 3.223376e-04	k: 336	n:1160000
LLGL2   1160000 perm   782 sec   (1484 perm/sec)   p_kst 2.896552e-04   p_cons 9.643336e-01   p_joint 2.896552e-04

Joint ci ratio: 2.116290e-01	ci left: 2.621493e-04	ci right 3.249833e-04	k: 342	n:1170000
Cons ci ratio: 6.973355e-04	ci left: 9.639596e-01	ci right 9.646329e-01	k: 1128228	n:1170000
KS ci ratio: 2.116290e-01	ci left: 2.621493e-04	ci right 3.249833e-04	k: 342	n:1170000
LLGL2   1170000 perm   794 sec   (1474 perm/sec)   p_kst 2.923077e-04   p_cons 9.642974e-01   p_joint 2.923077e-04

Joint ci ratio: 2.116293e-01	ci left: 2.599276e-04	ci right 3.222293e-04	k: 342	n:1180000
Cons ci ratio: 6.944681e-04	ci left: 9.639517e-01	ci right 9.646222e-01	k: 1137860	n:1180000
KS ci ratio: 2.116293e-01	ci left: 2.599276e-04	ci right 3.222293e-04	k: 342	n:1180000
LLGL2   1180000 perm   805 sec   (1466 perm/sec)   p_kst 2.898305e-04   p_cons 9.642881e-01   p_joint 2.898305e-04

Joint ci ratio: 2.095019e-01	ci left: 2.633156e-04	ci right 3.257135e-04	k: 349	n:1190000
Cons ci ratio: 6.917117e-04	ci left: 9.639364e-01	ci right 9.646042e-01	k: 1147483	n:1190000
KS ci ratio: 2.095019e-01	ci left: 2.633156e-04	ci right 3.257135e-04	k: 349	n:1190000
LLGL2   1190000 perm   816 sec   (1458 perm/sec)   p_kst 2.932773e-04   p_cons 9.642714e-01   p_joint 2.932773e-04

Joint ci ratio: 2.095022e-01	ci left: 2.611213e-04	ci right 3.229993e-04	k: 349	n:1200000
Cons ci ratio: 6.886295e-04	ci left: 9.639573e-01	ci right 9.646221e-01	k: 1157149	n:1200000
KS ci ratio: 2.095022e-01	ci left: 2.611213e-04	ci right 3.229993e-04	k: 349	n:1200000
LLGL2   1200000 perm   828 sec   (1450 perm/sec)   p_kst 2.908333e-04   p_cons 9.642908e-01   p_joint 2.908333e-04

Joint ci ratio: 2.092037e-01	ci left: 2.597464e-04	ci right 3.211996e-04	k: 350	n:1210000
Cons ci ratio: 6.855879e-04	ci left: 9.639778e-01	ci right 9.646398e-01	k: 1166815	n:1210000
KS ci ratio: 2.092037e-01	ci left: 2.597464e-04	ci right 3.211996e-04	k: 350	n:1210000
LLGL2   1210000 perm   839 sec   (1442 perm/sec)   p_kst 2.892562e-04   p_cons 9.643099e-01   p_joint 2.892562e-04

Joint ci ratio: 2.083153e-01	ci left: 2.599478e-04	ci right 3.211542e-04	k: 353	n:1220000
Cons ci ratio: 6.827893e-04	ci left: 9.639775e-01	ci right 9.646367e-01	k: 1176456	n:1220000
KS ci ratio: 2.083153e-01	ci left: 2.599478e-04	ci right 3.211542e-04	k: 353	n:1220000
LLGL2   1220000 perm   851 sec   (1434 perm/sec)   p_kst 2.893443e-04   p_cons 9.643082e-01   p_joint 2.893443e-04

Joint ci ratio: 2.074382e-01	ci left: 2.601464e-04	ci right 3.211090e-04	k: 356	n:1230000
Cons ci ratio: 6.800890e-04	ci left: 9.639706e-01	ci right 9.646272e-01	k: 1186089	n:1230000
KS ci ratio: 2.074382e-01	ci left: 2.601464e-04	ci right 3.211090e-04	k: 356	n:1230000
LLGL2   1230000 perm   862 sec   (1427 perm/sec)   p_kst 2.894309e-04   p_cons 9.643000e-01   p_joint 2.894309e-04

Joint ci ratio: 2.065721e-01	ci left: 2.603424e-04	ci right 3.210640e-04	k: 359	n:1240000
Cons ci ratio: 6.774998e-04	ci left: 9.639557e-01	ci right 9.646098e-01	k: 1195712	n:1240000
KS ci ratio: 2.065721e-01	ci left: 2.603424e-04	ci right 3.210640e-04	k: 359	n:1240000
LLGL2   1240000 perm   874 sec   (1419 perm/sec)   p_kst 2.895161e-04   p_cons 9.642839e-01   p_joint 2.895161e-04

Joint ci ratio: 2.054338e-01	ci left: 2.612946e-04	ci right 3.218603e-04	k: 363	n:1250000
Cons ci ratio: 6.747595e-04	ci left: 9.639596e-01	ci right 9.646110e-01	k: 1205358	n:1250000
KS ci ratio: 2.054338e-01	ci left: 2.612946e-04	ci right 3.218603e-04	k: 363	n:1250000
LLGL2   1250000 perm   886 sec   (1412 perm/sec)   p_kst 2.904000e-04   p_cons 9.642864e-01   p_joint 2.904000e-04

Joint ci ratio: 2.040371e-01	ci left: 2.629857e-04	ci right 3.234772e-04	k: 368	n:1260000
Cons ci ratio: 6.721142e-04	ci left: 9.639570e-01	ci right 9.646059e-01	k: 1214996	n:1260000
KS ci ratio: 2.040371e-01	ci left: 2.629857e-04	ci right 3.234772e-04	k: 368	n:1260000
LLGL2   1260000 perm   897 sec   (1404 perm/sec)   p_kst 2.920635e-04   p_cons 9.642825e-01   p_joint 2.920635e-04

Joint ci ratio: 2.023980e-01	ci left: 2.653990e-04	ci right 3.258946e-04	k: 374	n:1270000
Cons ci ratio: 6.694921e-04	ci left: 9.639553e-01	ci right 9.646016e-01	k: 1224635	n:1270000
KS ci ratio: 2.023980e-01	ci left: 2.653990e-04	ci right 3.258946e-04	k: 374	n:1270000
LLGL2   1270000 perm   909 sec   (1397 perm/sec)   p_kst 2.944882e-04   p_cons 9.642795e-01   p_joint 2.944882e-04

Joint ci ratio: 2.018605e-01	ci left: 2.648090e-04	ci right 3.249900e-04	k: 376	n:1280000
Cons ci ratio: 6.670667e-04	ci left: 9.639363e-01	ci right 9.645803e-01	k: 1234252	n:1280000
KS ci ratio: 2.018605e-01	ci left: 2.648090e-04	ci right 3.249900e-04	k: 376	n:1280000
LLGL2   1280000 perm   922 sec   (1389 perm/sec)   p_kst 2.937500e-04   p_cons 9.642594e-01   p_joint 2.937500e-04

Joint ci ratio: 2.013272e-01	ci left: 2.642283e-04	ci right 3.240993e-04	k: 378	n:1290000
Cons ci ratio: 6.642563e-04	ci left: 9.639605e-01	ci right 9.646018e-01	k: 1243924	n:1290000
KS ci ratio: 2.013272e-01	ci left: 2.642283e-04	ci right 3.240993e-04	k: 378	n:1290000
LLGL2   1290000 perm   934 sec   (1382 perm/sec)   p_kst 2.930233e-04   p_cons 9.642822e-01   p_joint 2.930233e-04

Joint ci ratio: 2.013274e-01	ci left: 2.621958e-04	ci right 3.216062e-04	k: 378	n:1300000
Cons ci ratio: 6.615770e-04	ci left: 9.639742e-01	ci right 9.646129e-01	k: 1253583	n:1300000
KS ci ratio: 2.013274e-01	ci left: 2.621958e-04	ci right 3.216062e-04	k: 378	n:1300000
LLGL2   1300000 perm   946 sec   (1374 perm/sec)   p_kst 2.907692e-04   p_cons 9.642946e-01   p_joint 2.907692e-04

Joint ci ratio: 2.005353e-01	ci left: 2.623691e-04	ci right 3.215564e-04	k: 381	n:1310000
Cons ci ratio: 6.589078e-04	ci left: 9.639901e-01	ci right 9.646262e-01	k: 1263245	n:1310000
KS ci ratio: 2.005353e-01	ci left: 2.623691e-04	ci right 3.215564e-04	k: 381	n:1310000
LLGL2   1310000 perm   958 sec   (1367 perm/sec)   p_kst 2.908397e-04   p_cons 9.643092e-01   p_joint 2.908397e-04

Joint ci ratio: 1.994935e-01	ci left: 2.632601e-04	ci right 3.223022e-04	k: 385	n:1320000
Cons ci ratio: 6.565667e-04	ci left: 9.639745e-01	ci right 9.646083e-01	k: 1272866	n:1320000
KS ci ratio: 1.994935e-01	ci left: 2.632601e-04	ci right 3.223022e-04	k: 385	n:1320000
LLGL2   1320000 perm   971 sec   (1360 perm/sec)   p_kst 2.916667e-04   p_cons 9.642924e-01   p_joint 2.916667e-04

Joint ci ratio: 1.989787e-01	ci left: 2.627094e-04	ci right 3.214576e-04	k: 387	n:1330000
Cons ci ratio: 6.541431e-04	ci left: 9.639704e-01	ci right 9.646020e-01	k: 1282502	n:1330000
KS ci ratio: 1.989787e-01	ci left: 2.627094e-04	ci right 3.214576e-04	k: 387	n:1330000
LLGL2   1330000 perm   983 sec   (1353 perm/sec)   p_kst 2.909774e-04   p_cons 9.642872e-01   p_joint 2.909774e-04

Joint ci ratio: 1.987230e-01	ci left: 2.614580e-04	ci right 3.198420e-04	k: 388	n:1340000
Cons ci ratio: 6.516827e-04	ci left: 9.639732e-01	ci right 9.646024e-01	k: 1292147	n:1340000
KS ci ratio: 1.987230e-01	ci left: 2.614580e-04	ci right 3.198420e-04	k: 388	n:1340000
LLGL2   1340000 perm   996 sec   (1346 perm/sec)   p_kst 2.895522e-04   p_cons 9.642888e-01   p_joint 2.895522e-04

Joint ci ratio: 1.982141e-01	ci left: 2.609291e-04	ci right 3.190278e-04	k: 390	n:1350000
Cons ci ratio: 6.492428e-04	ci left: 9.639767e-01	ci right 9.646035e-01	k: 1301793	n:1350000
KS ci ratio: 1.982141e-01	ci left: 2.609291e-04	ci right 3.190278e-04	k: 390	n:1350000
LLGL2   1350000 perm   1008 sec   (1339 perm/sec)   p_kst 2.888889e-04   p_cons 9.642911e-01   p_joint 2.888889e-04

Joint ci ratio: 1.979613e-01	ci left: 2.597093e-04	ci right 3.174538e-04	k: 391	n:1360000
Cons ci ratio: 6.468508e-04	ci left: 9.639780e-01	ci right 9.646024e-01	k: 1311436	n:1360000
KS ci ratio: 1.979613e-01	ci left: 2.597093e-04	ci right 3.174538e-04	k: 391	n:1360000
LLGL2   1360000 perm   1020 sec   (1333 perm/sec)   p_kst 2.875000e-04   p_cons 9.642912e-01   p_joint 2.875000e-04

Joint ci ratio: 1.974583e-01	ci left: 2.592012e-04	ci right 3.166686e-04	k: 393	n:1370000
Cons ci ratio: 6.446217e-04	ci left: 9.639645e-01	ci right 9.645868e-01	k: 1321059	n:1370000
KS ci ratio: 1.974583e-01	ci left: 2.592012e-04	ci right 3.166686e-04	k: 393	n:1370000
LLGL2   1370000 perm   1033 sec   (1326 perm/sec)   p_kst 2.868613e-04   p_cons 9.642766e-01   p_joint 2.868613e-04

Joint ci ratio: 1.969591e-01	ci left: 2.587007e-04	ci right 3.158947e-04	k: 395	n:1380000
Cons ci ratio: 6.423140e-04	ci left: 9.639622e-01	ci right 9.645823e-01	k: 1330697	n:1380000
KS ci ratio: 1.969591e-01	ci left: 2.587007e-04	ci right 3.158947e-04	k: 395	n:1380000
LLGL2   1380000 perm   1046 sec   (1320 perm/sec)   p_kst 2.862319e-04   p_cons 9.642732e-01   p_joint 2.862319e-04

Joint ci ratio: 1.964636e-01	ci left: 2.582075e-04	ci right 3.151317e-04	k: 397	n:1390000
Cons ci ratio: 6.399574e-04	ci left: 9.639678e-01	ci right 9.645856e-01	k: 1340346	n:1390000
KS ci ratio: 1.964636e-01	ci left: 2.582075e-04	ci right 3.151317e-04	k: 397	n:1390000
LLGL2   1390000 perm   1059 sec   (1313 perm/sec)   p_kst 2.856115e-04   p_cons 9.642777e-01   p_joint 2.856115e-04

Joint ci ratio: 1.949991e-01	ci left: 2.604389e-04	ci right 3.173762e-04	k: 403	n:1400000
Cons ci ratio: 6.374282e-04	ci left: 9.639949e-01	ci right 9.646103e-01	k: 1350025	n:1400000
KS ci ratio: 1.949991e-01	ci left: 2.604389e-04	ci right 3.173762e-04	k: 403	n:1400000
LLGL2   1400000 perm   1071 sec   (1307 perm/sec)   p_kst 2.878571e-04   p_cons 9.643036e-01   p_joint 2.878571e-04

Joint ci ratio: 1.935668e-01	ci left: 2.626402e-04	ci right 3.195873e-04	k: 409	n:1410000
Cons ci ratio: 6.349415e-04	ci left: 9.640202e-01	ci right 9.646332e-01	k: 1359702	n:1410000
KS ci ratio: 1.935668e-01	ci left: 2.626402e-04	ci right 3.195873e-04	k: 409	n:1410000
LLGL2   1410000 perm   1085 sec   (1300 perm/sec)   p_kst 2.900709e-04   p_cons 9.643277e-01   p_joint 2.900709e-04

Joint ci ratio: 1.933313e-01	ci left: 2.614607e-04	ci right 3.180750e-04	k: 410	n:1420000
Cons ci ratio: 6.326388e-04	ci left: 9.640282e-01	ci right 9.646389e-01	k: 1369355	n:1420000
KS ci ratio: 1.933313e-01	ci left: 2.614607e-04	ci right 3.180750e-04	k: 410	n:1420000
LLGL2   1420000 perm   1098 sec   (1293 perm/sec)   p_kst 2.887324e-04   p_cons 9.643345e-01   p_joint 2.887324e-04

Joint ci ratio: 1.928627e-01	ci left: 2.609633e-04	ci right 3.173168e-04	k: 412	n:1430000
Cons ci ratio: 6.304828e-04	ci left: 9.640227e-01	ci right 9.646314e-01	k: 1378989	n:1430000
KS ci ratio: 1.928627e-01	ci left: 2.609633e-04	ci right 3.173168e-04	k: 412	n:1430000
LLGL2   1430000 perm   1111 sec   (1287 perm/sec)   p_kst 2.881119e-04   p_cons 9.643280e-01   p_joint 2.881119e-04

Joint ci ratio: 1.914766e-01	ci left: 2.631173e-04	ci right 3.194801e-04	k: 418	n:1440000
Cons ci ratio: 6.283549e-04	ci left: 9.640166e-01	ci right 9.646232e-01	k: 1388622	n:1440000
KS ci ratio: 1.914766e-01	ci left: 2.631173e-04	ci right 3.194801e-04	k: 418	n:1440000
LLGL2   1440000 perm   1125 sec   (1280 perm/sec)   p_kst 2.902778e-04   p_cons 9.643208e-01   p_joint 2.902778e-04

Joint ci ratio: 1.907948e-01	ci left: 2.632726e-04	ci right 3.194446e-04	k: 421	n:1450000
Cons ci ratio: 6.262422e-04	ci left: 9.640113e-01	ci right 9.646158e-01	k: 1398256	n:1450000
KS ci ratio: 1.907948e-01	ci left: 2.632726e-04	ci right 3.194446e-04	k: 421	n:1450000
LLGL2   1450000 perm   1138 sec   (1274 perm/sec)   p_kst 2.903448e-04   p_cons 9.643145e-01   p_joint 2.903448e-04

Joint ci ratio: 1.894525e-01	ci left: 2.653834e-04	ci right 3.215616e-04	k: 427	n:1460000
Cons ci ratio: 6.242562e-04	ci left: 9.639943e-01	ci right 9.645970e-01	k: 1407873	n:1460000
KS ci ratio: 1.894525e-01	ci left: 2.653834e-04	ci right 3.215616e-04	k: 427	n:1460000
LLGL2   1460000 perm   1152 sec   (1267 perm/sec)   p_kst 2.924658e-04   p_cons 9.642966e-01   p_joint 2.924658e-04

Joint ci ratio: 1.885733e-01	ci left: 2.661704e-04	ci right 3.222238e-04	k: 431	n:1470000
Cons ci ratio: 6.221413e-04	ci left: 9.639940e-01	ci right 9.645946e-01	k: 1417514	n:1470000
KS ci ratio: 1.885733e-01	ci left: 2.661704e-04	ci right 3.222238e-04	k: 431	n:1470000
LLGL2   1470000 perm   1165 sec   (1261 perm/sec)   p_kst 2.931973e-04   p_cons 9.642952e-01   p_joint 2.931973e-04

Joint ci ratio: 1.881384e-01	ci left: 2.656596e-04	ci right 3.214616e-04	k: 433	n:1480000
Cons ci ratio: 5.959664e-04	ci left: 9.666343e-01	ci right 9.672112e-01	k: 1431047	n:1480000
KS ci ratio: 1.881384e-01	ci left: 2.656596e-04	ci right 3.214616e-04	k: 433	n:1480000
LLGL2   1480000 perm   1179 sec   (1255 perm/sec)   p_kst 2.925676e-04   p_cons 9.669236e-01   p_joint 2.925676e-04

Joint ci ratio: 1.866390e-01	ci left: 2.683543e-04	ci right 3.242222e-04	k: 440	n:1490000
Cons ci ratio: 5.939708e-04	ci left: 9.666344e-01	ci right 9.672094e-01	k: 1440715	n:1490000
KS ci ratio: 1.866390e-01	ci left: 2.683543e-04	ci right 3.242222e-04	k: 440	n:1490000
LLGL2   1490000 perm   1193 sec   (1249 perm/sec)   p_kst 2.953020e-04   p_cons 9.669228e-01   p_joint 2.953020e-04

Joint ci ratio: 1.851749e-01	ci left: 2.710148e-04	ci right 3.269443e-04	k: 447	n:1500000
Cons ci ratio: 5.920445e-04	ci left: 9.666292e-01	ci right 9.672023e-01	k: 1450375	n:1500000
KS ci ratio: 1.851749e-01	ci left: 2.710148e-04	ci right 3.269443e-04	k: 447	n:1500000
LLGL2   1500000 perm   1207 sec   (1243 perm/sec)   p_kst 2.980000e-04   p_cons 9.669167e-01   p_joint 2.980000e-04

Joint ci ratio: 1.847630e-01	ci left: 2.704832e-04	ci right 3.261648e-04	k: 449	n:1510000
Cons ci ratio: 5.902345e-04	ci left: 9.666134e-01	ci right 9.671848e-01	k: 1460019	n:1510000
KS ci ratio: 1.847630e-01	ci left: 2.704832e-04	ci right 3.261648e-04	k: 449	n:1510000
LLGL2   1510000 perm   1221 sec   (1237 perm/sec)   p_kst 2.973510e-04   p_cons 9.669000e-01   p_joint 2.973510e-04

Joint ci ratio: 1.843538e-01	ci left: 2.699587e-04	ci right 3.253955e-04	k: 451	n:1520000
Cons ci ratio: 5.882353e-04	ci left: 9.666203e-01	ci right 9.671897e-01	k: 1469697	n:1520000
KS ci ratio: 1.843538e-01	ci left: 2.699587e-04	ci right 3.253955e-04	k: 451	n:1520000
LLGL2   1520000 perm   1234 sec   (1231 perm/sec)   p_kst 2.967105e-04   p_cons 9.669059e-01   p_joint 2.967105e-04

Joint ci ratio: 1.837450e-01	ci left: 2.700647e-04	ci right 3.253198e-04	k: 454	n:1530000
Cons ci ratio: 5.863281e-04	ci left: 9.666193e-01	ci right 9.671868e-01	k: 1479363	n:1530000
KS ci ratio: 1.837450e-01	ci left: 2.700647e-04	ci right 3.253198e-04	k: 454	n:1530000
LLGL2   1530000 perm   1248 sec   (1226 perm/sec)   p_kst 2.967320e-04   p_cons 9.669039e-01   p_joint 2.967320e-04

Joint ci ratio: 1.831423e-01	ci left: 2.701696e-04	ci right 3.252447e-04	k: 457	n:1540000
Cons ci ratio: 5.845164e-04	ci left: 9.666097e-01	ci right 9.671755e-01	k: 1489016	n:1540000
KS ci ratio: 1.831423e-01	ci left: 2.701696e-04	ci right 3.252447e-04	k: 457	n:1540000
LLGL2   1540000 perm   1262 sec   (1220 perm/sec)   p_kst 2.967532e-04   p_cons 9.668935e-01   p_joint 2.967532e-04

Joint ci ratio: 1.817583e-01	ci left: 2.727365e-04	ci right 3.278685e-04	k: 464	n:1550000
Cons ci ratio: 5.827213e-04	ci left: 9.666003e-01	ci right 9.671644e-01	k: 1498669	n:1550000
KS ci ratio: 1.817583e-01	ci left: 2.727365e-04	ci right 3.278685e-04	k: 464	n:1550000
LLGL2   1550000 perm   1276 sec   (1215 perm/sec)   p_kst 2.993548e-04   p_cons 9.668832e-01   p_joint 2.993548e-04

Joint ci ratio: 1.807888e-01	ci left: 2.740479e-04	ci right 3.291172e-04	k: 469	n:1560000
Cons ci ratio: 5.807565e-04	ci left: 9.666116e-01	ci right 9.671738e-01	k: 1508354	n:1560000
KS ci ratio: 1.807888e-01	ci left: 2.740479e-04	ci right 3.291172e-04	k: 469	n:1560000
LLGL2   1560000 perm   1290 sec   (1209 perm/sec)   p_kst 3.006410e-04   p_cons 9.668936e-01   p_joint 3.006410e-04

Joint ci ratio: 1.796456e-01	ci left: 2.759517e-04	ci right 3.310147e-04	k: 475	n:1570000
Cons ci ratio: 5.787308e-04	ci left: 9.666318e-01	ci right 9.671920e-01	k: 1518053	n:1570000
KS ci ratio: 1.796456e-01	ci left: 2.759517e-04	ci right 3.310147e-04	k: 475	n:1570000
LLGL2   1570000 perm   1304 sec   (1204 perm/sec)   p_kst 3.025478e-04   p_cons 9.669127e-01   p_joint 3.025478e-04

Joint ci ratio: 1.794573e-01	ci left: 2.748096e-04	ci right 3.295810e-04	k: 476	n:1580000
Cons ci ratio: 5.768287e-04	ci left: 9.666402e-01	ci right 9.671986e-01	k: 1527734	n:1580000
KS ci ratio: 1.794573e-01	ci left: 2.748096e-04	ci right 3.295810e-04	k: 476	n:1580000
LLGL2   1580000 perm   1318 sec   (1199 perm/sec)   p_kst 3.012658e-04   p_cons 9.669203e-01   p_joint 3.012658e-04

Joint ci ratio: 1.785240e-01	ci left: 2.760850e-04	ci right 3.307936e-04	k: 481	n:1590000
Cons ci ratio: 5.748943e-04	ci left: 9.666542e-01	ci right 9.672107e-01	k: 1537424	n:1590000
KS ci ratio: 1.785240e-01	ci left: 2.760850e-04	ci right 3.307936e-04	k: 481	n:1590000
LLGL2   1590000 perm   1333 sec   (1193 perm/sec)   p_kst 3.025157e-04   p_cons 9.669333e-01   p_joint 3.025157e-04

Joint ci ratio: 1.783392e-01	ci left: 2.749565e-04	ci right 3.293790e-04	k: 482	n:1600000
Cons ci ratio: 5.731640e-04	ci left: 9.666474e-01	ci right 9.672022e-01	k: 1547081	n:1600000
KS ci ratio: 1.783392e-01	ci left: 2.749565e-04	ci right 3.293790e-04	k: 482	n:1600000
LLGL2   1600000 perm   1347 sec   (1188 perm/sec)   p_kst 3.012500e-04   p_cons 9.669256e-01   p_joint 3.012500e-04

Joint ci ratio: 1.776052e-01	ci left: 2.756225e-04	ci right 3.299282e-04	k: 486	n:1610000
Cons ci ratio: 5.714603e-04	ci left: 9.666393e-01	ci right 9.671925e-01	k: 1556736	n:1610000
KS ci ratio: 1.776052e-01	ci left: 2.756225e-04	ci right 3.299282e-04	k: 486	n:1610000
LLGL2   1610000 perm   1361 sec   (1183 perm/sec)   p_kst 3.018634e-04   p_cons 9.669168e-01   p_joint 3.018634e-04

Joint ci ratio: 1.770607e-01	ci left: 2.756908e-04	ci right 3.298256e-04	k: 489	n:1620000
Cons ci ratio: 5.695078e-04	ci left: 9.666612e-01	ci right 9.672125e-01	k: 1566439	n:1620000
KS ci ratio: 1.770607e-01	ci left: 2.756908e-04	ci right 3.298256e-04	k: 489	n:1620000
LLGL2   1620000 perm   1376 sec   (1178 perm/sec)   p_kst 3.018519e-04   p_cons 9.669377e-01   p_joint 3.018519e-04

Joint ci ratio: 1.768804e-01	ci left: 2.745858e-04	ci right 3.284428e-04	k: 490	n:1630000
Cons ci ratio: 5.677057e-04	ci left: 9.666680e-01	ci right 9.672175e-01	k: 1576118	n:1630000
KS ci ratio: 1.768804e-01	ci left: 2.745858e-04	ci right 3.284428e-04	k: 490	n:1630000
LLGL2   1630000 perm   1391 sec   (1172 perm/sec)   p_kst 3.006135e-04   p_cons 9.669436e-01   p_joint 3.006135e-04

Joint ci ratio: 1.767007e-01	ci left: 2.734942e-04	ci right 3.270768e-04	k: 491	n:1640000
Cons ci ratio: 5.658828e-04	ci left: 9.666789e-01	ci right 9.672267e-01	k: 1585804	n:1640000
KS ci ratio: 1.767007e-01	ci left: 2.734942e-04	ci right 3.270768e-04	k: 491	n:1640000
LLGL2   1640000 perm   1405 sec   (1167 perm/sec)   p_kst 2.993902e-04   p_cons 9.669537e-01   p_joint 2.993902e-04

Joint ci ratio: 1.765215e-01	ci left: 2.724159e-04	ci right 3.257274e-04	k: 492	n:1650000
Cons ci ratio: 5.642110e-04	ci left: 9.666746e-01	ci right 9.672207e-01	k: 1595465	n:1650000
KS ci ratio: 1.765215e-01	ci left: 2.724159e-04	ci right 3.257274e-04	k: 492	n:1650000
LLGL2   1650000 perm   1421 sec   (1161 perm/sec)   p_kst 2.981818e-04   p_cons 9.669485e-01   p_joint 2.981818e-04

Joint ci ratio: 1.758097e-01	ci left: 2.730783e-04	ci right 3.262809e-04	k: 496	n:1660000
Cons ci ratio: 5.626123e-04	ci left: 9.666636e-01	ci right 9.672082e-01	k: 1605115	n:1660000
KS ci ratio: 1.758097e-01	ci left: 2.730783e-04	ci right 3.262809e-04	k: 496	n:1660000
LLGL2   1660000 perm   1436 sec   (1156 perm/sec)   p_kst 2.987952e-04   p_cons 9.669367e-01   p_joint 2.987952e-04

Joint ci ratio: 1.752814e-01	ci left: 2.731606e-04	ci right 3.262024e-04	k: 499	n:1670000
Cons ci ratio: 5.611950e-04	ci left: 9.666336e-01	ci right 9.671768e-01	k: 1614733	n:1670000
KS ci ratio: 1.752814e-01	ci left: 2.731606e-04	ci right 3.262024e-04	k: 499	n:1670000
LLGL2   1670000 perm   1452 sec   (1150 perm/sec)   p_kst 2.988024e-04   p_cons 9.669060e-01   p_joint 2.988024e-04

Joint ci ratio: 1.747579e-01	ci left: 2.732421e-04	ci right 3.261246e-04	k: 502	n:1680000
Cons ci ratio: 5.594758e-04	ci left: 9.666397e-01	ci right 9.671813e-01	k: 1624411	n:1680000
KS ci ratio: 1.747579e-01	ci left: 2.732421e-04	ci right 3.261246e-04	k: 502	n:1680000
LLGL2   1680000 perm   1467 sec   (1145 perm/sec)   p_kst 2.988095e-04   p_cons 9.669113e-01   p_joint 2.988095e-04

Joint ci ratio: 1.744116e-01	ci left: 2.727570e-04	ci right 3.254299e-04	k: 504	n:1690000
Cons ci ratio: 5.577361e-04	ci left: 9.666500e-01	ci right 9.671898e-01	k: 1634096	n:1690000
KS ci ratio: 1.744116e-01	ci left: 2.727570e-04	ci right 3.254299e-04	k: 504	n:1690000
LLGL2   1690000 perm   1482 sec   (1140 perm/sec)   p_kst 2.982249e-04   p_cons 9.669207e-01   p_joint 2.982249e-04

Joint ci ratio: 1.735544e-01	ci left: 2.739657e-04	ci right 3.265848e-04	k: 509	n:1700000
Cons ci ratio: 5.560790e-04	ci left: 9.666524e-01	ci right 9.671907e-01	k: 1643768	n:1700000
KS ci ratio: 1.735544e-01	ci left: 2.739657e-04	ci right 3.265848e-04	k: 509	n:1700000
LLGL2   1700000 perm   1497 sec   (1135 perm/sec)   p_kst 2.994118e-04   p_cons 9.669224e-01   p_joint 2.994118e-04

Joint ci ratio: 1.727098e-01	ci left: 2.751608e-04	ci right 3.277254e-04	k: 514	n:1710000
Cons ci ratio: 5.543503e-04	ci left: 9.666648e-01	ci right 9.672014e-01	k: 1653457	n:1710000
KS ci ratio: 1.727098e-01	ci left: 2.751608e-04	ci right 3.277254e-04	k: 514	n:1710000
LLGL2   1710000 perm   1513 sec   (1130 perm/sec)   p_kst 3.005848e-04   p_cons 9.669339e-01   p_joint 3.005848e-04

Joint ci ratio: 1.725424e-01	ci left: 2.741173e-04	ci right 3.264266e-04	k: 515	n:1720000
Cons ci ratio: 5.528186e-04	ci left: 9.666561e-01	ci right 9.671912e-01	k: 1663110	n:1720000
KS ci ratio: 1.725424e-01	ci left: 2.741173e-04	ci right 3.264266e-04	k: 515	n:1720000
LLGL2   1720000 perm   1529 sec   (1125 perm/sec)   p_kst 2.994186e-04   p_cons 9.669244e-01   p_joint 2.994186e-04

Joint ci ratio: 1.720430e-01	ci left: 2.741921e-04	ci right 3.263485e-04	k: 518	n:1730000
Cons ci ratio: 5.513144e-04	ci left: 9.666457e-01	ci right 9.671793e-01	k: 1672760	n:1730000
KS ci ratio: 1.720430e-01	ci left: 2.741921e-04	ci right 3.263485e-04	k: 518	n:1730000
LLGL2   1730000 perm   1544 sec   (1120 perm/sec)   p_kst 2.994220e-04   p_cons 9.669133e-01   p_joint 2.994220e-04

Joint ci ratio: 1.715480e-01	ci left: 2.742663e-04	ci right 3.262711e-04	k: 521	n:1740000
Cons ci ratio: 5.497976e-04	ci left: 9.666383e-01	ci right 9.671705e-01	k: 1682415	n:1740000
KS ci ratio: 1.715480e-01	ci left: 2.742663e-04	ci right 3.262711e-04	k: 521	n:1740000
LLGL2   1740000 perm   1560 sec   (1115 perm/sec)   p_kst 2.994253e-04   p_cons 9.669052e-01   p_joint 2.994253e-04

Joint ci ratio: 1.710571e-01	ci left: 2.743399e-04	ci right 3.261945e-04	k: 524	n:1750000
Cons ci ratio: 5.483373e-04	ci left: 9.666259e-01	ci right 9.671566e-01	k: 1692061	n:1750000
KS ci ratio: 1.710571e-01	ci left: 2.743399e-04	ci right 3.261945e-04	k: 524	n:1750000
LLGL2   1750000 perm   1576 sec   (1111 perm/sec)   p_kst 2.994286e-04   p_cons 9.668920e-01   p_joint 2.994286e-04

Joint ci ratio: 1.707323e-01	ci left: 2.738689e-04	ci right 3.255260e-04	k: 526	n:1760000
Cons ci ratio: 5.466459e-04	ci left: 9.666421e-01	ci right 9.671712e-01	k: 1701757	n:1760000
KS ci ratio: 1.707323e-01	ci left: 2.738689e-04	ci right 3.255260e-04	k: 526	n:1760000
LLGL2   1760000 perm   1591 sec   (1106 perm/sec)   p_kst 2.988636e-04   p_cons 9.669074e-01   p_joint 2.988636e-04

Joint ci ratio: 1.700879e-01	ci left: 2.744851e-04	ci right 3.260430e-04	k: 530	n:1770000
Cons ci ratio: 5.450661e-04	ci left: 9.666467e-01	ci right 9.671743e-01	k: 1711433	n:1770000
KS ci ratio: 1.700879e-01	ci left: 2.744851e-04	ci right 3.260430e-04	k: 530	n:1770000
LLGL2   1770000 perm   1607 sec   (1101 perm/sec)   p_kst 2.994350e-04   p_cons 9.669113e-01   p_joint 2.994350e-04

Joint ci ratio: 1.697686e-01	ci left: 2.740189e-04	ci right 3.253827e-04	k: 532	n:1780000
Cons ci ratio: 5.435382e-04	ci left: 9.666469e-01	ci right 9.671730e-01	k: 1721101	n:1780000
KS ci ratio: 1.697686e-01	ci left: 2.740189e-04	ci right 3.253827e-04	k: 532	n:1780000
LLGL2   1780000 perm   1623 sec   (1097 perm/sec)   p_kst 2.988764e-04   p_cons 9.669107e-01   p_joint 2.988764e-04

Joint ci ratio: 1.692928e-01	ci left: 2.740929e-04	ci right 3.253119e-04	k: 535	n:1790000
Cons ci ratio: 5.420561e-04	ci left: 9.666431e-01	ci right 9.671677e-01	k: 1730762	n:1790000
KS ci ratio: 1.692928e-01	ci left: 2.740929e-04	ci right 3.253119e-04	k: 535	n:1790000
LLGL2   1790000 perm   1639 sec   (1092 perm/sec)   p_kst 2.988827e-04   p_cons 9.669061e-01   p_joint 2.988827e-04

Joint ci ratio: 1.689779e-01	ci left: 2.736342e-04	ci right 3.246627e-04	k: 537	n:1800000
Cons ci ratio: 5.406330e-04	ci left: 9.666337e-01	ci right 9.671570e-01	k: 1740413	n:1800000
KS ci ratio: 1.689779e-01	ci left: 2.736342e-04	ci right 3.246627e-04	k: 537	n:1800000
LLGL2   1800000 perm   1655 sec   (1088 perm/sec)   p_kst 2.983333e-04   p_cons 9.668961e-01   p_joint 2.983333e-04

Joint ci ratio: 1.685087e-01	ci left: 2.737099e-04	ci right 3.245964e-04	k: 540	n:1810000
Cons ci ratio: 5.391373e-04	ci left: 9.666345e-01	ci right 9.671563e-01	k: 1750082	n:1810000
KS ci ratio: 1.685087e-01	ci left: 2.737099e-04	ci right 3.245964e-04	k: 540	n:1810000
LLGL2   1810000 perm   1671 sec   (1083 perm/sec)   p_kst 2.983425e-04   p_cons 9.668961e-01   p_joint 2.983425e-04

Joint ci ratio: 1.681982e-01	ci left: 2.732586e-04	ci right 3.239581e-04	k: 542	n:1820000
Cons ci ratio: 5.377324e-04	ci left: 9.666258e-01	ci right 9.671463e-01	k: 1759734	n:1820000
KS ci ratio: 1.681982e-01	ci left: 2.732586e-04	ci right 3.239581e-04	k: 542	n:1820000
LLGL2   1820000 perm   1688 sec   (1078 perm/sec)   p_kst 2.978022e-04   p_cons 9.668868e-01   p_joint 2.978022e-04

Joint ci ratio: 1.675820e-01	ci left: 2.738593e-04	ci right 3.244654e-04	k: 546	n:1830000
Cons ci ratio: 5.363154e-04	ci left: 9.666200e-01	ci right 9.671391e-01	k: 1769391	n:1830000
KS ci ratio: 1.675820e-01	ci left: 2.738593e-04	ci right 3.244654e-04	k: 546	n:1830000
LLGL2   1830000 perm   1704 sec   (1074 perm/sec)   p_kst 2.983607e-04   p_cons 9.668803e-01   p_joint 2.983607e-04

Joint ci ratio: 1.668212e-01	ci left: 2.749747e-04	ci right 3.255330e-04	k: 551	n:1840000
Cons ci ratio: 5.349867e-04	ci left: 9.666050e-01	ci right 9.671228e-01	k: 1779031	n:1840000
KS ci ratio: 1.668212e-01	ci left: 2.749747e-04	ci right 3.255330e-04	k: 551	n:1840000
LLGL2   1840000 perm   1732 sec   (1063 perm/sec)   p_kst 2.994565e-04   p_cons 9.668647e-01   p_joint 2.994565e-04

Joint ci ratio: 1.662200e-01	ci left: 2.755604e-04	ci right 3.260255e-04	k: 555	n:1850000
Cons ci ratio: 5.336093e-04	ci left: 9.665973e-01	ci right 9.671137e-01	k: 1788684	n:1850000
KS ci ratio: 1.662200e-01	ci left: 2.755604e-04	ci right 3.260255e-04	k: 555	n:1850000
LLGL2   1850000 perm   1753 sec   (1055 perm/sec)   p_kst 3.000000e-04   p_cons 9.668562e-01   p_joint 3.000000e-04

Joint ci ratio: 1.653302e-01	ci left: 2.771709e-04	ci right 3.276322e-04	k: 561	n:1860000
Cons ci ratio: 5.320906e-04	ci left: 9.666079e-01	ci right 9.671229e-01	k: 1798371	n:1860000
KS ci ratio: 1.653302e-01	ci left: 2.771709e-04	ci right 3.276322e-04	k: 561	n:1860000
LLGL2   1860000 perm   1771 sec   (1050 perm/sec)   p_kst 3.016129e-04   p_cons 9.668661e-01   p_joint 3.016129e-04

Joint ci ratio: 1.648907e-01	ci left: 2.772267e-04	ci right 3.275506e-04	k: 564	n:1870000
Cons ci ratio: 5.307043e-04	ci left: 9.666040e-01	ci right 9.671176e-01	k: 1808031	n:1870000
KS ci ratio: 1.648907e-01	ci left: 2.772267e-04	ci right 3.275506e-04	k: 564	n:1870000
LLGL2   1870000 perm   1788 sec   (1046 perm/sec)   p_kst 3.016043e-04   p_cons 9.668615e-01   p_joint 3.016043e-04

Joint ci ratio: 1.647450e-01	ci left: 2.762620e-04	ci right 3.263622e-04	k: 565	n:1880000
Cons ci ratio: 5.291662e-04	ci left: 9.666198e-01	ci right 9.671320e-01	k: 1817728	n:1880000
KS ci ratio: 1.647450e-01	ci left: 2.762620e-04	ci right 3.263622e-04	k: 565	n:1880000
LLGL2   1880000 perm   1805 sec   (1042 perm/sec)   p_kst 3.005319e-04   p_cons 9.668766e-01   p_joint 3.005319e-04

Joint ci ratio: 1.647452e-01	ci left: 2.748003e-04	ci right 3.246354e-04	k: 565	n:1890000
Cons ci ratio: 5.277983e-04	ci left: 9.666164e-01	ci right 9.671272e-01	k: 1827389	n:1890000
KS ci ratio: 1.647452e-01	ci left: 2.748003e-04	ci right 3.246354e-04	k: 565	n:1890000
LLGL2   1890000 perm   1822 sec   (1037 perm/sec)   p_kst 2.989418e-04   p_cons 9.668725e-01   p_joint 2.989418e-04

Joint ci ratio: 1.643103e-01	ci left: 2.748679e-04	ci right 3.245707e-04	k: 568	n:1900000
Cons ci ratio: 5.263587e-04	ci left: 9.666230e-01	ci right 9.671324e-01	k: 1837069	n:1900000
KS ci ratio: 1.643103e-01	ci left: 2.748679e-04	ci right 3.245707e-04	k: 568	n:1900000
LLGL2   1900000 perm   1847 sec   (1029 perm/sec)   p_kst 2.989474e-04   p_cons 9.668784e-01   p_joint 2.989474e-04

Joint ci ratio: 1.638788e-01	ci left: 2.749350e-04	ci right 3.245065e-04	k: 571	n:1910000
Cons ci ratio: 5.249867e-04	ci left: 9.666227e-01	ci right 9.671308e-01	k: 1846736	n:1910000
KS ci ratio: 1.638788e-01	ci left: 2.749350e-04	ci right 3.245065e-04	k: 571	n:1910000
LLGL2   1910000 perm   1866 sec   (1024 perm/sec)   p_kst 2.989529e-04   p_cons 9.668775e-01   p_joint 2.989529e-04

Joint ci ratio: 1.635931e-01	ci left: 2.745020e-04	ci right 3.239007e-04	k: 573	n:1920000
Cons ci ratio: 5.236466e-04	ci left: 9.666198e-01	ci right 9.671267e-01	k: 1856398	n:1920000
KS ci ratio: 1.635931e-01	ci left: 2.745020e-04	ci right 3.239007e-04	k: 573	n:1920000
LLGL2   1920000 perm   1888 sec   (1017 perm/sec)   p_kst 2.984375e-04   p_cons 9.668740e-01   p_joint 2.984375e-04

Joint ci ratio: 1.634509e-01	ci left: 2.735767e-04	ci right 3.227618e-04	k: 574	n:1930000
Cons ci ratio: 5.224138e-04	ci left: 9.666050e-01	ci right 9.671107e-01	k: 1866037	n:1930000
KS ci ratio: 1.634509e-01	ci left: 2.735767e-04	ci right 3.227618e-04	k: 574	n:1930000
LLGL2   1930000 perm   1906 sec   (1013 perm/sec)   p_kst 2.974093e-04   p_cons 9.668585e-01   p_joint 2.974093e-04

Joint ci ratio: 1.631674e-01	ci left: 2.731553e-04	ci right 3.221711e-04	k: 576	n:1940000
Cons ci ratio: 5.211184e-04	ci left: 9.665992e-01	ci right 9.671035e-01	k: 1875693	n:1940000
KS ci ratio: 1.631674e-01	ci left: 2.731553e-04	ci right 3.221711e-04	k: 576	n:1940000
LLGL2   1940000 perm   1924 sec   (1009 perm/sec)   p_kst 2.969072e-04   p_cons 9.668521e-01   p_joint 2.969072e-04

Joint ci ratio: 1.626047e-01	ci left: 2.737221e-04	ci right 3.226538e-04	k: 580	n:1950000
Cons ci ratio: 5.197701e-04	ci left: 9.666011e-01	ci right 9.671042e-01	k: 1885364	n:1950000
KS ci ratio: 1.626047e-01	ci left: 2.737221e-04	ci right 3.226538e-04	k: 580	n:1950000
LLGL2   1950000 perm   1941 sec   (1005 perm/sec)   p_kst 2.974359e-04   p_cons 9.668533e-01   p_joint 2.974359e-04

Joint ci ratio: 1.623256e-01	ci left: 2.733045e-04	ci right 3.220694e-04	k: 582	n:1960000
Cons ci ratio: 5.184116e-04	ci left: 9.666056e-01	ci right 9.671073e-01	k: 1895040	n:1960000
KS ci ratio: 1.623256e-01	ci left: 2.733045e-04	ci right 3.220694e-04	k: 582	n:1960000
LLGL2   1960000 perm   1958 sec   (1001 perm/sec)   p_kst 2.969388e-04   p_cons 9.668571e-01   p_joint 2.969388e-04

Joint ci ratio: 1.621867e-01	ci left: 2.724042e-04	ci right 3.209628e-04	k: 583	n:1970000
Cons ci ratio: 5.169982e-04	ci left: 9.666182e-01	ci right 9.671185e-01	k: 1904732	n:1970000
KS ci ratio: 1.621867e-01	ci left: 2.724042e-04	ci right 3.209628e-04	k: 583	n:1970000
LLGL2   1970000 perm   1977 sec   (997 perm/sec)   p_kst 2.959391e-04   p_cons 9.668690e-01   p_joint 2.959391e-04

Joint ci ratio: 1.617717e-01	ci left: 2.724821e-04	ci right 3.209183e-04	k: 586	n:1980000
Cons ci ratio: 5.156491e-04	ci left: 9.666240e-01	ci right 9.671231e-01	k: 1914411	n:1980000
KS ci ratio: 1.617717e-01	ci left: 2.724821e-04	ci right 3.209183e-04	k: 586	n:1980000
LLGL2   1980000 perm   1994 sec   (993 perm/sec)   p_kst 2.959596e-04   p_cons 9.668742e-01   p_joint 2.959596e-04

Joint ci ratio: 1.609511e-01	ci left: 2.740062e-04	ci right 3.224423e-04	k: 592	n:1990000
Cons ci ratio: 5.144839e-04	ci left: 9.666081e-01	ci right 9.671061e-01	k: 1924047	n:1990000
KS ci ratio: 1.609511e-01	ci left: 2.740062e-04	ci right 3.224423e-04	k: 592	n:1990000
LLGL2   1990000 perm   2012 sec   (989 perm/sec)   p_kst 2.974874e-04   p_cons 9.668578e-01   p_joint 2.974874e-04

Joint ci ratio: 1.608156e-01	ci left: 2.731161e-04	ci right 3.213502e-04	k: 593	n:2000000
Cons ci ratio: 5.132545e-04	ci left: 9.666015e-01	ci right 9.670982e-01	k: 1933701	n:2000000
KS ci ratio: 1.608156e-01	ci left: 2.731161e-04	ci right 3.213502e-04	k: 593	n:2000000
LLGL2   2000000 perm   2030 sec   (985 perm/sec)   p_kst 2.965000e-04   p_cons 9.668505e-01   p_joint 2.965000e-04

Joint ci ratio: 1.606805e-01	ci left: 2.722348e-04	ci right 3.202690e-04	k: 594	n:2010000
Cons ci ratio: 5.119384e-04	ci left: 9.666068e-01	ci right 9.671023e-01	k: 1943379	n:2010000
KS ci ratio: 1.606805e-01	ci left: 2.722348e-04	ci right 3.202690e-04	k: 594	n:2010000
LLGL2   2010000 perm   2048 sec   (982 perm/sec)   p_kst 2.955224e-04   p_cons 9.668552e-01   p_joint 2.955224e-04

Joint ci ratio: 1.594787e-01	ci left: 2.751641e-04	ci right 3.233172e-04	k: 603	n:2020000
Cons ci ratio: 5.108335e-04	ci left: 9.665868e-01	ci right 9.670812e-01	k: 1953006	n:2020000
KS ci ratio: 1.594787e-01	ci left: 2.751641e-04	ci right 3.233172e-04	k: 603	n:2020000
LLGL2   2020000 perm   2066 sec   (978 perm/sec)   p_kst 2.985149e-04   p_cons 9.668347e-01   p_joint 2.985149e-04

Joint ci ratio: 1.590841e-01	ci left: 2.752275e-04	ci right 3.232612e-04	k: 606	n:2030000
Cons ci ratio: 5.096025e-04	ci left: 9.665838e-01	ci right 9.670770e-01	k: 1962667	n:2030000
KS ci ratio: 1.590841e-01	ci left: 2.752275e-04	ci right 3.232612e-04	k: 606	n:2030000
LLGL2   2030000 perm   2084 sec   (974 perm/sec)   p_kst 2.985222e-04   p_cons 9.668310e-01   p_joint 2.985222e-04

Joint ci ratio: 1.589533e-01	ci left: 2.743490e-04	ci right 3.221863e-04	k: 607	n:2040000
Cons ci ratio: 5.083842e-04	ci left: 9.665803e-01	ci right 9.670723e-01	k: 1972327	n:2040000
KS ci ratio: 1.589533e-01	ci left: 2.743490e-04	ci right 3.221863e-04	k: 607	n:2040000
LLGL2   2040000 perm   2102 sec   (970 perm/sec)   p_kst 2.975490e-04   p_cons 9.668270e-01   p_joint 2.975490e-04

Joint ci ratio: 1.585626e-01	ci left: 2.744160e-04	ci right 3.221362e-04	k: 610	n:2050000
Cons ci ratio: 5.071283e-04	ci left: 9.665827e-01	ci right 9.670735e-01	k: 1981999	n:2050000
KS ci ratio: 1.585626e-01	ci left: 2.744160e-04	ci right 3.221362e-04	k: 610	n:2050000
LLGL2   2050000 perm   2121 sec   (966 perm/sec)   p_kst 2.975610e-04   p_cons 9.668288e-01   p_joint 2.975610e-04

Joint ci ratio: 1.579176e-01	ci left: 2.754150e-04	ci right 3.230956e-04	k: 615	n:2060000
Cons ci ratio: 5.058702e-04	ci left: 9.665866e-01	ci right 9.670762e-01	k: 1991674	n:2060000
KS ci ratio: 1.579176e-01	ci left: 2.754150e-04	ci right 3.230956e-04	k: 615	n:2060000
LLGL2   2060000 perm   2141 sec   (962 perm/sec)   p_kst 2.985437e-04   p_cons 9.668320e-01   p_joint 2.985437e-04

Joint ci ratio: 1.575345e-01	ci left: 2.754766e-04	ci right 3.230412e-04	k: 618	n:2070000
Cons ci ratio: 5.046442e-04	ci left: 9.665875e-01	ci right 9.670759e-01	k: 2001343	n:2070000
KS ci ratio: 1.575345e-01	ci left: 2.754766e-04	ci right 3.230412e-04	k: 618	n:2070000
LLGL2   2070000 perm   2159 sec   (959 perm/sec)   p_kst 2.985507e-04   p_cons 9.668324e-01   p_joint 2.985507e-04

Joint ci ratio: 1.572807e-01	ci left: 2.750758e-04	ci right 3.224875e-04	k: 620	n:2080000
Cons ci ratio: 5.033742e-04	ci left: 9.665952e-01	ci right 9.670823e-01	k: 2011026	n:2080000
KS ci ratio: 1.572807e-01	ci left: 2.750758e-04	ci right 3.224875e-04	k: 620	n:2080000
LLGL2   2080000 perm   2177 sec   (955 perm/sec)   p_kst 2.980769e-04   p_cons 9.668394e-01   p_joint 2.980769e-04

Joint ci ratio: 1.570280e-01	ci left: 2.746790e-04	ci right 3.219390e-04	k: 622	n:2090000
Cons ci ratio: 5.022112e-04	ci left: 9.665903e-01	ci right 9.670763e-01	k: 2020683	n:2090000
KS ci ratio: 1.570280e-01	ci left: 2.746790e-04	ci right 3.219390e-04	k: 622	n:2090000
LLGL2   2090000 perm   2195 sec   (952 perm/sec)   p_kst 2.976077e-04   p_cons 9.668340e-01   p_joint 2.976077e-04

Joint ci ratio: 1.566513e-01	ci left: 2.747435e-04	ci right 3.218906e-04	k: 625	n:2100000
Cons ci ratio: 5.009335e-04	ci left: 9.666012e-01	ci right 9.670860e-01	k: 2030373	n:2100000
KS ci ratio: 1.566513e-01	ci left: 2.747435e-04	ci right 3.218906e-04	k: 625	n:2100000
LLGL2   2100000 perm   2214 sec   (949 perm/sec)   p_kst 2.976190e-04   p_cons 9.668443e-01   p_joint 2.976190e-04

Joint ci ratio: 1.559058e-01	ci left: 2.761738e-04	ci right 3.233197e-04	k: 631	n:2110000
Cons ci ratio: 4.996173e-04	ci left: 9.666183e-01	ci right 9.671018e-01	k: 2040076	n:2110000
KS ci ratio: 1.559058e-01	ci left: 2.761738e-04	ci right 3.233197e-04	k: 631	n:2110000
LLGL2   2110000 perm   2232 sec   (945 perm/sec)   p_kst 2.990521e-04   p_cons 9.668607e-01   p_joint 2.990521e-04

Joint ci ratio: 1.551709e-01	ci left: 2.775911e-04	ci right 3.247349e-04	k: 637	n:2120000
Cons ci ratio: 4.985755e-04	ci left: 9.666010e-01	ci right 9.670835e-01	k: 2049707	n:2120000
KS ci ratio: 1.551709e-01	ci left: 2.775911e-04	ci right 3.247349e-04	k: 637	n:2120000
LLGL2   2120000 perm   2251 sec   (942 perm/sec)   p_kst 3.004717e-04   p_cons 9.668429e-01   p_joint 3.004717e-04

Joint ci ratio: 1.546867e-01	ci left: 2.780930e-04	ci right 3.251610e-04	k: 641	n:2130000
Cons ci ratio: 4.974636e-04	ci left: 9.665939e-01	ci right 9.670753e-01	k: 2059359	n:2130000
KS ci ratio: 1.546867e-01	ci left: 2.780930e-04	ci right 3.251610e-04	k: 641	n:2130000
LLGL2   2130000 perm   2270 sec   (938 perm/sec)   p_kst 3.009390e-04   p_cons 9.668352e-01   p_joint 3.009390e-04

Joint ci ratio: 1.539688e-01	ci left: 2.794890e-04	ci right 3.265534e-04	k: 647	n:2140000
Cons ci ratio: 4.964711e-04	ci left: 9.665722e-01	ci right 9.670527e-01	k: 2068980	n:2140000
KS ci ratio: 1.539688e-01	ci left: 2.794890e-04	ci right 3.265534e-04	k: 647	n:2140000
LLGL2   2140000 perm   2288 sec   (935 perm/sec)   p_kst 3.023364e-04   p_cons 9.668131e-01   p_joint 3.023364e-04

Joint ci ratio: 1.538502e-01	ci left: 2.786363e-04	ci right 3.255176e-04	k: 648	n:2150000
Cons ci ratio: 4.953444e-04	ci left: 9.665690e-01	ci right 9.670484e-01	k: 2078640	n:2150000
KS ci ratio: 1.538502e-01	ci left: 2.786363e-04	ci right 3.255176e-04	k: 648	n:2150000
LLGL2   2150000 perm   2307 sec   (932 perm/sec)   p_kst 3.013953e-04   p_cons 9.668093e-01   p_joint 3.013953e-04

Joint ci ratio: 1.534958e-01	ci left: 2.786818e-04	ci right 3.254528e-04	k: 651	n:2160000
Cons ci ratio: 4.941611e-04	ci left: 9.665742e-01	ci right 9.670524e-01	k: 2088318	n:2160000
KS ci ratio: 1.534958e-01	ci left: 2.786818e-04	ci right 3.254528e-04	k: 651	n:2160000
LLGL2   2160000 perm   2326 sec   (929 perm/sec)   p_kst 3.013889e-04   p_cons 9.668139e-01   p_joint 3.013889e-04

Joint ci ratio: 1.532610e-01	ci left: 2.782838e-04	ci right 3.249101e-04	k: 653	n:2170000
Cons ci ratio: 4.930712e-04	ci left: 9.665682e-01	ci right 9.670453e-01	k: 2097972	n:2170000
KS ci ratio: 1.532610e-01	ci left: 2.782838e-04	ci right 3.249101e-04	k: 653	n:2170000
LLGL2   2170000 perm   2345 sec   (926 perm/sec)   p_kst 3.009217e-04   p_cons 9.668074e-01   p_joint 3.009217e-04

Joint ci ratio: 1.529107e-01	ci left: 2.783307e-04	ci right 3.248485e-04	k: 656	n:2180000
Cons ci ratio: 4.919357e-04	ci left: 9.665692e-01	ci right 9.670452e-01	k: 2107641	n:2180000
KS ci ratio: 1.529107e-01	ci left: 2.783307e-04	ci right 3.248485e-04	k: 656	n:2180000
LLGL2   2180000 perm   2364 sec   (922 perm/sec)   p_kst 3.009174e-04   p_cons 9.668078e-01   p_joint 3.009174e-04

Joint ci ratio: 1.524473e-01	ci left: 2.788165e-04	ci right 3.252614e-04	k: 660	n:2190000
Cons ci ratio: 4.908221e-04	ci left: 9.665683e-01	ci right 9.670433e-01	k: 2117306	n:2190000
KS ci ratio: 1.524473e-01	ci left: 2.788165e-04	ci right 3.252614e-04	k: 660	n:2190000
LLGL2   2190000 perm   2383 sec   (919 perm/sec)   p_kst 3.013699e-04   p_cons 9.668064e-01   p_joint 3.013699e-04

Joint ci ratio: 1.521025e-01	ci left: 2.788608e-04	ci right 3.251984e-04	k: 663	n:2200000
Cons ci ratio: 4.897090e-04	ci left: 9.665683e-01	ci right 9.670422e-01	k: 2126973	n:2200000
KS ci ratio: 1.521025e-01	ci left: 2.788608e-04	ci right 3.251984e-04	k: 663	n:2200000
LLGL2   2200000 perm   2403 sec   (916 perm/sec)   p_kst 3.013636e-04   p_cons 9.668059e-01   p_joint 3.013636e-04

Joint ci ratio: 1.519882e-01	ci left: 2.780343e-04	ci right 3.241967e-04	k: 664	n:2210000
Cons ci ratio: 4.885621e-04	ci left: 9.665739e-01	ci right 9.670466e-01	k: 2136652	n:2210000
KS ci ratio: 1.519882e-01	ci left: 2.780343e-04	ci right 3.241967e-04	k: 664	n:2210000
LLGL2   2210000 perm   2422 sec   (912 perm/sec)   p_kst 3.004525e-04   p_cons 9.668109e-01   p_joint 3.004525e-04

Joint ci ratio: 1.516465e-01	ci left: 2.780819e-04	ci right 3.241390e-04	k: 667	n:2220000
Cons ci ratio: 4.874197e-04	ci left: 9.665798e-01	ci right 9.670514e-01	k: 2146332	n:2220000
KS ci ratio: 1.516465e-01	ci left: 2.780819e-04	ci right 3.241390e-04	k: 667	n:2220000
LLGL2   2220000 perm   2441 sec   (909 perm/sec)   p_kst 3.004505e-04   p_cons 9.668162e-01   p_joint 3.004505e-04

Joint ci ratio: 1.514200e-01	ci left: 2.776977e-04	ci right 3.236163e-04	k: 669	n:2230000
Cons ci ratio: 4.863466e-04	ci left: 9.665775e-01	ci right 9.670482e-01	k: 2155994	n:2230000
KS ci ratio: 1.514200e-01	ci left: 2.776977e-04	ci right 3.236163e-04	k: 669	n:2230000
LLGL2   2230000 perm   2460 sec   (906 perm/sec)   p_kst 3.000000e-04   p_cons 9.668135e-01   p_joint 3.000000e-04

Joint ci ratio: 1.507464e-01	ci left: 2.790353e-04	ci right 3.249513e-04	k: 675	n:2240000
Cons ci ratio: 4.852197e-04	ci left: 9.665834e-01	ci right 9.670529e-01	k: 2165674	n:2240000
KS ci ratio: 1.507464e-01	ci left: 2.790353e-04	ci right 3.249513e-04	k: 675	n:2240000
LLGL2   2240000 perm   2480 sec   (903 perm/sec)   p_kst 3.013393e-04   p_cons 9.668187e-01   p_joint 3.013393e-04

Joint ci ratio: 1.505240e-01	ci left: 2.786506e-04	ci right 3.244294e-04	k: 677	n:2250000
Cons ci ratio: 4.841174e-04	ci left: 9.665869e-01	ci right 9.670554e-01	k: 2175349	n:2250000
KS ci ratio: 1.505240e-01	ci left: 2.786506e-04	ci right 3.244294e-04	k: 677	n:2250000
LLGL2   2250000 perm   2500 sec   (900 perm/sec)   p_kst 3.008889e-04   p_cons 9.668218e-01   p_joint 3.008889e-04

Joint ci ratio: 1.503025e-01	ci left: 2.782692e-04	ci right 3.239122e-04	k: 679	n:2260000
Cons ci ratio: 4.831191e-04	ci left: 9.665776e-01	ci right 9.670451e-01	k: 2184995	n:2260000
KS ci ratio: 1.503025e-01	ci left: 2.782692e-04	ci right 3.239122e-04	k: 679	n:2260000
LLGL2   2260000 perm   2520 sec   (897 perm/sec)   p_kst 3.004425e-04   p_cons 9.668119e-01   p_joint 3.004425e-04

Joint ci ratio: 1.497529e-01	ci left: 2.791633e-04	ci right 3.247705e-04	k: 684	n:2270000
Cons ci ratio: 4.820112e-04	ci left: 9.665838e-01	ci right 9.670502e-01	k: 2194676	n:2270000
KS ci ratio: 1.497529e-01	ci left: 2.791633e-04	ci right 3.247705e-04	k: 684	n:2270000
LLGL2   2270000 perm   2540 sec   (894 perm/sec)   p_kst 3.013216e-04   p_cons 9.668176e-01   p_joint 3.013216e-04

Joint ci ratio: 1.494260e-01	ci left: 2.792055e-04	ci right 3.247111e-04	k: 687	n:2280000
Cons ci ratio: 4.808911e-04	ci left: 9.665926e-01	ci right 9.670580e-01	k: 2204363	n:2280000
KS ci ratio: 1.494260e-01	ci left: 2.792055e-04	ci right 3.247111e-04	k: 687	n:2280000
LLGL2   2280000 perm   2559 sec   (891 perm/sec)   p_kst 3.013158e-04   p_cons 9.668259e-01   p_joint 3.013158e-04

Joint ci ratio: 1.492093e-01	ci left: 2.788270e-04	ci right 3.241991e-04	k: 689	n:2290000
Cons ci ratio: 4.798310e-04	ci left: 9.665943e-01	ci right 9.670587e-01	k: 2214034	n:2290000
KS ci ratio: 1.492093e-01	ci left: 2.788270e-04	ci right 3.241991e-04	k: 689	n:2290000
LLGL2   2290000 perm   2579 sec   (888 perm/sec)   p_kst 3.008734e-04   p_cons 9.668271e-01   p_joint 3.008734e-04

Joint ci ratio: 1.492094e-01	ci left: 2.776147e-04	ci right 3.227895e-04	k: 689	n:2300000
Cons ci ratio: 4.789336e-04	ci left: 9.665751e-01	ci right 9.670385e-01	k: 2223657	n:2300000
KS ci ratio: 1.492094e-01	ci left: 2.776147e-04	ci right 3.227895e-04	k: 689	n:2300000
LLGL2   2300000 perm   2599 sec   (885 perm/sec)   p_kst 2.995652e-04   p_cons 9.668074e-01   p_joint 2.995652e-04

Joint ci ratio: 1.487788e-01	ci left: 2.780799e-04	ci right 3.231883e-04	k: 693	n:2310000
Cons ci ratio: 4.779090e-04	ci left: 9.665738e-01	ci right 9.670363e-01	k: 2233321	n:2310000
KS ci ratio: 1.487788e-01	ci left: 2.780799e-04	ci right 3.231883e-04	k: 693	n:2310000
LLGL2   2310000 perm   2619 sec   (882 perm/sec)   p_kst 3.000000e-04   p_cons 9.668056e-01   p_joint 3.000000e-04

Joint ci ratio: 1.481397e-01	ci left: 2.793715e-04	ci right 3.244774e-04	k: 699	n:2320000
Cons ci ratio: 4.768973e-04	ci left: 9.665717e-01	ci right 9.670332e-01	k: 2242983	n:2320000
KS ci ratio: 1.481397e-01	ci left: 2.793715e-04	ci right 3.244774e-04	k: 699	n:2320000
LLGL2   2320000 perm   2639 sec   (879 perm/sec)   p_kst 3.012931e-04   p_cons 9.668030e-01   p_joint 3.012931e-04

Joint ci ratio: 1.479285e-01	ci left: 2.789990e-04	ci right 3.239750e-04	k: 701	n:2330000
Cons ci ratio: 4.758538e-04	ci left: 9.665748e-01	ci right 9.670352e-01	k: 2252657	n:2330000
KS ci ratio: 1.479285e-01	ci left: 2.789990e-04	ci right 3.239750e-04	k: 701	n:2330000
LLGL2   2330000 perm   2659 sec   (876 perm/sec)   p_kst 3.008584e-04   p_cons 9.668056e-01   p_joint 3.008584e-04

Joint ci ratio: 1.474045e-01	ci left: 2.798645e-04	ci right 3.248061e-04	k: 706	n:2340000
Cons ci ratio: 4.748519e-04	ci left: 9.665731e-01	ci right 9.670326e-01	k: 2262320	n:2340000
KS ci ratio: 1.474045e-01	ci left: 2.798645e-04	ci right 3.248061e-04	k: 706	n:2340000
LLGL2   2340000 perm   2679 sec   (873 perm/sec)   p_kst 3.017094e-04   p_cons 9.668034e-01   p_joint 3.017094e-04

Joint ci ratio: 1.468859e-01	ci left: 2.807230e-04	ci right 3.256298e-04	k: 711	n:2350000
Cons ci ratio: 4.737275e-04	ci left: 9.665889e-01	ci right 9.670474e-01	k: 2272024	n:2350000
KS ci ratio: 1.468859e-01	ci left: 2.807230e-04	ci right 3.256298e-04	k: 711	n:2350000
LLGL2   2350000 perm   2700 sec   (871 perm/sec)   p_kst 3.025532e-04   p_cons 9.668187e-01   p_joint 3.025532e-04

Joint ci ratio: 1.467829e-01	ci left: 2.799416e-04	ci right 3.246894e-04	k: 712	n:2360000
Cons ci ratio: 4.726203e-04	ci left: 9.666034e-01	ci right 9.670607e-01	k: 2281725	n:2360000
KS ci ratio: 1.467829e-01	ci left: 2.799416e-04	ci right 3.246894e-04	k: 712	n:2360000
LLGL2   2360000 perm   2720 sec   (868 perm/sec)   p_kst 3.016949e-04   p_cons 9.668326e-01   p_joint 3.016949e-04

Joint ci ratio: 1.462709e-01	ci left: 2.807928e-04	ci right 3.255063e-04	k: 717	n:2370000
Cons ci ratio: 4.716107e-04	ci left: 9.666054e-01	ci right 9.670618e-01	k: 2291397	n:2370000
KS ci ratio: 1.462709e-01	ci left: 2.807928e-04	ci right 3.255063e-04	k: 717	n:2370000
LLGL2   2370000 perm   2740 sec   (865 perm/sec)   p_kst 3.025316e-04   p_cons 9.668342e-01   p_joint 3.025316e-04

Joint ci ratio: 1.458651e-01	ci left: 2.812322e-04	ci right 3.258807e-04	k: 721	n:2380000
Cons ci ratio: 4.707618e-04	ci left: 9.665864e-01	ci right 9.670419e-01	k: 2301019	n:2380000
KS ci ratio: 1.458651e-01	ci left: 2.812322e-04	ci right 3.258807e-04	k: 721	n:2380000
LLGL2   2380000 perm   2760 sec   (862 perm/sec)   p_kst 3.029412e-04   p_cons 9.668147e-01   p_joint 3.029412e-04

Joint ci ratio: 1.458652e-01	ci left: 2.800555e-04	ci right 3.245172e-04	k: 721	n:2390000
Cons ci ratio: 4.697059e-04	ci left: 9.665964e-01	ci right 9.670510e-01	k: 2310710	n:2390000
KS ci ratio: 1.458652e-01	ci left: 2.800555e-04	ci right 3.245172e-04	k: 721	n:2390000
LLGL2   2390000 perm   2780 sec   (860 perm/sec)   p_kst 3.016736e-04   p_cons 9.668243e-01   p_joint 3.016736e-04

Joint ci ratio: 1.454628e-01	ci left: 2.804946e-04	ci right 3.248924e-04	k: 725	n:2400000
Cons ci ratio: 4.687727e-04	ci left: 9.665905e-01	ci right 9.670442e-01	k: 2320363	n:2400000
KS ci ratio: 1.454628e-01	ci left: 2.804946e-04	ci right 3.248924e-04	k: 725	n:2400000
LLGL2   2400000 perm   2801 sec   (857 perm/sec)   p_kst 3.020833e-04   p_cons 9.668179e-01   p_joint 3.020833e-04

Joint ci ratio: 1.453628e-01	ci left: 2.797305e-04	ci right 3.239744e-04	k: 726	n:2410000
Cons ci ratio: 4.678148e-04	ci left: 9.665889e-01	ci right 9.670416e-01	k: 2330026	n:2410000
KS ci ratio: 1.453628e-01	ci left: 2.797305e-04	ci right 3.239744e-04	k: 726	n:2410000
LLGL2   2410000 perm   2821 sec   (854 perm/sec)   p_kst 3.012448e-04   p_cons 9.668158e-01   p_joint 3.012448e-04

Joint ci ratio: 1.449645e-01	ci left: 2.801675e-04	ci right 3.243485e-04	k: 730	n:2420000
Cons ci ratio: 4.668477e-04	ci left: 9.665893e-01	ci right 9.670410e-01	k: 2339694	n:2420000
KS ci ratio: 1.449645e-01	ci left: 2.801675e-04	ci right 3.243485e-04	k: 730	n:2420000
LLGL2   2420000 perm   2842 sec   (851 perm/sec)   p_kst 3.016529e-04   p_cons 9.668157e-01   p_joint 3.016529e-04

Joint ci ratio: 1.447666e-01	ci left: 2.798077e-04	ci right 3.238666e-04	k: 732	n:2430000
Cons ci ratio: 4.658298e-04	ci left: 9.665975e-01	ci right 9.670483e-01	k: 2349381	n:2430000
KS ci ratio: 1.447666e-01	ci left: 2.798077e-04	ci right 3.238666e-04	k: 732	n:2430000
LLGL2   2430000 perm   2863 sec   (849 perm/sec)   p_kst 3.012346e-04   p_cons 9.668235e-01   p_joint 3.012346e-04

Joint ci ratio: 1.443732e-01	ci left: 2.802410e-04	ci right 3.242379e-04	k: 736	n:2440000
Cons ci ratio: 4.649224e-04	ci left: 9.665913e-01	ci right 9.670412e-01	k: 2359033	n:2440000
KS ci ratio: 1.443732e-01	ci left: 2.802410e-04	ci right 3.242379e-04	k: 736	n:2440000
LLGL2   2440000 perm   2883 sec   (846 perm/sec)   p_kst 3.016393e-04   p_cons 9.668168e-01   p_joint 3.016393e-04

Joint ci ratio: 1.440803e-01	ci left: 2.802775e-04	ci right 3.241831e-04	k: 739	n:2450000
Cons ci ratio: 4.639643e-04	ci left: 9.665929e-01	ci right 9.670419e-01	k: 2368704	n:2450000
KS ci ratio: 1.440803e-01	ci left: 2.802775e-04	ci right 3.241831e-04	k: 739	n:2450000
LLGL2   2450000 perm   2903 sec   (844 perm/sec)   p_kst 3.016327e-04   p_cons 9.668180e-01   p_joint 3.016327e-04

Joint ci ratio: 1.439831e-01	ci left: 2.795300e-04	ci right 3.232864e-04	k: 740	n:2460000
Cons ci ratio: 4.630296e-04	ci left: 9.665921e-01	ci right 9.670401e-01	k: 2378369	n:2460000
KS ci ratio: 1.439831e-01	ci left: 2.795300e-04	ci right 3.232864e-04	k: 740	n:2460000
LLGL2   2460000 perm   2924 sec   (841 perm/sec)   p_kst 3.008130e-04   p_cons 9.668167e-01   p_joint 3.008130e-04

Joint ci ratio: 1.434997e-01	ci left: 2.803498e-04	ci right 3.240746e-04	k: 745	n:2470000
Cons ci ratio: 4.620393e-04	ci left: 9.665998e-01	ci right 9.670469e-01	k: 2388055	n:2470000
KS ci ratio: 1.434997e-01	ci left: 2.803498e-04	ci right 3.240746e-04	k: 745	n:2470000
LLGL2   2470000 perm   2945 sec   (839 perm/sec)   p_kst 3.016194e-04   p_cons 9.668239e-01   p_joint 3.016194e-04

Joint ci ratio: 1.432120e-01	ci left: 2.803856e-04	ci right 3.240209e-04	k: 748	n:2480000
Cons ci ratio: 4.610467e-04	ci left: 9.666086e-01	ci right 9.670548e-01	k: 2397744	n:2480000
KS ci ratio: 1.432120e-01	ci left: 2.803856e-04	ci right 3.240209e-04	k: 748	n:2480000
LLGL2   2480000 perm   2966 sec   (836 perm/sec)   p_kst 3.016129e-04   p_cons 9.668323e-01   p_joint 3.016129e-04

Joint ci ratio: 1.428311e-01	ci left: 2.808085e-04	ci right 3.243835e-04	k: 752	n:2490000
Cons ci ratio: 4.601843e-04	ci left: 9.666001e-01	ci right 9.670454e-01	k: 2407390	n:2490000
KS ci ratio: 1.428311e-01	ci left: 2.808085e-04	ci right 3.243835e-04	k: 752	n:2490000
LLGL2   2490000 perm   2987 sec   (833 perm/sec)   p_kst 3.020080e-04   p_cons 9.668233e-01   p_joint 3.020080e-04

Joint ci ratio: 1.424532e-01	ci left: 2.812282e-04	ci right 3.247430e-04	k: 756	n:2500000
Cons ci ratio: 4.592722e-04	ci left: 9.665992e-01	ci right 9.670437e-01	k: 2417055	n:2500000
KS ci ratio: 1.424532e-01	ci left: 2.812282e-04	ci right 3.247430e-04	k: 756	n:2500000
LLGL2   2500000 perm   3009 sec   (831 perm/sec)   p_kst 3.024000e-04   p_cons 9.668220e-01   p_joint 3.024000e-04

Joint ci ratio: 1.422654e-01	ci left: 2.808762e-04	ci right 3.242744e-04	k: 758	n:2510000
Cons ci ratio: 4.583200e-04	ci left: 9.666048e-01	ci right 9.670483e-01	k: 2426736	n:2510000
KS ci ratio: 1.422654e-01	ci left: 2.808762e-04	ci right 3.242744e-04	k: 758	n:2510000
LLGL2   2510000 perm   3030 sec   (828 perm/sec)   p_kst 3.019920e-04   p_cons 9.668271e-01   p_joint 3.019920e-04

Joint ci ratio: 1.420784e-01	ci left: 2.805270e-04	ci right 3.238094e-04	k: 760	n:2520000
Cons ci ratio: 4.574105e-04	ci left: 9.666051e-01	ci right 9.670478e-01	k: 2436404	n:2520000
KS ci ratio: 1.420784e-01	ci left: 2.805270e-04	ci right 3.238094e-04	k: 760	n:2520000
LLGL2   2520000 perm   3051 sec   (826 perm/sec)   p_kst 3.015873e-04   p_cons 9.668270e-01   p_joint 3.015873e-04

Joint ci ratio: 1.416139e-01	ci left: 2.813244e-04	ci right 3.245759e-04	k: 765	n:2530000
Cons ci ratio: 4.564867e-04	ci left: 9.666082e-01	ci right 9.670500e-01	k: 2446079	n:2530000
KS ci ratio: 1.416139e-01	ci left: 2.813244e-04	ci right 3.245759e-04	k: 765	n:2530000
LLGL2   2530000 perm   3072 sec   (823 perm/sec)   p_kst 3.023715e-04   p_cons 9.668296e-01   p_joint 3.023715e-04

Joint ci ratio: 1.413374e-01	ci left: 2.813561e-04	ci right 3.245209e-04	k: 768	n:2540000
Cons ci ratio: 4.555769e-04	ci left: 9.666101e-01	ci right 9.670510e-01	k: 2455751	n:2540000
KS ci ratio: 1.413374e-01	ci left: 2.813561e-04	ci right 3.245209e-04	k: 768	n:2540000
LLGL2   2540000 perm   3094 sec   (821 perm/sec)   p_kst 3.023622e-04   p_cons 9.668311e-01   p_joint 3.023622e-04

Joint ci ratio: 1.409712e-01	ci left: 2.817660e-04	ci right 3.248723e-04	k: 772	n:2550000
Cons ci ratio: 4.546863e-04	ci left: 9.666101e-01	ci right 9.670501e-01	k: 2465418	n:2550000
KS ci ratio: 1.409712e-01	ci left: 2.817660e-04	ci right 3.248723e-04	k: 772	n:2550000
LLGL2   2550000 perm   3116 sec   (818 perm/sec)   p_kst 3.027451e-04   p_cons 9.668306e-01   p_joint 3.027451e-04

Joint ci ratio: 1.407892e-01	ci left: 2.814190e-04	ci right 3.244120e-04	k: 774	n:2560000
Cons ci ratio: 4.538618e-04	ci left: 9.666014e-01	ci right 9.670405e-01	k: 2475063	n:2560000
KS ci ratio: 1.407892e-01	ci left: 2.814190e-04	ci right 3.244120e-04	k: 774	n:2560000
LLGL2   2560000 perm   3137 sec   (816 perm/sec)   p_kst 3.023437e-04   p_cons 9.668215e-01   p_joint 3.023437e-04

Joint ci ratio: 1.405175e-01	ci left: 2.814503e-04	ci right 3.243581e-04	k: 777	n:2570000
Cons ci ratio: 4.530307e-04	ci left: 9.665943e-01	ci right 9.670327e-01	k: 2484712	n:2570000
KS ci ratio: 1.405175e-01	ci left: 2.814503e-04	ci right 3.243581e-04	k: 777	n:2570000
LLGL2   2570000 perm   3158 sec   (814 perm/sec)   p_kst 3.023346e-04   p_cons 9.668140e-01   p_joint 3.023346e-04

Joint ci ratio: 1.404273e-01	ci left: 2.807333e-04	ci right 3.235021e-04	k: 778	n:2580000
Cons ci ratio: 4.522861e-04	ci left: 9.665756e-01	ci right 9.670133e-01	k: 2494331	n:2580000
KS ci ratio: 1.404273e-01	ci left: 2.807333e-04	ci right 3.235021e-04	k: 778	n:2580000
LLGL2   2580000 perm   3180 sec   (811 perm/sec)   p_kst 3.015504e-04   p_cons 9.667950e-01   p_joint 3.015504e-04

Joint ci ratio: 1.403374e-01	ci left: 2.800220e-04	ci right 3.226527e-04	k: 779	n:2590000
Cons ci ratio: 4.513767e-04	ci left: 9.665811e-01	ci right 9.670179e-01	k: 2504012	n:2590000
KS ci ratio: 1.403374e-01	ci left: 2.800220e-04	ci right 3.226527e-04	k: 779	n:2590000
LLGL2   2590000 perm   3201 sec   (809 perm/sec)   p_kst 3.007722e-04   p_cons 9.668000e-01   p_joint 3.007722e-04

Joint ci ratio: 1.401578e-01	ci left: 2.796872e-04	ci right 3.222080e-04	k: 781	n:2600000
Cons ci ratio: 4.505213e-04	ci left: 9.665796e-01	ci right 9.670155e-01	k: 2513675	n:2600000
KS ci ratio: 1.401578e-01	ci left: 2.796872e-04	ci right 3.222080e-04	k: 781	n:2600000
LLGL2   2600000 perm   3223 sec   (807 perm/sec)   p_kst 3.003846e-04   p_cons 9.667981e-01   p_joint 3.003846e-04

Joint ci ratio: 1.399789e-01	ci left: 2.793550e-04	ci right 3.217666e-04	k: 783	n:2610000
Cons ci ratio: 4.496842e-04	ci left: 9.665762e-01	ci right 9.670113e-01	k: 2523333	n:2610000
KS ci ratio: 1.399789e-01	ci left: 2.793550e-04	ci right 3.217666e-04	k: 783	n:2610000
LLGL2   2610000 perm   3245 sec   (804 perm/sec)   p_kst 3.000000e-04   p_cons 9.667943e-01   p_joint 3.000000e-04

Joint ci ratio: 1.398898e-01	ci left: 2.786571e-04	ci right 3.209335e-04	k: 784	n:2620000
Cons ci ratio: 4.488437e-04	ci left: 9.665739e-01	ci right 9.670082e-01	k: 2532994	n:2620000
KS ci ratio: 1.398898e-01	ci left: 2.786571e-04	ci right 3.209335e-04	k: 784	n:2620000
LLGL2   2620000 perm   3267 sec   (802 perm/sec)   p_kst 2.992366e-04   p_cons 9.667916e-01   p_joint 2.992366e-04

Joint ci ratio: 1.396233e-01	ci left: 2.786984e-04	ci right 3.208938e-04	k: 787	n:2630000
Cons ci ratio: 4.479787e-04	ci left: 9.665759e-01	ci right 9.670094e-01	k: 2542666	n:2630000
KS ci ratio: 1.396233e-01	ci left: 2.786984e-04	ci right 3.208938e-04	k: 787	n:2630000
LLGL2   2630000 perm   3289 sec   (800 perm/sec)   p_kst 2.992395e-04   p_cons 9.667932e-01   p_joint 2.992395e-04

Joint ci ratio: 1.392702e-01	ci left: 2.791050e-04	ci right 3.212462e-04	k: 791	n:2640000
Cons ci ratio: 4.470396e-04	ci left: 9.665893e-01	ci right 9.670218e-01	k: 2552368	n:2640000
KS ci ratio: 1.392702e-01	ci left: 2.791050e-04	ci right 3.212462e-04	k: 791	n:2640000
LLGL2   2640000 perm   3311 sec   (797 perm/sec)   p_kst 2.996212e-04   p_cons 9.668061e-01   p_joint 2.996212e-04

Joint ci ratio: 1.392703e-01	ci left: 2.780517e-04	ci right 3.200340e-04	k: 791	n:2650000
Cons ci ratio: 4.462164e-04	ci left: 9.665866e-01	ci right 9.670184e-01	k: 2562028	n:2650000
KS ci ratio: 1.392703e-01	ci left: 2.780517e-04	ci right 3.200340e-04	k: 791	n:2650000
LLGL2   2650000 perm   3334 sec   (795 perm/sec)   p_kst 2.984906e-04   p_cons 9.668030e-01   p_joint 2.984906e-04

Joint ci ratio: 1.390948e-01	ci left: 2.777321e-04	ci right 3.196089e-04	k: 793	n:2660000
Cons ci ratio: 4.453665e-04	ci left: 9.665885e-01	ci right 9.670195e-01	k: 2571700	n:2660000
KS ci ratio: 1.390948e-01	ci left: 2.777321e-04	ci right 3.196089e-04	k: 793	n:2660000
LLGL2   2660000 perm   3356 sec   (793 perm/sec)   p_kst 2.981203e-04   p_cons 9.668045e-01   p_joint 2.981203e-04

Joint ci ratio: 1.388328e-01	ci left: 2.777765e-04	ci right 3.195745e-04	k: 796	n:2670000
Cons ci ratio: 4.445344e-04	ci left: 9.665885e-01	ci right 9.670187e-01	k: 2581367	n:2670000
KS ci ratio: 1.388328e-01	ci left: 2.777765e-04	ci right 3.195745e-04	k: 796	n:2670000
LLGL2   2670000 perm   3379 sec   (790 perm/sec)   p_kst 2.981273e-04   p_cons 9.668041e-01   p_joint 2.981273e-04

Joint ci ratio: 1.384857e-01	ci left: 2.781808e-04	ci right 3.199263e-04	k: 800	n:2680000
Cons ci ratio: 4.437044e-04	ci left: 9.665889e-01	ci right 9.670183e-01	k: 2591035	n:2680000
KS ci ratio: 1.384857e-01	ci left: 2.781808e-04	ci right 3.199263e-04	k: 800	n:2680000
LLGL2   2680000 perm   3401 sec   (788 perm/sec)   p_kst 2.985075e-04   p_cons 9.668041e-01   p_joint 2.985075e-04

Joint ci ratio: 1.383131e-01	ci left: 2.778644e-04	ci right 3.195063e-04	k: 802	n:2690000
Cons ci ratio: 4.428867e-04	ci left: 9.665882e-01	ci right 9.670167e-01	k: 2600700	n:2690000
KS ci ratio: 1.383131e-01	ci left: 2.778644e-04	ci right 3.195063e-04	k: 802	n:2690000
LLGL2   2690000 perm   3424 sec   (786 perm/sec)   p_kst 2.981413e-04   p_cons 9.668030e-01   p_joint 2.981413e-04

Joint ci ratio: 1.380555e-01	ci left: 2.779079e-04	ci right 3.194724e-04	k: 805	n:2700000
Cons ci ratio: 4.420505e-04	ci left: 9.665908e-01	ci right 9.670186e-01	k: 2610374	n:2700000
KS ci ratio: 1.380555e-01	ci left: 2.779079e-04	ci right 3.194724e-04	k: 805	n:2700000
LLGL2   2700000 perm   3447 sec   (783 perm/sec)   p_kst 2.981481e-04   p_cons 9.668052e-01   p_joint 2.981481e-04

Joint ci ratio: 1.377141e-01	ci left: 2.783076e-04	ci right 3.198204e-04	k: 809	n:2710000
Cons ci ratio: 4.412622e-04	ci left: 9.665871e-01	ci right 9.670141e-01	k: 2620031	n:2710000
KS ci ratio: 1.377141e-01	ci left: 2.783076e-04	ci right 3.198204e-04	k: 809	n:2710000
LLGL2   2710000 perm   3469 sec   (781 perm/sec)   p_kst 2.985240e-04   p_cons 9.668011e-01   p_joint 2.985240e-04

Joint ci ratio: 1.376293e-01	ci left: 2.776393e-04	ci right 3.190249e-04	k: 810	n:2720000
Cons ci ratio: 4.404730e-04	ci left: 9.665842e-01	ci right 9.670104e-01	k: 2629690	n:2720000
KS ci ratio: 1.376293e-01	ci left: 2.776393e-04	ci right 3.190249e-04	k: 810	n:2720000
LLGL2   2720000 perm   3491 sec   (779 perm/sec)   p_kst 2.977941e-04   p_cons 9.667978e-01   p_joint 2.977941e-04

Joint ci ratio: 1.374599e-01	ci left: 2.773297e-04	ci right 3.186141e-04	k: 812	n:2730000
Cons ci ratio: 4.396806e-04	ci left: 9.665824e-01	ci right 9.670078e-01	k: 2639352	n:2730000
KS ci ratio: 1.374599e-01	ci left: 2.773297e-04	ci right 3.186141e-04	k: 812	n:2730000
LLGL2   2730000 perm   3514 sec   (777 perm/sec)   p_kst 2.974359e-04   p_cons 9.667956e-01   p_joint 2.974359e-04

Joint ci ratio: 1.372070e-01	ci left: 2.773749e-04	ci right 3.185838e-04	k: 815	n:2740000
Cons ci ratio: 4.388948e-04	ci left: 9.665802e-01	ci right 9.670049e-01	k: 2649013	n:2740000
KS ci ratio: 1.372070e-01	ci left: 2.773749e-04	ci right 3.185838e-04	k: 815	n:2740000
LLGL2   2740000 perm   3537 sec   (775 perm/sec)   p_kst 2.974453e-04   p_cons 9.667931e-01   p_joint 2.974453e-04

Joint ci ratio: 1.366221e-01	ci left: 2.788245e-04	ci right 3.200579e-04	k: 822	n:2750000
Cons ci ratio: 4.381729e-04	ci left: 9.665693e-01	ci right 9.669933e-01	k: 2658650	n:2750000
KS ci ratio: 1.366221e-01	ci left: 2.788245e-04	ci right 3.200579e-04	k: 822	n:2750000
LLGL2   2750000 perm   3560 sec   (773 perm/sec)   p_kst 2.989091e-04   p_cons 9.667818e-01   p_joint 2.989091e-04

Joint ci ratio: 1.365393e-01	ci left: 2.781642e-04	ci right 3.192729e-04	k: 823	n:2760000
Cons ci ratio: 4.374198e-04	ci left: 9.665636e-01	ci right 9.669869e-01	k: 2668301	n:2760000
KS ci ratio: 1.365393e-01	ci left: 2.781642e-04	ci right 3.192729e-04	k: 823	n:2760000
LLGL2   2760000 perm   3583 sec   (770 perm/sec)   p_kst 2.981884e-04   p_cons 9.667757e-01   p_joint 2.981884e-04

Joint ci ratio: 1.363739e-01	ci left: 2.778574e-04	ci right 3.188670e-04	k: 825	n:2770000
Cons ci ratio: 4.365799e-04	ci left: 9.665713e-01	ci right 9.669938e-01	k: 2677989	n:2770000
KS ci ratio: 1.363739e-01	ci left: 2.778574e-04	ci right 3.188670e-04	k: 825	n:2770000
LLGL2   2770000 perm   3605 sec   (768 perm/sec)   p_kst 2.978339e-04   p_cons 9.667830e-01   p_joint 2.978339e-04

Joint ci ratio: 1.360448e-01	ci left: 2.782477e-04	ci right 3.192078e-04	k: 829	n:2780000
Cons ci ratio: 4.358594e-04	ci left: 9.665620e-01	ci right 9.669838e-01	k: 2687630	n:2780000
KS ci ratio: 1.360448e-01	ci left: 2.782477e-04	ci right 3.192078e-04	k: 829	n:2780000
LLGL2   2780000 perm   3628 sec   (766 perm/sec)   p_kst 2.982014e-04   p_cons 9.667734e-01   p_joint 2.982014e-04

Joint ci ratio: 1.355557e-01	ci left: 2.793279e-04	ci right 3.202873e-04	k: 835	n:2790000
Cons ci ratio: 4.351570e-04	ci left: 9.665506e-01	ci right 9.669717e-01	k: 2697265	n:2790000
KS ci ratio: 1.355557e-01	ci left: 2.793279e-04	ci right 3.202873e-04	k: 835	n:2790000
LLGL2   2790000 perm   3651 sec   (764 perm/sec)   p_kst 2.992832e-04   p_cons 9.667616e-01   p_joint 2.992832e-04

Joint ci ratio: 1.352325e-01	ci left: 2.797105e-04	ci right 3.206203e-04	k: 839	n:2800000
Cons ci ratio: 4.344194e-04	ci left: 9.665451e-01	ci right 9.669654e-01	k: 2706916	n:2800000
KS ci ratio: 1.352325e-01	ci left: 2.797105e-04	ci right 3.206203e-04	k: 839	n:2800000
LLGL2   2800000 perm   3674 sec   (762 perm/sec)   p_kst 2.996429e-04   p_cons 9.667557e-01   p_joint 2.996429e-04

Joint ci ratio: 1.349117e-01	ci left: 2.800905e-04	ci right 3.209509e-04	k: 843	n:2810000
Cons ci ratio: 4.336542e-04	ci left: 9.665442e-01	ci right 9.669638e-01	k: 2716580	n:2810000
KS ci ratio: 1.349117e-01	ci left: 2.800905e-04	ci right 3.209509e-04	k: 843	n:2810000
LLGL2   2810000 perm   3697 sec   (760 perm/sec)   p_kst 3.000000e-04   p_cons 9.667544e-01   p_joint 3.000000e-04

Joint ci ratio: 1.346725e-01	ci left: 2.801252e-04	ci right 3.209124e-04	k: 846	n:2820000
Cons ci ratio: 4.328143e-04	ci left: 9.665550e-01	ci right 9.669738e-01	k: 2726277	n:2820000
KS ci ratio: 1.346725e-01	ci left: 2.801252e-04	ci right 3.209124e-04	k: 846	n:2820000
LLGL2   2820000 perm   3720 sec   (758 perm/sec)   p_kst 3.000000e-04   p_cons 9.667649e-01   p_joint 3.000000e-04

Joint ci ratio: 1.345932e-01	ci left: 2.794768e-04	ci right 3.201437e-04	k: 847	n:2830000
Cons ci ratio: 4.319887e-04	ci left: 9.665644e-01	ci right 9.669824e-01	k: 2735970	n:2830000
KS ci ratio: 1.345932e-01	ci left: 2.794768e-04	ci right 3.201437e-04	k: 847	n:2830000
LLGL2   2830000 perm   3743 sec   (756 perm/sec)   p_kst 2.992933e-04   p_cons 9.667739e-01   p_joint 2.992933e-04

Joint ci ratio: 1.342768e-01	ci left: 2.798538e-04	ci right 3.204722e-04	k: 851	n:2840000
Cons ci ratio: 4.312812e-04	ci left: 9.665567e-01	ci right 9.669740e-01	k: 2745615	n:2840000
KS ci ratio: 1.342768e-01	ci left: 2.798538e-04	ci right 3.204722e-04	k: 851	n:2840000
LLGL2   2840000 perm   3767 sec   (754 perm/sec)   p_kst 2.996479e-04   p_cons 9.667658e-01   p_joint 2.996479e-04

Joint ci ratio: 1.339627e-01	ci left: 2.802283e-04	ci right 3.207983e-04	k: 855	n:2850000
Cons ci ratio: 4.305396e-04	ci left: 9.665547e-01	ci right 9.669713e-01	k: 2755276	n:2850000
KS ci ratio: 1.339627e-01	ci left: 2.802283e-04	ci right 3.207983e-04	k: 855	n:2850000
LLGL2   2850000 perm   3790 sec   (752 perm/sec)   p_kst 3.000000e-04   p_cons 9.667635e-01   p_joint 3.000000e-04

Joint ci ratio: 1.335731e-01	ci left: 2.809382e-04	ci right 3.214834e-04	k: 860	n:2860000
Cons ci ratio: 4.297643e-04	ci left: 9.665584e-01	ci right 9.669742e-01	k: 2764953	n:2860000
KS ci ratio: 1.335731e-01	ci left: 2.809382e-04	ci right 3.214834e-04	k: 860	n:2860000
LLGL2   2860000 perm   3813 sec   (750 perm/sec)   p_kst 3.006993e-04   p_cons 9.667668e-01   p_joint 3.006993e-04

Joint ci ratio: 1.335732e-01	ci left: 2.799593e-04	ci right 3.203632e-04	k: 860	n:2870000
Cons ci ratio: 4.290537e-04	ci left: 9.665529e-01	ci right 9.669681e-01	k: 2774604	n:2870000
KS ci ratio: 1.335732e-01	ci left: 2.799593e-04	ci right 3.203632e-04	k: 860	n:2870000
LLGL2   2870000 perm   3837 sec   (748 perm/sec)   p_kst 2.996516e-04   p_cons 9.667610e-01   p_joint 2.996516e-04

Joint ci ratio: 1.334183e-01	ci left: 2.796585e-04	ci right 3.199685e-04	k: 862	n:2880000
Cons ci ratio: 4.282448e-04	ci left: 9.665628e-01	ci right 9.669772e-01	k: 2784299	n:2880000
KS ci ratio: 1.334183e-01	ci left: 2.796585e-04	ci right 3.199685e-04	k: 862	n:2880000
LLGL2   2880000 perm   3861 sec   (746 perm/sec)   p_kst 2.993056e-04   p_cons 9.667705e-01   p_joint 2.993056e-04

Joint ci ratio: 1.332640e-01	ci left: 2.793598e-04	ci right 3.195765e-04	k: 864	n:2890000
Cons ci ratio: 4.275279e-04	ci left: 9.665595e-01	ci right 9.669731e-01	k: 2793956	n:2890000
KS ci ratio: 1.332640e-01	ci left: 2.793598e-04	ci right 3.195765e-04	k: 864	n:2890000
LLGL2   2890000 perm   3885 sec   (744 perm/sec)   p_kst 2.989619e-04   p_cons 9.667668e-01   p_joint 2.989619e-04

Joint ci ratio: 1.329569e-01	ci left: 2.797299e-04	ci right 3.198997e-04	k: 868	n:2900000
Cons ci ratio: 4.267481e-04	ci left: 9.665662e-01	ci right 9.669791e-01	k: 2803642	n:2900000
KS ci ratio: 1.329569e-01	ci left: 2.797299e-04	ci right 3.198997e-04	k: 868	n:2900000
LLGL2   2900000 perm   3908 sec   (742 perm/sec)   p_kst 2.993103e-04   p_cons 9.667731e-01   p_joint 2.993103e-04

Joint ci ratio: 1.328042e-01	ci left: 2.794330e-04	ci right 3.195105e-04	k: 870	n:2910000
Cons ci ratio: 4.259817e-04	ci left: 9.665715e-01	ci right 9.669836e-01	k: 2813324	n:2910000
KS ci ratio: 1.328042e-01	ci left: 2.794330e-04	ci right 3.195105e-04	k: 870	n:2910000
LLGL2   2910000 perm   3932 sec   (740 perm/sec)   p_kst 2.989691e-04   p_cons 9.667780e-01   p_joint 2.989691e-04

Joint ci ratio: 1.325003e-01	ci left: 2.798005e-04	ci right 3.198316e-04	k: 874	n:2920000
Cons ci ratio: 4.252512e-04	ci left: 9.665719e-01	ci right 9.669833e-01	k: 2822992	n:2920000
KS ci ratio: 1.325003e-01	ci left: 2.798005e-04	ci right 3.198316e-04	k: 874	n:2920000
LLGL2   2920000 perm   3957 sec   (738 perm/sec)   p_kst 2.993151e-04   p_cons 9.667781e-01   p_joint 2.993151e-04

Joint ci ratio: 1.322737e-01	ci left: 2.798355e-04	ci right 3.197978e-04	k: 877	n:2930000
Cons ci ratio: 4.245582e-04	ci left: 9.665672e-01	ci right 9.669780e-01	k: 2832645	n:2930000
KS ci ratio: 1.322737e-01	ci left: 2.798355e-04	ci right 3.197978e-04	k: 877	n:2930000
LLGL2   2930000 perm   3982 sec   (736 perm/sec)   p_kst 2.993174e-04   p_cons 9.667730e-01   p_joint 2.993174e-04

Joint ci ratio: 1.319734e-01	ci left: 2.801992e-04	ci right 3.201155e-04	k: 881	n:2940000
Cons ci ratio: 4.238596e-04	ci left: 9.665639e-01	ci right 9.669740e-01	k: 2842302	n:2940000
KS ci ratio: 1.319734e-01	ci left: 2.801992e-04	ci right 3.201155e-04	k: 881	n:2940000
LLGL2   2940000 perm   4006 sec   (734 perm/sec)   p_kst 2.996599e-04   p_cons 9.667694e-01   p_joint 2.996599e-04

Joint ci ratio: 1.318987e-01	ci left: 2.795772e-04	ci right 3.193806e-04	k: 882	n:2950000
Cons ci ratio: 4.230707e-04	ci left: 9.665749e-01	ci right 9.669842e-01	k: 2852001	n:2950000
KS ci ratio: 1.318987e-01	ci left: 2.795772e-04	ci right 3.193806e-04	k: 882	n:2950000
LLGL2   2950000 perm   4031 sec   (732 perm/sec)   p_kst 2.989831e-04   p_cons 9.667800e-01   p_joint 2.989831e-04

Joint ci ratio: 1.315268e-01	ci left: 2.802662e-04	ci right 3.200464e-04	k: 887	n:2960000
Cons ci ratio: 4.223439e-04	ci left: 9.665770e-01	ci right 9.669856e-01	k: 2861674	n:2960000
KS ci ratio: 1.315268e-01	ci left: 2.802662e-04	ci right 3.200464e-04	k: 887	n:2960000
LLGL2   2960000 perm   4055 sec   (730 perm/sec)   p_kst 2.996622e-04   p_cons 9.667818e-01   p_joint 2.996622e-04

Joint ci ratio: 1.313790e-01	ci left: 2.799738e-04	ci right 3.196643e-04	k: 889	n:2970000
Cons ci ratio: 4.216739e-04	ci left: 9.665710e-01	ci right 9.669790e-01	k: 2871323	n:2970000
KS ci ratio: 1.313790e-01	ci left: 2.799738e-04	ci right 3.196643e-04	k: 889	n:2970000
LLGL2   2970000 perm   4080 sec   (728 perm/sec)   p_kst 2.993266e-04   p_cons 9.667754e-01   p_joint 2.993266e-04

Joint ci ratio: 1.313791e-01	ci left: 2.790343e-04	ci right 3.185916e-04	k: 889	n:2980000
Cons ci ratio: 4.210180e-04	ci left: 9.665633e-01	ci right 9.669707e-01	k: 2880967	n:2980000
KS ci ratio: 1.313791e-01	ci left: 2.790343e-04	ci right 3.185916e-04	k: 889	n:2980000
LLGL2   2980000 perm   4104 sec   (726 perm/sec)   p_kst 2.983221e-04   p_cons 9.667674e-01   p_joint 2.983221e-04

Joint ci ratio: 1.311582e-01	ci left: 2.790715e-04	ci right 3.185624e-04	k: 892	n:2990000
Cons ci ratio: 4.203236e-04	ci left: 9.665621e-01	ci right 9.669688e-01	k: 2890630	n:2990000
KS ci ratio: 1.311582e-01	ci left: 2.790715e-04	ci right 3.185624e-04	k: 892	n:2990000
LLGL2   2990000 perm   4128 sec   (724 perm/sec)   p_kst 2.983278e-04   p_cons 9.667659e-01   p_joint 2.983278e-04

Joint ci ratio: 1.305021e-01	ci left: 2.810431e-04	ci right 3.205986e-04	k: 901	n:3000000
Cons ci ratio: 4.196239e-04	ci left: 9.665622e-01	ci right 9.669682e-01	k: 2900297	n:3000000
KS ci ratio: 1.305021e-01	ci left: 2.810431e-04	ci right 3.205986e-04	k: 901	n:3000000
LLGL2   3000000 perm   4153 sec   (722 perm/sec)   p_kst 3.003333e-04   p_cons 9.667657e-01   p_joint 3.003333e-04

Joint ci ratio: 1.304298e-01	ci left: 2.804308e-04	ci right 3.198766e-04	k: 902	n:3010000
Cons ci ratio: 4.189407e-04	ci left: 9.665603e-01	ci right 9.669657e-01	k: 2909958	n:3010000
KS ci ratio: 1.304298e-01	ci left: 2.804308e-04	ci right 3.198766e-04	k: 902	n:3010000
LLGL2   3010000 perm   4178 sec   (720 perm/sec)   p_kst 2.996678e-04   p_cons 9.667635e-01   p_joint 2.996678e-04

Joint ci ratio: 1.300702e-01	ci left: 2.811039e-04	ci right 3.205269e-04	k: 907	n:3020000
Cons ci ratio: 4.182953e-04	ci left: 9.665532e-01	ci right 9.669579e-01	k: 2919603	n:3020000
KS ci ratio: 1.300702e-01	ci left: 2.811039e-04	ci right 3.205269e-04	k: 907	n:3020000
LLGL2   3020000 perm   4203 sec   (719 perm/sec)   p_kst 3.003311e-04   p_cons 9.667560e-01   p_joint 3.003311e-04

Joint ci ratio: 1.299272e-01	ci left: 2.808147e-04	ci right 3.201506e-04	k: 909	n:3030000
Cons ci ratio: 4.176206e-04	ci left: 9.665510e-01	ci right 9.669550e-01	k: 2929263	n:3030000
KS ci ratio: 1.299272e-01	ci left: 2.808147e-04	ci right 3.201506e-04	k: 909	n:3030000
LLGL2   3030000 perm   4229 sec   (717 perm/sec)   p_kst 3.000000e-04   p_cons 9.667535e-01   p_joint 3.000000e-04

Joint ci ratio: 1.296426e-01	ci left: 2.811641e-04	ci right 3.204559e-04	k: 913	n:3040000
Cons ci ratio: 4.169322e-04	ci left: 9.665515e-01	ci right 9.669549e-01	k: 2938931	n:3040000
KS ci ratio: 1.296426e-01	ci left: 2.811641e-04	ci right 3.204559e-04	k: 913	n:3040000
LLGL2   3040000 perm   4254 sec   (715 perm/sec)   p_kst 3.003289e-04   p_cons 9.667536e-01   p_joint 3.003289e-04

Joint ci ratio: 1.293598e-01	ci left: 2.815112e-04	ci right 3.207592e-04	k: 917	n:3050000
Cons ci ratio: 4.162259e-04	ci left: 9.665553e-01	ci right 9.669580e-01	k: 2948609	n:3050000
KS ci ratio: 1.293598e-01	ci left: 2.815112e-04	ci right 3.207592e-04	k: 917	n:3050000
LLGL2   3050000 perm   4279 sec   (713 perm/sec)   p_kst 3.006557e-04   p_cons 9.667570e-01   p_joint 3.006557e-04

Joint ci ratio: 1.290089e-01	ci left: 2.821724e-04	ci right 3.213977e-04	k: 922	n:3060000
Cons ci ratio: 4.155274e-04	ci left: 9.665583e-01	ci right 9.669604e-01	k: 2958285	n:3060000
KS ci ratio: 1.290089e-01	ci left: 2.821724e-04	ci right 3.213977e-04	k: 922	n:3060000
LLGL2   3060000 perm   4304 sec   (711 perm/sec)   p_kst 3.013072e-04   p_cons 9.667598e-01   p_joint 3.013072e-04

Joint ci ratio: 1.287997e-01	ci left: 2.821990e-04	ci right 3.213595e-04	k: 925	n:3070000
Cons ci ratio: 4.148472e-04	ci left: 9.665591e-01	ci right 9.669605e-01	k: 2967954	n:3070000
KS ci ratio: 1.287997e-01	ci left: 2.821990e-04	ci right 3.213595e-04	k: 925	n:3070000
LLGL2   3070000 perm   4329 sec   (709 perm/sec)   p_kst 3.013029e-04   p_cons 9.667603e-01   p_joint 3.013029e-04

Joint ci ratio: 1.285224e-01	ci left: 2.825397e-04	ci right 3.216566e-04	k: 929	n:3080000
Cons ci ratio: 4.141661e-04	ci left: 9.665606e-01	ci right 9.669613e-01	k: 2977625	n:3080000
KS ci ratio: 1.285224e-01	ci left: 2.825397e-04	ci right 3.216566e-04	k: 929	n:3080000
LLGL2   3080000 perm   4355 sec   (707 perm/sec)   p_kst 3.016234e-04   p_cons 9.667614e-01   p_joint 3.016234e-04

Joint ci ratio: 1.282469e-01	ci left: 2.828782e-04	ci right 3.219517e-04	k: 933	n:3090000
Cons ci ratio: 4.134737e-04	ci left: 9.665643e-01	ci right 9.669643e-01	k: 2987303	n:3090000
KS ci ratio: 1.282469e-01	ci left: 2.828782e-04	ci right 3.219517e-04	k: 933	n:3090000
LLGL2   3090000 perm   4381 sec   (705 perm/sec)   p_kst 3.019417e-04   p_cons 9.667647e-01   p_joint 3.019417e-04

Joint ci ratio: 1.279732e-01	ci left: 2.832147e-04	ci right 3.222448e-04	k: 937	n:3100000
Cons ci ratio: 4.128014e-04	ci left: 9.665653e-01	ci right 9.669647e-01	k: 2996973	n:3100000
KS ci ratio: 1.279732e-01	ci left: 2.832147e-04	ci right 3.222448e-04	k: 937	n:3100000
LLGL2   3100000 perm   4406 sec   (704 perm/sec)   p_kst 3.022581e-04   p_cons 9.667655e-01   p_joint 3.022581e-04

Joint ci ratio: 1.277690e-01	ci left: 2.832378e-04	ci right 3.222041e-04	k: 940	n:3110000
Cons ci ratio: 4.121736e-04	ci left: 9.665600e-01	ci right 9.669588e-01	k: 3006623	n:3110000
KS ci ratio: 1.277690e-01	ci left: 2.832378e-04	ci right 3.222041e-04	k: 940	n:3110000
LLGL2   3110000 perm   4433 sec   (702 perm/sec)   p_kst 3.022508e-04   p_cons 9.667598e-01   p_joint 3.022508e-04

Joint ci ratio: 1.277012e-01	ci left: 2.826403e-04	ci right 3.215022e-04	k: 941	n:3120000
Cons ci ratio: 4.115076e-04	ci left: 9.665611e-01	ci right 9.669592e-01	k: 3016293	n:3120000
KS ci ratio: 1.277012e-01	ci left: 2.826403e-04	ci right 3.215022e-04	k: 941	n:3120000
LLGL2   3120000 perm   4458 sec   (700 perm/sec)   p_kst 3.016026e-04   p_cons 9.667606e-01   p_joint 3.016026e-04

Joint ci ratio: 1.274983e-01	ci left: 2.826651e-04	ci right 3.214640e-04	k: 944	n:3130000
Cons ci ratio: 4.107938e-04	ci left: 9.665702e-01	ci right 9.669676e-01	k: 3025988	n:3130000
KS ci ratio: 1.274983e-01	ci left: 2.826651e-04	ci right 3.214640e-04	k: 944	n:3130000
LLGL2   3130000 perm   4484 sec   (698 perm/sec)   p_kst 3.015974e-04   p_cons 9.667693e-01   p_joint 3.015974e-04

Joint ci ratio: 1.273637e-01	ci left: 2.823816e-04	ci right 3.210975e-04	k: 946	n:3140000
Cons ci ratio: 4.100368e-04	ci left: 9.665866e-01	ci right 9.669833e-01	k: 3035706	n:3140000
KS ci ratio: 1.273637e-01	ci left: 2.823816e-04	ci right 3.210975e-04	k: 946	n:3140000
LLGL2   3140000 perm   4511 sec   (696 perm/sec)   p_kst 3.012739e-04   p_cons 9.667854e-01   p_joint 3.012739e-04

Joint ci ratio: 1.272965e-01	ci left: 2.817924e-04	ci right 3.204057e-04	k: 947	n:3150000
Cons ci ratio: 4.093811e-04	ci left: 9.665876e-01	ci right 9.669836e-01	k: 3045376	n:3150000
KS ci ratio: 1.272965e-01	ci left: 2.817924e-04	ci right 3.204057e-04	k: 947	n:3150000
LLGL2   3150000 perm   4537 sec   (694 perm/sec)   p_kst 3.006349e-04   p_cons 9.667860e-01   p_joint 3.006349e-04

Joint ci ratio: 1.272295e-01	ci left: 2.812071e-04	ci right 3.197183e-04	k: 948	n:3160000
Cons ci ratio: 4.087688e-04	ci left: 9.665822e-01	ci right 9.669777e-01	k: 3055026	n:3160000
KS ci ratio: 1.272295e-01	ci left: 2.812071e-04	ci right 3.197183e-04	k: 948	n:3160000
LLGL2   3160000 perm   4563 sec   (693 perm/sec)   p_kst 3.000000e-04   p_cons 9.667804e-01   p_joint 3.000000e-04

Joint ci ratio: 1.271625e-01	ci left: 2.806254e-04	ci right 3.190352e-04	k: 949	n:3170000
Cons ci ratio: 4.081512e-04	ci left: 9.665781e-01	ci right 9.669730e-01	k: 3064680	n:3170000
KS ci ratio: 1.271625e-01	ci left: 2.806254e-04	ci right 3.190352e-04	k: 949	n:3170000
LLGL2   3170000 perm   4589 sec   (691 perm/sec)   p_kst 2.993691e-04   p_cons 9.667760e-01   p_joint 2.993691e-04

Joint ci ratio: 1.270289e-01	ci left: 2.803519e-04	ci right 3.186809e-04	k: 951	n:3180000
Cons ci ratio: 4.075344e-04	ci left: 9.665744e-01	ci right 9.669687e-01	k: 3074335	n:3180000
KS ci ratio: 1.270289e-01	ci left: 2.803519e-04	ci right 3.186809e-04	k: 951	n:3180000
LLGL2   3180000 perm   4616 sec   (689 perm/sec)   p_kst 2.990566e-04   p_cons 9.667720e-01   p_joint 2.990566e-04

Joint ci ratio: 1.265644e-01	ci left: 2.815978e-04	ci right 3.199458e-04	k: 958	n:3190000
Cons ci ratio: 4.068747e-04	ci left: 9.665780e-01	ci right 9.669716e-01	k: 3084013	n:3190000
KS ci ratio: 1.265644e-01	ci left: 2.815978e-04	ci right 3.199458e-04	k: 958	n:3190000
LLGL2   3190000 perm   4642 sec   (687 perm/sec)   p_kst 3.003135e-04   p_cons 9.667752e-01   p_joint 3.003135e-04

Joint ci ratio: 1.263012e-01	ci left: 2.819283e-04	ci right 3.202355e-04	k: 962	n:3200000
Cons ci ratio: 4.061886e-04	ci left: 9.665862e-01	ci right 9.669792e-01	k: 3093706	n:3200000
KS ci ratio: 1.263012e-01	ci left: 2.819283e-04	ci right 3.202355e-04	k: 962	n:3200000
LLGL2   3200000 perm   4669 sec   (685 perm/sec)   p_kst 3.006250e-04   p_cons 9.667831e-01   p_joint 3.006250e-04

Joint ci ratio: 1.261703e-01	ci left: 2.816534e-04	ci right 3.198806e-04	k: 964	n:3210000
Cons ci ratio: 4.055649e-04	ci left: 9.665850e-01	ci right 9.669774e-01	k: 3103369	n:3210000
KS ci ratio: 1.261703e-01	ci left: 2.816534e-04	ci right 3.198806e-04	k: 964	n:3210000
LLGL2   3210000 perm   4695 sec   (684 perm/sec)   p_kst 3.003115e-04   p_cons 9.667816e-01   p_joint 3.003115e-04

Joint ci ratio: 1.259746e-01	ci left: 2.816809e-04	ci right 3.198482e-04	k: 967	n:3220000
Cons ci ratio: 4.049186e-04	ci left: 9.665879e-01	ci right 9.669796e-01	k: 3113045	n:3220000
KS ci ratio: 1.259746e-01	ci left: 2.816809e-04	ci right 3.198482e-04	k: 967	n:3220000
LLGL2   3220000 perm   4721 sec   (682 perm/sec)   p_kst 3.003106e-04   p_cons 9.667842e-01   p_joint 3.003106e-04

Joint ci ratio: 1.259096e-01	ci left: 2.811087e-04	ci right 3.191773e-04	k: 968	n:3230000
Cons ci ratio: 4.042988e-04	ci left: 9.665870e-01	ci right 9.669781e-01	k: 3122709	n:3230000
KS ci ratio: 1.259096e-01	ci left: 2.811087e-04	ci right 3.191773e-04	k: 968	n:3230000
LLGL2   3230000 perm   4748 sec   (680 perm/sec)   p_kst 2.996904e-04   p_cons 9.667830e-01   p_joint 2.996904e-04

Joint ci ratio: 1.256505e-01	ci left: 2.814368e-04	ci right 3.194656e-04	k: 972	n:3240000
Cons ci ratio: 4.036935e-04	ci left: 9.665842e-01	ci right 9.669748e-01	k: 3132367	n:3240000
KS ci ratio: 1.256505e-01	ci left: 2.814368e-04	ci right 3.194656e-04	k: 972	n:3240000
LLGL2   3240000 perm   4774 sec   (679 perm/sec)   p_kst 3.000000e-04   p_cons 9.667799e-01   p_joint 3.000000e-04

Joint ci ratio: 1.254573e-01	ci left: 2.814649e-04	ci right 3.194347e-04	k: 975	n:3250000
Cons ci ratio: 4.031430e-04	ci left: 9.665732e-01	ci right 9.669632e-01	k: 3141998	n:3250000
KS ci ratio: 1.254573e-01	ci left: 2.814649e-04	ci right 3.194347e-04	k: 975	n:3250000
LLGL2   3250000 perm   4801 sec   (677 perm/sec)   p_kst 3.000000e-04   p_cons 9.667686e-01   p_joint 3.000000e-04

Joint ci ratio: 1.250734e-01	ci left: 2.823844e-04	ci right 3.203529e-04	k: 981	n:3260000
Cons ci ratio: 4.025428e-04	ci left: 9.665705e-01	ci right 9.669600e-01	k: 3151656	n:3260000
KS ci ratio: 1.250734e-01	ci left: 2.823844e-04	ci right 3.203529e-04	k: 981	n:3260000
LLGL2   3260000 perm   4827 sec   (675 perm/sec)   p_kst 3.009202e-04   p_cons 9.667656e-01   p_joint 3.009202e-04

Joint ci ratio: 1.248828e-01	ci left: 2.824096e-04	ci right 3.203194e-04	k: 984	n:3270000
Cons ci ratio: 4.019089e-04	ci left: 9.665737e-01	ci right 9.669625e-01	k: 3161333	n:3270000
KS ci ratio: 1.248828e-01	ci left: 2.824096e-04	ci right 3.203194e-04	k: 984	n:3270000
LLGL2   3270000 perm   4854 sec   (674 perm/sec)   p_kst 3.009174e-04   p_cons 9.667685e-01   p_joint 3.009174e-04

Joint ci ratio: 1.245670e-01	ci left: 2.830254e-04	ci right 3.209147e-04	k: 989	n:3280000
Cons ci ratio: 4.012914e-04	ci left: 9.665747e-01	ci right 9.669629e-01	k: 3171003	n:3280000
KS ci ratio: 1.245670e-01	ci left: 2.830254e-04	ci right 3.209147e-04	k: 989	n:3280000
LLGL2   3280000 perm   4880 sec   (672 perm/sec)   p_kst 3.015244e-04   p_cons 9.667692e-01   p_joint 3.015244e-04

Joint ci ratio: 1.243160e-01	ci left: 2.833431e-04	ci right 3.211929e-04	k: 993	n:3290000
Cons ci ratio: 4.006786e-04	ci left: 9.665754e-01	ci right 9.669630e-01	k: 3180672	n:3290000
KS ci ratio: 1.243160e-01	ci left: 2.833431e-04	ci right 3.211929e-04	k: 993	n:3290000
LLGL2   3290000 perm   4907 sec   (670 perm/sec)   p_kst 3.018237e-04   p_cons 9.667696e-01   p_joint 3.018237e-04

Joint ci ratio: 1.241912e-01	ci left: 2.830717e-04	ci right 3.208445e-04	k: 995	n:3300000
Cons ci ratio: 4.000440e-04	ci left: 9.665800e-01	ci right 9.669671e-01	k: 3190354	n:3300000
KS ci ratio: 1.241912e-01	ci left: 2.830717e-04	ci right 3.208445e-04	k: 995	n:3300000
LLGL2   3300000 perm   4934 sec   (669 perm/sec)   p_kst 3.015152e-04   p_cons 9.667739e-01   p_joint 3.015152e-04

Joint ci ratio: 1.237570e-01	ci left: 2.842657e-04	ci right 3.220555e-04	k: 1002	n:3310000
Cons ci ratio: 3.994369e-04	ci left: 9.665807e-01	ci right 9.669671e-01	k: 3200023	n:3310000
KS ci ratio: 1.237570e-01	ci left: 2.842657e-04	ci right 3.220555e-04	k: 1002	n:3310000
LLGL2   3310000 perm   4961 sec   (667 perm/sec)   p_kst 3.027190e-04   p_cons 9.667743e-01   p_joint 3.027190e-04

Joint ci ratio: 1.233884e-01	ci left: 2.851609e-04	ci right 3.229485e-04	k: 1008	n:3320000
Cons ci ratio: 3.988157e-04	ci left: 9.665841e-01	ci right 9.669699e-01	k: 3209701	n:3320000
KS ci ratio: 1.233884e-01	ci left: 2.851609e-04	ci right 3.229485e-04	k: 1008	n:3320000
LLGL2   3320000 perm   4988 sec   (666 perm/sec)   p_kst 3.036145e-04   p_cons 9.667774e-01   p_joint 3.036145e-04

Joint ci ratio: 1.232054e-01	ci left: 2.851777e-04	ci right 3.229074e-04	k: 1011	n:3330000
Cons ci ratio: 3.982160e-04	ci left: 9.665844e-01	ci right 9.669697e-01	k: 3219369	n:3330000
KS ci ratio: 1.232054e-01	ci left: 2.851777e-04	ci right 3.229074e-04	k: 1011	n:3330000
LLGL2   3330000 perm   5015 sec   (664 perm/sec)   p_kst 3.036036e-04   p_cons 9.667775e-01   p_joint 3.036036e-04

Joint ci ratio: 1.229626e-01	ci left: 2.854846e-04	ci right 3.231750e-04	k: 1015	n:3340000
Cons ci ratio: 3.976709e-04	ci left: 9.665764e-01	ci right 9.669611e-01	k: 3229009	n:3340000
KS ci ratio: 1.229626e-01	ci left: 2.854846e-04	ci right 3.231750e-04	k: 1015	n:3340000
LLGL2   3340000 perm   5042 sec   (662 perm/sec)   p_kst 3.038922e-04   p_cons 9.667692e-01   p_joint 3.038922e-04

Joint ci ratio: 1.226611e-01	ci left: 2.860791e-04	ci right 3.237487e-04	k: 1020	n:3350000
Cons ci ratio: 3.970708e-04	ci left: 9.665777e-01	ci right 9.669618e-01	k: 3238680	n:3350000
KS ci ratio: 1.226611e-01	ci left: 2.860791e-04	ci right 3.237487e-04	k: 1020	n:3350000
LLGL2   3350000 perm   5070 sec   (661 perm/sec)   p_kst 3.044776e-04   p_cons 9.667701e-01   p_joint 3.044776e-04

Joint ci ratio: 1.224813e-01	ci left: 2.860931e-04	ci right 3.237054e-04	k: 1023	n:3360000
Cons ci ratio: 3.964863e-04	ci left: 9.665768e-01	ci right 9.669604e-01	k: 3248344	n:3360000
KS ci ratio: 1.224813e-01	ci left: 2.860931e-04	ci right 3.237054e-04	k: 1023	n:3360000
LLGL2   3360000 perm   5097 sec   (659 perm/sec)   p_kst 3.044643e-04   p_cons 9.667690e-01   p_joint 3.044643e-04

Joint ci ratio: 1.224216e-01	ci left: 2.855318e-04	ci right 3.230507e-04	k: 1024	n:3370000
Cons ci ratio: 3.959244e-04	ci left: 9.665728e-01	ci right 9.669558e-01	k: 3257997	n:3370000
KS ci ratio: 1.224216e-01	ci left: 2.855318e-04	ci right 3.230507e-04	k: 1024	n:3370000
LLGL2   3370000 perm   5125 sec   (658 perm/sec)   p_kst 3.038576e-04   p_cons 9.667647e-01   p_joint 3.038576e-04

Joint ci ratio: 1.222428e-01	ci left: 2.855475e-04	ci right 3.230096e-04	k: 1027	n:3380000
Cons ci ratio: 3.953304e-04	ci left: 9.665743e-01	ci right 9.669568e-01	k: 3267669	n:3380000
KS ci ratio: 1.222428e-01	ci left: 2.855475e-04	ci right 3.230096e-04	k: 1027	n:3380000
LLGL2   3380000 perm   5153 sec   (656 perm/sec)   p_kst 3.038462e-04   p_cons 9.667660e-01   p_joint 3.038462e-04

Joint ci ratio: 1.220648e-01	ci left: 2.855631e-04	ci right 3.229688e-04	k: 1030	n:3390000
Cons ci ratio: 3.947408e-04	ci left: 9.665756e-01	ci right 9.669575e-01	k: 3277340	n:3390000
KS ci ratio: 1.220648e-01	ci left: 2.855631e-04	ci right 3.229688e-04	k: 1030	n:3390000
LLGL2   3390000 perm   5181 sec   (654 perm/sec)   p_kst 3.038348e-04   p_cons 9.667670e-01   p_joint 3.038348e-04

Joint ci ratio: 1.220057e-01	ci left: 2.850083e-04	ci right 3.223220e-04	k: 1031	n:3400000
Cons ci ratio: 3.941972e-04	ci left: 9.665698e-01	ci right 9.669512e-01	k: 3286987	n:3400000
KS ci ratio: 1.220057e-01	ci left: 2.850083e-04	ci right 3.223220e-04	k: 1031	n:3400000
LLGL2   3400000 perm   5208 sec   (653 perm/sec)   p_kst 3.032353e-04   p_cons 9.667609e-01   p_joint 3.032353e-04

Joint ci ratio: 1.218288e-01	ci left: 2.850255e-04	ci right 3.222833e-04	k: 1034	n:3410000
Cons ci ratio: 3.935857e-04	ci left: 9.665755e-01	ci right 9.669563e-01	k: 3296673	n:3410000
KS ci ratio: 1.218288e-01	ci left: 2.850255e-04	ci right 3.222833e-04	k: 1034	n:3410000
LLGL2   3410000 perm   5236 sec   (651 perm/sec)   p_kst 3.032258e-04   p_cons 9.667663e-01   p_joint 3.032258e-04

Joint ci ratio: 1.217113e-01	ci left: 2.847590e-04	ci right 3.219436e-04	k: 1036	n:3420000
Cons ci ratio: 3.930110e-04	ci left: 9.665756e-01	ci right 9.669558e-01	k: 3306340	n:3420000
KS ci ratio: 1.217113e-01	ci left: 2.847590e-04	ci right 3.219436e-04	k: 1036	n:3420000
LLGL2   3420000 perm   5264 sec   (650 perm/sec)   p_kst 3.029240e-04   p_cons 9.667661e-01   p_joint 3.029240e-04

Joint ci ratio: 1.215356e-01	ci left: 2.847768e-04	ci right 3.219062e-04	k: 1039	n:3430000
Cons ci ratio: 3.924709e-04	ci left: 9.665704e-01	ci right 9.669501e-01	k: 3315989	n:3430000
KS ci ratio: 1.215356e-01	ci left: 2.847768e-04	ci right 3.219062e-04	k: 1039	n:3430000
LLGL2   3430000 perm   5293 sec   (648 perm/sec)   p_kst 3.029155e-04   p_cons 9.667606e-01   p_joint 3.029155e-04

Joint ci ratio: 1.214772e-01	ci left: 2.842309e-04	ci right 3.212699e-04	k: 1040	n:3440000
Cons ci ratio: 3.918462e-04	ci left: 9.665795e-01	ci right 9.669586e-01	k: 3325687	n:3440000
KS ci ratio: 1.214772e-01	ci left: 2.842309e-04	ci right 3.212699e-04	k: 1040	n:3440000
LLGL2   3440000 perm   5321 sec   (646 perm/sec)   p_kst 3.023256e-04   p_cons 9.667695e-01   p_joint 3.023256e-04

Joint ci ratio: 1.213607e-01	ci left: 2.839691e-04	ci right 3.209360e-04	k: 1042	n:3450000
Cons ci ratio: 3.912738e-04	ci left: 9.665805e-01	ci right 9.669590e-01	k: 3335357	n:3450000
KS ci ratio: 1.213607e-01	ci left: 2.839691e-04	ci right 3.209360e-04	k: 1042	n:3450000
LLGL2   3450000 perm   5350 sec   (645 perm/sec)   p_kst 3.020290e-04   p_cons 9.667701e-01   p_joint 3.020290e-04

Joint ci ratio: 1.212446e-01	ci left: 2.837089e-04	ci right 3.206040e-04	k: 1044	n:3460000
Cons ci ratio: 3.907250e-04	ci left: 9.665779e-01	ci right 9.669560e-01	k: 3345015	n:3460000
KS ci ratio: 1.212446e-01	ci left: 2.837089e-04	ci right 3.206040e-04	k: 1044	n:3460000
LLGL2   3460000 perm   5378 sec   (643 perm/sec)   p_kst 3.017341e-04   p_cons 9.667673e-01   p_joint 3.017341e-04

Joint ci ratio: 1.210709e-01	ci left: 2.837296e-04	ci right 3.205709e-04	k: 1047	n:3470000
Cons ci ratio: 3.901330e-04	ci left: 9.665829e-01	ci right 9.669604e-01	k: 3354699	n:3470000
KS ci ratio: 1.210709e-01	ci left: 2.837296e-04	ci right 3.205709e-04	k: 1047	n:3470000
LLGL2   3470000 perm   5407 sec   (642 perm/sec)   p_kst 3.017291e-04   p_cons 9.667720e-01   p_joint 3.017291e-04

Joint ci ratio: 1.209556e-01	ci left: 2.834716e-04	ci right 3.202418e-04	k: 1049	n:3480000
Cons ci ratio: 3.895611e-04	ci left: 9.665850e-01	ci right 9.669619e-01	k: 3364373	n:3480000
KS ci ratio: 1.209556e-01	ci left: 2.834716e-04	ci right 3.202418e-04	k: 1049	n:3480000
LLGL2   3480000 perm   5435 sec   (640 perm/sec)   p_kst 3.014368e-04   p_cons 9.667739e-01   p_joint 3.014368e-04

Joint ci ratio: 1.207831e-01	ci left: 2.834930e-04	ci right 3.202098e-04	k: 1052	n:3490000
Cons ci ratio: 3.889935e-04	ci left: 9.665868e-01	ci right 9.669631e-01	k: 3374046	n:3490000
KS ci ratio: 1.207831e-01	ci left: 2.834930e-04	ci right 3.202098e-04	k: 1052	n:3490000
LLGL2   3490000 perm   5463 sec   (639 perm/sec)   p_kst 3.014327e-04   p_cons 9.667754e-01   p_joint 3.014327e-04

Joint ci ratio: 1.207259e-01	ci left: 2.829601e-04	ci right 3.195892e-04	k: 1053	n:3500000
Cons ci ratio: 3.884318e-04	ci left: 9.665880e-01	ci right 9.669638e-01	k: 3383717	n:3500000
KS ci ratio: 1.207259e-01	ci left: 2.829601e-04	ci right 3.195892e-04	k: 1053	n:3500000
LLGL2   3500000 perm   5492 sec   (637 perm/sec)   p_kst 3.008571e-04   p_cons 9.667763e-01   p_joint 3.008571e-04

Joint ci ratio: 1.206687e-01	ci left: 2.824302e-04	ci right 3.189722e-04	k: 1054	n:3510000
Cons ci ratio: 3.878880e-04	ci left: 9.665866e-01	ci right 9.669619e-01	k: 3393379	n:3510000
KS ci ratio: 1.206687e-01	ci left: 2.824302e-04	ci right 3.189722e-04	k: 1054	n:3510000
LLGL2   3510000 perm   5521 sec   (636 perm/sec)   p_kst 3.002849e-04   p_cons 9.667746e-01   p_joint 3.002849e-04

Joint ci ratio: 1.204405e-01	ci left: 2.827300e-04	ci right 3.192367e-04	k: 1058	n:3520000
Cons ci ratio: 3.873276e-04	ci left: 9.665884e-01	ci right 9.669631e-01	k: 3403052	n:3520000
KS ci ratio: 1.204405e-01	ci left: 2.827300e-04	ci right 3.192367e-04	k: 1058	n:3520000
LLGL2   3520000 perm   5550 sec   (634 perm/sec)   p_kst 3.005682e-04   p_cons 9.667761e-01   p_joint 3.005682e-04

Joint ci ratio: 1.202703e-01	ci left: 2.827533e-04	ci right 3.192077e-04	k: 1061	n:3530000
Cons ci ratio: 3.867765e-04	ci left: 9.665890e-01	ci right 9.669632e-01	k: 3412721	n:3530000
KS ci ratio: 1.202703e-01	ci left: 2.827533e-04	ci right 3.192077e-04	k: 1061	n:3530000
LLGL2   3530000 perm   5578 sec   (633 perm/sec)   p_kst 3.005666e-04   p_cons 9.667765e-01   p_joint 3.005666e-04

Joint ci ratio: 1.201572e-01	ci left: 2.825026e-04	ci right 3.188880e-04	k: 1063	n:3540000
Cons ci ratio: 3.862039e-04	ci left: 9.665936e-01	ci right 9.669672e-01	k: 3422404	n:3540000
KS ci ratio: 1.201572e-01	ci left: 2.825026e-04	ci right 3.188880e-04	k: 1063	n:3540000
LLGL2   3540000 perm   5606 sec   (631 perm/sec)   p_kst 3.002825e-04   p_cons 9.667808e-01   p_joint 3.002825e-04

Joint ci ratio: 1.198198e-01	ci left: 2.833462e-04	ci right 3.197305e-04	k: 1069	n:3550000
Cons ci ratio: 3.856491e-04	ci left: 9.665956e-01	ci right 9.669687e-01	k: 3432078	n:3550000
KS ci ratio: 1.198198e-01	ci left: 2.833462e-04	ci right 3.197305e-04	k: 1069	n:3550000
LLGL2   3550000 perm   5635 sec   (630 perm/sec)   p_kst 3.011268e-04   p_cons 9.667825e-01   p_joint 3.011268e-04

Joint ci ratio: 1.197080e-01	ci left: 2.830953e-04	ci right 3.194110e-04	k: 1071	n:3560000
Cons ci ratio: 3.851320e-04	ci left: 9.665917e-01	ci right 9.669643e-01	k: 3441731	n:3560000
KS ci ratio: 1.197080e-01	ci left: 2.830953e-04	ci right 3.194110e-04	k: 1071	n:3560000
LLGL2   3560000 perm   5664 sec   (629 perm/sec)   p_kst 3.008427e-04   p_cons 9.667784e-01   p_joint 3.008427e-04

Joint ci ratio: 1.195409e-01	ci left: 2.831175e-04	ci right 3.193818e-04	k: 1074	n:3570000
Cons ci ratio: 3.845466e-04	ci left: 9.665996e-01	ci right 9.669716e-01	k: 3451426	n:3570000
KS ci ratio: 1.195409e-01	ci left: 2.831175e-04	ci right 3.193818e-04	k: 1074	n:3570000
LLGL2   3570000 perm   5693 sec   (627 perm/sec)   p_kst 3.008403e-04   p_cons 9.667860e-01   p_joint 3.008403e-04

Joint ci ratio: 1.193744e-01	ci left: 2.831396e-04	ci right 3.193527e-04	k: 1077	n:3580000
Cons ci ratio: 3.840473e-04	ci left: 9.665935e-01	ci right 9.669650e-01	k: 3461071	n:3580000
KS ci ratio: 1.193744e-01	ci left: 2.831396e-04	ci right 3.193527e-04	k: 1077	n:3580000
LLGL2   3580000 perm   5722 sec   (626 perm/sec)   p_kst 3.008380e-04   p_cons 9.667796e-01   p_joint 3.008380e-04

Joint ci ratio: 1.191535e-01	ci left: 2.834319e-04	ci right 3.196105e-04	k: 1081	n:3590000
Cons ci ratio: 3.835616e-04	ci left: 9.665854e-01	ci right 9.669565e-01	k: 3470709	n:3590000
KS ci ratio: 1.191535e-01	ci left: 2.834319e-04	ci right 3.196105e-04	k: 1081	n:3590000
LLGL2   3590000 perm   5752 sec   (624 perm/sec)   p_kst 3.011142e-04   p_cons 9.667713e-01   p_joint 3.011142e-04

Joint ci ratio: 1.189887e-01	ci left: 2.834531e-04	ci right 3.195809e-04	k: 1084	n:3600000
Cons ci ratio: 3.829900e-04	ci left: 9.665921e-01	ci right 9.669627e-01	k: 3480400	n:3600000
KS ci ratio: 1.189887e-01	ci left: 2.834531e-04	ci right 3.195809e-04	k: 1084	n:3600000
LLGL2   3600000 perm   5783 sec   (623 perm/sec)   p_kst 3.011111e-04   p_cons 9.667778e-01   p_joint 3.011111e-04

Joint ci ratio: 1.188245e-01	ci left: 2.834742e-04	ci right 3.195513e-04	k: 1087	n:3610000
Cons ci ratio: 3.824423e-04	ci left: 9.665952e-01	ci right 9.669652e-01	k: 3490078	n:3610000
KS ci ratio: 1.188245e-01	ci left: 2.834742e-04	ci right 3.195513e-04	k: 1087	n:3610000
LLGL2   3610000 perm   5812 sec   (621 perm/sec)   p_kst 3.011080e-04   p_cons 9.667806e-01   p_joint 3.011080e-04

Joint ci ratio: 1.187155e-01	ci left: 2.832272e-04	ci right 3.192375e-04	k: 1089	n:3620000
Cons ci ratio: 3.819626e-04	ci left: 9.665872e-01	ci right 9.669568e-01	k: 3499716	n:3620000
KS ci ratio: 1.187155e-01	ci left: 2.832272e-04	ci right 3.192375e-04	k: 1089	n:3620000
LLGL2   3620000 perm   5841 sec   (620 perm/sec)   p_kst 3.008287e-04   p_cons 9.667724e-01   p_joint 3.008287e-04

Joint ci ratio: 1.186611e-01	ci left: 2.827142e-04	ci right 3.186417e-04	k: 1090	n:3630000
Cons ci ratio: 3.814226e-04	ci left: 9.665898e-01	ci right 9.669588e-01	k: 3509392	n:3630000
KS ci ratio: 1.186611e-01	ci left: 2.827142e-04	ci right 3.186417e-04	k: 1090	n:3630000
LLGL2   3630000 perm   5871 sec   (618 perm/sec)   p_kst 3.002755e-04   p_cons 9.667747e-01   p_joint 3.002755e-04

Joint ci ratio: 1.184983e-01	ci left: 2.827373e-04	ci right 3.186149e-04	k: 1093	n:3640000
Cons ci ratio: 3.808946e-04	ci left: 9.665906e-01	ci right 9.669592e-01	k: 3519062	n:3640000
KS ci ratio: 1.184983e-01	ci left: 2.827373e-04	ci right 3.186149e-04	k: 1093	n:3640000
LLGL2   3640000 perm   5902 sec   (617 perm/sec)   p_kst 3.002747e-04   p_cons 9.667753e-01   p_joint 3.002747e-04

Joint ci ratio: 1.181209e-01	ci left: 2.838237e-04	ci right 3.197165e-04	k: 1100	n:3650000
Cons ci ratio: 3.803656e-04	ci left: 9.665921e-01	ci right 9.669601e-01	k: 3528734	n:3650000
KS ci ratio: 1.181209e-01	ci left: 2.838237e-04	ci right 3.197165e-04	k: 1100	n:3650000
LLGL2   3650000 perm   5932 sec   (615 perm/sec)   p_kst 3.013699e-04   p_cons 9.667764e-01   p_joint 3.013699e-04

Joint ci ratio: 1.179069e-01	ci left: 2.841089e-04	ci right 3.199681e-04	k: 1104	n:3660000
Cons ci ratio: 3.798566e-04	ci left: 9.665905e-01	ci right 9.669580e-01	k: 3538395	n:3660000
KS ci ratio: 1.179069e-01	ci left: 2.841089e-04	ci right 3.199681e-04	k: 1104	n:3660000
LLGL2   3660000 perm   5963 sec   (614 perm/sec)   p_kst 3.016393e-04   p_cons 9.667746e-01   p_joint 3.016393e-04

Joint ci ratio: 1.176941e-01	ci left: 2.843925e-04	ci right 3.202183e-04	k: 1108	n:3670000
Cons ci ratio: 3.793222e-04	ci left: 9.665935e-01	ci right 9.669605e-01	k: 3548073	n:3670000
KS ci ratio: 1.176941e-01	ci left: 2.843925e-04	ci right 3.202183e-04	k: 1108	n:3670000
LLGL2   3670000 perm   5995 sec   (612 perm/sec)   p_kst 3.019074e-04   p_cons 9.667774e-01   p_joint 3.019074e-04

Joint ci ratio: 1.173243e-01	ci left: 2.854660e-04	ci right 3.213062e-04	k: 1115	n:3680000
Cons ci ratio: 3.787997e-04	ci left: 9.665949e-01	ci right 9.669614e-01	k: 3557745	n:3680000
KS ci ratio: 1.173243e-01	ci left: 2.854660e-04	ci right 3.213062e-04	k: 1115	n:3680000
LLGL2   3680000 perm   6027 sec   (611 perm/sec)   p_kst 3.029891e-04   p_cons 9.667785e-01   p_joint 3.029891e-04

Joint ci ratio: 1.171146e-01	ci left: 2.857446e-04	ci right 3.215512e-04	k: 1119	n:3690000
Cons ci ratio: 3.782825e-04	ci left: 9.665958e-01	ci right 9.669618e-01	k: 3567415	n:3690000
KS ci ratio: 1.171146e-01	ci left: 2.857446e-04	ci right 3.215512e-04	k: 1119	n:3690000
LLGL2   3690000 perm   6057 sec   (609 perm/sec)   p_kst 3.032520e-04   p_cons 9.667791e-01   p_joint 3.032520e-04

Joint ci ratio: 1.170102e-01	ci left: 2.854971e-04	ci right 3.212385e-04	k: 1121	n:3700000
Cons ci ratio: 3.777754e-04	ci left: 9.665953e-01	ci right 9.669608e-01	k: 3577080	n:3700000
KS ci ratio: 1.170102e-01	ci left: 2.854971e-04	ci right 3.212385e-04	k: 1121	n:3700000
LLGL2   3700000 perm   6088 sec   (608 perm/sec)   p_kst 3.029730e-04   p_cons 9.667784e-01   p_joint 3.029730e-04

Joint ci ratio: 1.168541e-01	ci left: 2.855125e-04	ci right 3.212049e-04	k: 1124	n:3710000
Cons ci ratio: 3.771801e-04	ci left: 9.666102e-01	ci right 9.669751e-01	k: 3586802	n:3710000
KS ci ratio: 1.168541e-01	ci left: 2.855125e-04	ci right 3.212049e-04	k: 1124	n:3710000
LLGL2   3710000 perm   6118 sec   (606 perm/sec)   p_kst 3.029650e-04   p_cons 9.667930e-01   p_joint 3.029650e-04

Joint ci ratio: 1.168541e-01	ci left: 2.847450e-04	ci right 3.203415e-04	k: 1124	n:3720000
Cons ci ratio: 3.766806e-04	ci left: 9.666091e-01	ci right 9.669735e-01	k: 3596465	n:3720000
KS ci ratio: 1.168541e-01	ci left: 2.847450e-04	ci right 3.203415e-04	k: 1124	n:3720000
LLGL2   3720000 perm   6149 sec   (605 perm/sec)   p_kst 3.021505e-04   p_cons 9.667917e-01   p_joint 3.021505e-04

Joint ci ratio: 1.167504e-01	ci left: 2.845021e-04	ci right 3.200345e-04	k: 1126	n:3730000
Cons ci ratio: 3.761799e-04	ci left: 9.666085e-01	ci right 9.669725e-01	k: 3606130	n:3730000
KS ci ratio: 1.167504e-01	ci left: 2.845021e-04	ci right 3.200345e-04	k: 1126	n:3730000
LLGL2   3730000 perm   6179 sec   (604 perm/sec)   p_kst 3.018767e-04   p_cons 9.667909e-01   p_joint 3.018767e-04

Joint ci ratio: 1.167505e-01	ci left: 2.837414e-04	ci right 3.191788e-04	k: 1126	n:3740000
Cons ci ratio: 3.756984e-04	ci left: 9.666051e-01	ci right 9.669685e-01	k: 3615784	n:3740000
KS ci ratio: 1.167505e-01	ci left: 2.837414e-04	ci right 3.191788e-04	k: 1126	n:3740000
LLGL2   3740000 perm   6209 sec   (602 perm/sec)   p_kst 3.010695e-04   p_cons 9.667872e-01   p_joint 3.010695e-04

Joint ci ratio: 1.164923e-01	ci left: 2.842792e-04	ci right 3.196999e-04	k: 1131	n:3750000
Cons ci ratio: 3.751689e-04	ci left: 9.666102e-01	ci right 9.669731e-01	k: 3625470	n:3750000
KS ci ratio: 1.164923e-01	ci left: 2.842792e-04	ci right 3.196999e-04	k: 1131	n:3750000
LLGL2   3750000 perm   6239 sec   (601 perm/sec)   p_kst 3.016000e-04   p_cons 9.667920e-01   p_joint 3.016000e-04

Joint ci ratio: 1.164409e-01	ci left: 2.837814e-04	ci right 3.191233e-04	k: 1132	n:3760000
Cons ci ratio: 3.746742e-04	ci left: 9.666096e-01	ci right 9.669721e-01	k: 3635135	n:3760000
KS ci ratio: 1.164409e-01	ci left: 2.837814e-04	ci right 3.191233e-04	k: 1132	n:3760000
LLGL2   3760000 perm   6272 sec   (600 perm/sec)   p_kst 3.010638e-04   p_cons 9.667912e-01   p_joint 3.010638e-04

Joint ci ratio: 1.163383e-01	ci left: 2.835437e-04	ci right 3.188228e-04	k: 1134	n:3770000
Cons ci ratio: 3.741660e-04	ci left: 9.666117e-01	ci right 9.669737e-01	k: 3644810	n:3770000
KS ci ratio: 1.163383e-01	ci left: 2.835437e-04	ci right 3.188228e-04	k: 1134	n:3770000
LLGL2   3770000 perm   6302 sec   (598 perm/sec)   p_kst 3.007958e-04   p_cons 9.667931e-01   p_joint 3.007958e-04

Joint ci ratio: 1.161848e-01	ci left: 2.835641e-04	ci right 3.187961e-04	k: 1137	n:3780000
Cons ci ratio: 3.736321e-04	ci left: 9.666186e-01	ci right 9.669801e-01	k: 3654503	n:3780000
KS ci ratio: 1.161848e-01	ci left: 2.835641e-04	ci right 3.187961e-04	k: 1137	n:3780000
LLGL2   3780000 perm   6332 sec   (597 perm/sec)   p_kst 3.007937e-04   p_cons 9.667997e-01   p_joint 3.007937e-04

Joint ci ratio: 1.159304e-01	ci left: 2.840969e-04	ci right 3.193124e-04	k: 1142	n:3790000
Cons ci ratio: 3.731082e-04	ci left: 9.666242e-01	ci right 9.669851e-01	k: 3664191	n:3790000
KS ci ratio: 1.159304e-01	ci left: 2.840969e-04	ci right 3.193124e-04	k: 1142	n:3790000
LLGL2   3790000 perm   6364 sec   (596 perm/sec)   p_kst 3.013193e-04   p_cons 9.668050e-01   p_joint 3.013193e-04

Joint ci ratio: 1.157281e-01	ci left: 2.843714e-04	ci right 3.195553e-04	k: 1146	n:3800000
Cons ci ratio: 3.726246e-04	ci left: 9.666231e-01	ci right 9.669836e-01	k: 3673854	n:3800000
KS ci ratio: 1.157281e-01	ci left: 2.843714e-04	ci right 3.195553e-04	k: 1146	n:3800000
LLGL2   3800000 perm   6396 sec   (594 perm/sec)   p_kst 3.015789e-04   p_cons 9.668037e-01   p_joint 3.015789e-04

Joint ci ratio: 1.156777e-01	ci left: 2.838799e-04	ci right 3.189866e-04	k: 1147	n:3810000
Cons ci ratio: 3.721673e-04	ci left: 9.666178e-01	ci right 9.669778e-01	k: 3683501	n:3810000
KS ci ratio: 1.156777e-01	ci left: 2.838799e-04	ci right 3.189866e-04	k: 1147	n:3810000
LLGL2   3810000 perm   6427 sec   (593 perm/sec)   p_kst 3.010499e-04   p_cons 9.667982e-01   p_joint 3.010499e-04

Joint ci ratio: 1.154266e-01	ci left: 2.844078e-04	ci right 3.194983e-04	k: 1152	n:3820000
Cons ci ratio: 3.716692e-04	ci left: 9.666199e-01	ci right 9.669794e-01	k: 3693176	n:3820000
KS ci ratio: 1.154266e-01	ci left: 2.844078e-04	ci right 3.194983e-04	k: 1152	n:3820000
LLGL2   3820000 perm   6458 sec   (591 perm/sec)   p_kst 3.015707e-04   p_cons 9.668000e-01   p_joint 3.015707e-04

Joint ci ratio: 1.153266e-01	ci left: 2.841724e-04	ci right 3.192013e-04	k: 1154	n:3830000
Cons ci ratio: 3.711399e-04	ci left: 9.666277e-01	ci right 9.669868e-01	k: 3702873	n:3830000
KS ci ratio: 1.153266e-01	ci left: 2.841724e-04	ci right 3.192013e-04	k: 1154	n:3830000
LLGL2   3830000 perm   6489 sec   (590 perm/sec)   p_kst 3.013055e-04   p_cons 9.668076e-01   p_joint 3.013055e-04

Joint ci ratio: 1.149292e-01	ci left: 2.854557e-04	ci right 3.205133e-04	k: 1162	n:3840000
Cons ci ratio: 3.706369e-04	ci left: 9.666313e-01	ci right 9.669899e-01	k: 3712554	n:3840000
KS ci ratio: 1.149292e-01	ci left: 2.854557e-04	ci right 3.205133e-04	k: 1162	n:3840000
LLGL2   3840000 perm   6520 sec   (589 perm/sec)   p_kst 3.026042e-04   p_cons 9.668109e-01   p_joint 3.026042e-04

Joint ci ratio: 1.147813e-01	ci left: 2.854711e-04	ci right 3.204824e-04	k: 1165	n:3850000
Cons ci ratio: 3.701689e-04	ci left: 9.666292e-01	ci right 9.669873e-01	k: 3722213	n:3850000
KS ci ratio: 1.147813e-01	ci left: 2.854711e-04	ci right 3.204824e-04	k: 1165	n:3850000
LLGL2   3850000 perm   6552 sec   (588 perm/sec)   p_kst 3.025974e-04   p_cons 9.668086e-01   p_joint 3.025974e-04

Joint ci ratio: 1.145849e-01	ci left: 2.857381e-04	ci right 3.207182e-04	k: 1169	n:3860000
Cons ci ratio: 3.696370e-04	ci left: 9.666385e-01	ci right 9.669961e-01	k: 3731916	n:3860000
KS ci ratio: 1.145849e-01	ci left: 2.857381e-04	ci right 3.207182e-04	k: 1169	n:3860000
LLGL2   3860000 perm   6583 sec   (586 perm/sec)   p_kst 3.028497e-04   p_cons 9.668176e-01   p_joint 3.028497e-04

Joint ci ratio: 1.145360e-01	ci left: 2.852507e-04	ci right 3.201552e-04	k: 1170	n:3870000
Cons ci ratio: 3.691638e-04	ci left: 9.666379e-01	ci right 9.669950e-01	k: 3741581	n:3870000
KS ci ratio: 1.145360e-01	ci left: 2.852507e-04	ci right 3.201552e-04	k: 1170	n:3870000
LLGL2   3870000 perm   6614 sec   (585 perm/sec)   p_kst 3.023256e-04   p_cons 9.668168e-01   p_joint 3.023256e-04

Joint ci ratio: 1.144871e-01	ci left: 2.847659e-04	ci right 3.195952e-04	k: 1171	n:3880000
Cons ci ratio: 3.687058e-04	ci left: 9.666350e-01	ci right 9.669917e-01	k: 3751237	n:3880000
KS ci ratio: 1.144871e-01	ci left: 2.847659e-04	ci right 3.195952e-04	k: 1171	n:3880000
LLGL2   3880000 perm   6646 sec   (584 perm/sec)   p_kst 3.018041e-04   p_cons 9.668137e-01   p_joint 3.018041e-04

Joint ci ratio: 1.143896e-01	ci left: 2.845333e-04	ci right 3.193025e-04	k: 1173	n:3890000
Cons ci ratio: 3.682082e-04	ci left: 9.666393e-01	ci right 9.669955e-01	k: 3760921	n:3890000
KS ci ratio: 1.143896e-01	ci left: 2.845333e-04	ci right 3.193025e-04	k: 1173	n:3890000
LLGL2   3890000 perm   6678 sec   (583 perm/sec)   p_kst 3.015424e-04   p_cons 9.668177e-01   p_joint 3.015424e-04

Joint ci ratio: 1.141952e-01	ci left: 2.848000e-04	ci right 3.195387e-04	k: 1177	n:3900000
Cons ci ratio: 3.677140e-04	ci left: 9.666433e-01	ci right 9.669991e-01	k: 3770604	n:3900000
KS ci ratio: 1.141952e-01	ci left: 2.848000e-04	ci right 3.195387e-04	k: 1177	n:3900000
LLGL2   3900000 perm   6710 sec   (581 perm/sec)   p_kst 3.017949e-04   p_cons 9.668215e-01   p_joint 3.017949e-04

Joint ci ratio: 1.140984e-01	ci left: 2.845685e-04	ci right 3.192476e-04	k: 1179	n:3910000
Cons ci ratio: 3.672994e-04	ci left: 9.666337e-01	ci right 9.669891e-01	k: 3780234	n:3910000
KS ci ratio: 1.140984e-01	ci left: 2.845685e-04	ci right 3.192476e-04	k: 1179	n:3910000
LLGL2   3910000 perm   6741 sec   (580 perm/sec)   p_kst 3.015345e-04   p_cons 9.668118e-01   p_joint 3.015345e-04

Joint ci ratio: 1.139536e-01	ci left: 2.845861e-04	ci right 3.192203e-04	k: 1182	n:3920000
Cons ci ratio: 3.668964e-04	ci left: 9.666224e-01	ci right 9.669774e-01	k: 3789857	n:3920000
KS ci ratio: 1.139536e-01	ci left: 2.845861e-04	ci right 3.192203e-04	k: 1182	n:3920000
LLGL2   3920000 perm   6775 sec   (579 perm/sec)   p_kst 3.015306e-04   p_cons 9.668003e-01   p_joint 3.015306e-04

Joint ci ratio: 1.138094e-01	ci left: 2.846035e-04	ci right 3.191931e-04	k: 1185	n:3930000
Cons ci ratio: 3.664351e-04	ci left: 9.666216e-01	ci right 9.669762e-01	k: 3799521	n:3930000
KS ci ratio: 1.138094e-01	ci left: 2.846035e-04	ci right 3.191931e-04	k: 1185	n:3930000
LLGL2   3930000 perm   6806 sec   (577 perm/sec)   p_kst 3.015267e-04   p_cons 9.667992e-01   p_joint 3.015267e-04

Joint ci ratio: 1.137615e-01	ci left: 2.841278e-04	ci right 3.186440e-04	k: 1186	n:3940000
Cons ci ratio: 3.659684e-04	ci left: 9.666221e-01	ci right 9.669762e-01	k: 3809190	n:3940000
KS ci ratio: 1.137615e-01	ci left: 2.841278e-04	ci right 3.186440e-04	k: 1186	n:3940000
LLGL2   3940000 perm   6838 sec   (576 perm/sec)   p_kst 3.010152e-04   p_cons 9.667995e-01   p_joint 3.010152e-04

Joint ci ratio: 1.137136e-01	ci left: 2.836544e-04	ci right 3.180977e-04	k: 1187	n:3950000
Cons ci ratio: 3.655005e-04	ci left: 9.666231e-01	ci right 9.669767e-01	k: 3818861	n:3950000
KS ci ratio: 1.137136e-01	ci left: 2.836544e-04	ci right 3.180977e-04	k: 1187	n:3950000
LLGL2   3950000 perm   6870 sec   (575 perm/sec)   p_kst 3.005063e-04   p_cons 9.668003e-01   p_joint 3.005063e-04

Joint ci ratio: 1.135226e-01	ci left: 2.839195e-04	ci right 3.183332e-04	k: 1191	n:3960000
Cons ci ratio: 3.650344e-04	ci left: 9.666241e-01	ci right 9.669772e-01	k: 3828532	n:3960000
KS ci ratio: 1.135226e-01	ci left: 2.839195e-04	ci right 3.183332e-04	k: 1191	n:3960000
LLGL2   3960000 perm   6902 sec   (574 perm/sec)   p_kst 3.007576e-04   p_cons 9.668010e-01   p_joint 3.007576e-04

Joint ci ratio: 1.131907e-01	ci left: 2.849176e-04	ci right 3.193445e-04	k: 1198	n:3970000
Cons ci ratio: 3.645844e-04	ci left: 9.666225e-01	ci right 9.669753e-01	k: 3838193	n:3970000
KS ci ratio: 1.131907e-01	ci left: 2.849176e-04	ci right 3.193445e-04	k: 1198	n:3970000
LLGL2   3970000 perm   6934 sec   (573 perm/sec)   p_kst 3.017632e-04   p_cons 9.667992e-01   p_joint 3.017632e-04

Joint ci ratio: 1.130024e-01	ci left: 2.851783e-04	ci right 3.195756e-04	k: 1202	n:3980000
Cons ci ratio: 3.640904e-04	ci left: 9.666291e-01	ci right 9.669813e-01	k: 3847886	n:3980000
KS ci ratio: 1.130024e-01	ci left: 2.851783e-04	ci right 3.195756e-04	k: 1202	n:3980000
LLGL2   3980000 perm   6967 sec   (571 perm/sec)   p_kst 3.020101e-04   p_cons 9.668055e-01   p_joint 3.020101e-04

Joint ci ratio: 1.129555e-01	ci left: 2.847071e-04	ci right 3.190324e-04	k: 1203	n:3990000
Cons ci ratio: 3.636169e-04	ci left: 9.666323e-01	ci right 9.669841e-01	k: 3857566	n:3990000
KS ci ratio: 1.129555e-01	ci left: 2.847071e-04	ci right 3.190324e-04	k: 1203	n:3990000
LLGL2   3990000 perm   7000 sec   (570 perm/sec)   p_kst 3.015038e-04   p_cons 9.668085e-01   p_joint 3.015038e-04

Joint ci ratio: 1.129086e-01	ci left: 2.842383e-04	ci right 3.184919e-04	k: 1204	n:4000000
Cons ci ratio: 3.631722e-04	ci left: 9.666307e-01	ci right 9.669821e-01	k: 3867227	n:4000000
KS ci ratio: 1.129086e-01	ci left: 2.842383e-04	ci right 3.184919e-04	k: 1204	n:4000000
LLGL2   4000000 perm   7032 sec   (569 perm/sec)   p_kst 3.010000e-04   p_cons 9.668068e-01   p_joint 3.010000e-04

Joint ci ratio: 1.128150e-01	ci left: 2.840142e-04	ci right 3.182104e-04	k: 1206	n:4010000
Cons ci ratio: 3.627121e-04	ci left: 9.666322e-01	ci right 9.669831e-01	k: 3876900	n:4010000
KS ci ratio: 1.128150e-01	ci left: 2.840142e-04	ci right 3.182104e-04	k: 1206	n:4010000
LLGL2   4010000 perm   7065 sec   (568 perm/sec)   p_kst 3.007481e-04   p_cons 9.668080e-01   p_joint 3.007481e-04

Joint ci ratio: 1.127217e-01	ci left: 2.837911e-04	ci right 3.179304e-04	k: 1208	n:4020000
Cons ci ratio: 3.622285e-04	ci left: 9.666381e-01	ci right 9.669886e-01	k: 3886591	n:4020000
KS ci ratio: 1.127217e-01	ci left: 2.837911e-04	ci right 3.179304e-04	k: 1208	n:4020000
LLGL2   4020000 perm   7097 sec   (566 perm/sec)   p_kst 3.004975e-04   p_cons 9.668137e-01   p_joint 3.004975e-04

Joint ci ratio: 1.126286e-01	ci left: 2.835692e-04	ci right 3.176518e-04	k: 1210	n:4030000
Cons ci ratio: 3.617328e-04	ci left: 9.666465e-01	ci right 9.669965e-01	k: 3896292	n:4030000
KS ci ratio: 1.126286e-01	ci left: 2.835692e-04	ci right 3.176518e-04	k: 1210	n:4030000
LLGL2   4030000 perm   7131 sec   (565 perm/sec)   p_kst 3.002481e-04   p_cons 9.668218e-01   p_joint 3.002481e-04

Joint ci ratio: 1.124430e-01	ci left: 2.838296e-04	ci right 3.178835e-04	k: 1214	n:4040000
Cons ci ratio: 3.613186e-04	ci left: 9.666407e-01	ci right 9.669903e-01	k: 3905936	n:4040000
KS ci ratio: 1.124430e-01	ci left: 2.838296e-04	ci right 3.178835e-04	k: 1214	n:4040000
LLGL2   4040000 perm   7163 sec   (564 perm/sec)   p_kst 3.004950e-04   p_cons 9.668158e-01   p_joint 3.004950e-04

Joint ci ratio: 1.122584e-01	ci left: 2.840886e-04	ci right 3.181140e-04	k: 1218	n:4050000
Cons ci ratio: 3.608336e-04	ci left: 9.666478e-01	ci right 9.669969e-01	k: 3915632	n:4050000
KS ci ratio: 1.122584e-01	ci left: 2.840886e-04	ci right 3.181140e-04	k: 1218	n:4050000
LLGL2   4050000 perm   7196 sec   (563 perm/sec)   p_kst 3.007407e-04   p_cons 9.668227e-01   p_joint 3.007407e-04

Joint ci ratio: 1.121205e-01	ci left: 2.841071e-04	ci right 3.180901e-04	k: 1221	n:4060000
Cons ci ratio: 3.603768e-04	ci left: 9.666502e-01	ci right 9.669989e-01	k: 3925309	n:4060000
KS ci ratio: 1.121205e-01	ci left: 2.841071e-04	ci right 3.180901e-04	k: 1221	n:4060000
LLGL2   4060000 perm   7229 sec   (562 perm/sec)   p_kst 3.007389e-04   p_cons 9.668249e-01   p_joint 3.007389e-04

Joint ci ratio: 1.119831e-01	ci left: 2.841255e-04	ci right 3.180663e-04	k: 1224	n:4070000
Cons ci ratio: 3.599121e-04	ci left: 9.666543e-01	ci right 9.670025e-01	k: 3934993	n:4070000
KS ci ratio: 1.119831e-01	ci left: 2.841255e-04	ci right 3.180663e-04	k: 1224	n:4070000
LLGL2   4070000 perm   7261 sec   (560 perm/sec)   p_kst 3.007371e-04   p_cons 9.668287e-01   p_joint 3.007371e-04

Joint ci ratio: 1.119375e-01	ci left: 2.836673e-04	ci right 3.175387e-04	k: 1225	n:4080000
Cons ci ratio: 3.594739e-04	ci left: 9.666540e-01	ci right 9.670017e-01	k: 3944659	n:4080000
KS ci ratio: 1.119375e-01	ci left: 2.836673e-04	ci right 3.175387e-04	k: 1225	n:4080000
LLGL2   4080000 perm   7294 sec   (559 perm/sec)   p_kst 3.002451e-04   p_cons 9.668282e-01   p_joint 3.002451e-04

Joint ci ratio: 1.117553e-01	ci left: 2.839244e-04	ci right 3.177676e-04	k: 1229	n:4090000
Cons ci ratio: 3.590154e-04	ci left: 9.666575e-01	ci right 9.670049e-01	k: 3954341	n:4090000
KS ci ratio: 1.117553e-01	ci left: 2.839244e-04	ci right 3.177676e-04	k: 1229	n:4090000
LLGL2   4090000 perm   7327 sec   (558 perm/sec)   p_kst 3.004890e-04   p_cons 9.668315e-01   p_joint 3.004890e-04

Joint ci ratio: 1.116646e-01	ci left: 2.837061e-04	ci right 3.174940e-04	k: 1231	n:4100000
Cons ci ratio: 3.586132e-04	ci left: 9.666513e-01	ci right 9.669983e-01	k: 3963983	n:4100000
KS ci ratio: 1.116646e-01	ci left: 2.837061e-04	ci right 3.174940e-04	k: 1231	n:4100000
LLGL2   4100000 perm   7361 sec   (557 perm/sec)   p_kst 3.002439e-04   p_cons 9.668251e-01   p_joint 3.002439e-04

Joint ci ratio: 1.114837e-01	ci left: 2.839619e-04	ci right 3.177219e-04	k: 1235	n:4110000
Cons ci ratio: 3.581770e-04	ci left: 9.666515e-01	ci right 9.669980e-01	k: 3973651	n:4110000
KS ci ratio: 1.114837e-01	ci left: 2.839619e-04	ci right 3.177219e-04	k: 1235	n:4110000
LLGL2   4110000 perm   7394 sec   (556 perm/sec)   p_kst 3.004866e-04   p_cons 9.668251e-01   p_joint 3.004866e-04

Joint ci ratio: 1.113936e-01	ci left: 2.837446e-04	ci right 3.174497e-04	k: 1237	n:4120000
Cons ci ratio: 3.577342e-04	ci left: 9.666531e-01	ci right 9.669992e-01	k: 3983325	n:4120000
KS ci ratio: 1.113936e-01	ci left: 2.837446e-04	ci right 3.174497e-04	k: 1237	n:4120000
LLGL2   4120000 perm   7427 sec   (555 perm/sec)   p_kst 3.002427e-04   p_cons 9.668265e-01   p_joint 3.002427e-04

Joint ci ratio: 1.111694e-01	ci left: 2.842345e-04	ci right 3.179254e-04	k: 1242	n:4130000
Cons ci ratio: 3.572904e-04	ci left: 9.666552e-01	ci right 9.670008e-01	k: 3993001	n:4130000
KS ci ratio: 1.111694e-01	ci left: 2.842345e-04	ci right 3.179254e-04	k: 1242	n:4130000
LLGL2   4130000 perm   7460 sec   (554 perm/sec)   p_kst 3.007264e-04   p_cons 9.668283e-01   p_joint 3.007264e-04

Joint ci ratio: 1.108576e-01	ci left: 2.851918e-04	ci right 3.188952e-04	k: 1249	n:4140000
Cons ci ratio: 3.568483e-04	ci left: 9.666572e-01	ci right 9.670025e-01	k: 4002677	n:4140000
KS ci ratio: 1.108576e-01	ci left: 2.851918e-04	ci right 3.188952e-04	k: 1249	n:4140000
LLGL2   4140000 perm   7496 sec   (552 perm/sec)   p_kst 3.016908e-04   p_cons 9.668302e-01   p_joint 3.016908e-04

Joint ci ratio: 1.106806e-01	ci left: 2.854418e-04	ci right 3.191173e-04	k: 1253	n:4150000
Cons ci ratio: 3.564065e-04	ci left: 9.666596e-01	ci right 9.670044e-01	k: 4012354	n:4150000
KS ci ratio: 1.106806e-01	ci left: 2.854418e-04	ci right 3.191173e-04	k: 1253	n:4150000
LLGL2   4150000 perm   7529 sec   (551 perm/sec)   p_kst 3.019277e-04   p_cons 9.668323e-01   p_joint 3.019277e-04

Joint ci ratio: 1.106366e-01	ci left: 2.849893e-04	ci right 3.185972e-04	k: 1254	n:4160000
Cons ci ratio: 3.559943e-04	ci left: 9.666568e-01	ci right 9.670012e-01	k: 4022010	n:4160000
KS ci ratio: 1.106366e-01	ci left: 2.849893e-04	ci right 3.185972e-04	k: 1254	n:4160000
LLGL2   4160000 perm   7563 sec   (550 perm/sec)   p_kst 3.014423e-04   p_cons 9.668293e-01   p_joint 3.014423e-04

Joint ci ratio: 1.104168e-01	ci left: 2.854718e-04	ci right 3.190654e-04	k: 1259	n:4170000
Cons ci ratio: 3.555622e-04	ci left: 9.666579e-01	ci right 9.670019e-01	k: 4031682	n:4170000
KS ci ratio: 1.104168e-01	ci left: 2.854718e-04	ci right 3.190654e-04	k: 1259	n:4170000
LLGL2   4170000 perm   7597 sec   (549 perm/sec)   p_kst 3.019185e-04   p_cons 9.668302e-01   p_joint 3.019185e-04

Joint ci ratio: 1.102856e-01	ci left: 2.854867e-04	ci right 3.190396e-04	k: 1262	n:4180000
Cons ci ratio: 3.551344e-04	ci left: 9.666585e-01	ci right 9.670021e-01	k: 4041352	n:4180000
KS ci ratio: 1.102856e-01	ci left: 2.854867e-04	ci right 3.190396e-04	k: 1262	n:4180000
LLGL2   4180000 perm   7631 sec   (548 perm/sec)   p_kst 3.019139e-04   p_cons 9.668306e-01   p_joint 3.019139e-04

Joint ci ratio: 1.102420e-01	ci left: 2.850375e-04	ci right 3.185234e-04	k: 1263	n:4190000
Cons ci ratio: 3.547015e-04	ci left: 9.666603e-01	ci right 9.670035e-01	k: 4051027	n:4190000
KS ci ratio: 1.102420e-01	ci left: 2.850375e-04	ci right 3.185234e-04	k: 1263	n:4190000
LLGL2   4190000 perm   7668 sec   (546 perm/sec)   p_kst 3.014320e-04   p_cons 9.668322e-01   p_joint 3.014320e-04

Joint ci ratio: 1.101114e-01	ci left: 2.850534e-04	ci right 3.184990e-04	k: 1266	n:4200000
Cons ci ratio: 3.543031e-04	ci left: 9.666561e-01	ci right 9.669989e-01	k: 4060677	n:4200000
KS ci ratio: 1.101114e-01	ci left: 2.850534e-04	ci right 3.184990e-04	k: 1266	n:4200000
LLGL2   4200000 perm   7702 sec   (545 perm/sec)   p_kst 3.014286e-04   p_cons 9.668279e-01   p_joint 3.014286e-04

Joint ci ratio: 1.099380e-01	ci left: 2.853003e-04	ci right 3.187187e-04	k: 1270	n:4210000
Cons ci ratio: 3.538602e-04	ci left: 9.666603e-01	ci right 9.670027e-01	k: 4070362	n:4210000
KS ci ratio: 1.099380e-01	ci left: 2.853003e-04	ci right 3.187187e-04	k: 1270	n:4210000
LLGL2   4210000 perm   7736 sec   (544 perm/sec)   p_kst 3.016627e-04   p_cons 9.668318e-01   p_joint 3.016627e-04

Joint ci ratio: 1.098948e-01	ci left: 2.848547e-04	ci right 3.182069e-04	k: 1271	n:4220000
Cons ci ratio: 3.534162e-04	ci left: 9.666650e-01	ci right 9.670069e-01	k: 4080049	n:4220000
KS ci ratio: 1.098948e-01	ci left: 2.848547e-04	ci right 3.182069e-04	k: 1271	n:4220000
LLGL2   4220000 perm   7770 sec   (543 perm/sec)   p_kst 3.011848e-04   p_cons 9.668363e-01   p_joint 3.011848e-04

Joint ci ratio: 1.096365e-01	ci left: 2.855608e-04	ci right 3.189120e-04	k: 1277	n:4230000
Cons ci ratio: 3.530117e-04	ci left: 9.666627e-01	ci right 9.670043e-01	k: 4089707	n:4230000
KS ci ratio: 1.096365e-01	ci left: 2.855608e-04	ci right 3.189120e-04	k: 1277	n:4230000
LLGL2   4230000 perm   7806 sec   (542 perm/sec)   p_kst 3.018913e-04   p_cons 9.668338e-01   p_joint 3.018913e-04

Joint ci ratio: 1.093800e-01	ci left: 2.862636e-04	ci right 3.196137e-04	k: 1283	n:4240000
Cons ci ratio: 3.526021e-04	ci left: 9.666617e-01	ci right 9.670028e-01	k: 4099370	n:4240000
KS ci ratio: 1.093800e-01	ci left: 2.862636e-04	ci right 3.196137e-04	k: 1283	n:4240000
LLGL2   4240000 perm   7841 sec   (541 perm/sec)   p_kst 3.025943e-04   p_cons 9.668325e-01   p_joint 3.025943e-04

Joint ci ratio: 1.092100e-01	ci left: 2.865055e-04	ci right 3.198286e-04	k: 1287	n:4250000
Cons ci ratio: 3.522094e-04	ci left: 9.666578e-01	ci right 9.669985e-01	k: 4109021	n:4250000
KS ci ratio: 1.092100e-01	ci left: 2.865055e-04	ci right 3.198286e-04	k: 1287	n:4250000
LLGL2   4250000 perm   7876 sec   (540 perm/sec)   p_kst 3.028235e-04   p_cons 9.668285e-01   p_joint 3.028235e-04

Joint ci ratio: 1.091253e-01	ci left: 2.862896e-04	ci right 3.195601e-04	k: 1289	n:4260000
Cons ci ratio: 3.518026e-04	ci left: 9.666567e-01	ci right 9.669971e-01	k: 4118684	n:4260000
KS ci ratio: 1.091253e-01	ci left: 2.862896e-04	ci right 3.195601e-04	k: 1289	n:4260000
LLGL2   4260000 perm   7910 sec   (539 perm/sec)   p_kst 3.025822e-04   p_cons 9.668272e-01   p_joint 3.025822e-04

Joint ci ratio: 1.089565e-01	ci left: 2.865304e-04	ci right 3.197740e-04	k: 1293	n:4270000
Cons ci ratio: 3.513741e-04	ci left: 9.666599e-01	ci right 9.669999e-01	k: 4128365	n:4270000
KS ci ratio: 1.089565e-01	ci left: 2.865304e-04	ci right 3.197740e-04	k: 1293	n:4270000
LLGL2   4270000 perm   7945 sec   (537 perm/sec)   p_kst 3.028103e-04   p_cons 9.668302e-01   p_joint 3.028103e-04

Joint ci ratio: 1.088724e-01	ci left: 2.863155e-04	ci right 3.195069e-04	k: 1295	n:4280000
Cons ci ratio: 3.509688e-04	ci left: 9.666591e-01	ci right 9.669987e-01	k: 4138029	n:4280000
KS ci ratio: 1.088724e-01	ci left: 2.863155e-04	ci right 3.195069e-04	k: 1295	n:4280000
LLGL2   4280000 perm   7980 sec   (536 perm/sec)   p_kst 3.025701e-04   p_cons 9.668292e-01   p_joint 3.025701e-04

Joint ci ratio: 1.087466e-01	ci left: 2.863283e-04	ci right 3.194804e-04	k: 1298	n:4290000
Cons ci ratio: 3.505064e-04	ci left: 9.666691e-01	ci right 9.670082e-01	k: 4147739	n:4290000
KS ci ratio: 1.087466e-01	ci left: 2.863283e-04	ci right 3.194804e-04	k: 1298	n:4290000
LLGL2   4290000 perm   8015 sec   (535 perm/sec)   p_kst 3.025641e-04   p_cons 9.668389e-01   p_joint 3.025641e-04

Joint ci ratio: 1.087466e-01	ci left: 2.856625e-04	ci right 3.187375e-04	k: 1298	n:4300000
Cons ci ratio: 3.500699e-04	ci left: 9.666745e-01	ci right 9.670132e-01	k: 4157430	n:4300000
KS ci ratio: 1.087466e-01	ci left: 2.856625e-04	ci right 3.187375e-04	k: 1298	n:4300000
LLGL2   4300000 perm   8051 sec   (534 perm/sec)   p_kst 3.018605e-04   p_cons 9.668442e-01   p_joint 3.018605e-04

Joint ci ratio: 1.086213e-01	ci left: 2.856768e-04	ci right 3.187129e-04	k: 1301	n:4310000
Cons ci ratio: 3.496654e-04	ci left: 9.666744e-01	ci right 9.670127e-01	k: 4167097	n:4310000
KS ci ratio: 1.086213e-01	ci left: 2.856768e-04	ci right 3.187129e-04	k: 1301	n:4310000
LLGL2   4310000 perm   8086 sec   (533 perm/sec)   p_kst 3.018561e-04   p_cons 9.668439e-01   p_joint 3.018561e-04

Joint ci ratio: 1.084964e-01	ci left: 2.856911e-04	ci right 3.186884e-04	k: 1304	n:4320000
Cons ci ratio: 3.492812e-04	ci left: 9.666708e-01	ci right 9.670087e-01	k: 4176749	n:4320000
KS ci ratio: 1.084964e-01	ci left: 2.856911e-04	ci right 3.186884e-04	k: 1304	n:4320000
LLGL2   4320000 perm   8123 sec   (532 perm/sec)   p_kst 3.018519e-04   p_cons 9.668400e-01   p_joint 3.018519e-04

Joint ci ratio: 1.084548e-01	ci left: 2.852560e-04	ci right 3.181896e-04	k: 1305	n:4330000
Cons ci ratio: 3.488580e-04	ci left: 9.666746e-01	ci right 9.670121e-01	k: 4186433	n:4330000
KS ci ratio: 1.084548e-01	ci left: 2.852560e-04	ci right 3.181896e-04	k: 1305	n:4330000
LLGL2   4330000 perm   8159 sec   (531 perm/sec)   p_kst 3.013857e-04   p_cons 9.668436e-01   p_joint 3.013857e-04

Joint ci ratio: 1.083719e-01	ci left: 2.850470e-04	ci right 3.179298e-04	k: 1307	n:4340000
Cons ci ratio: 3.484263e-04	ci left: 9.666802e-01	ci right 9.670173e-01	k: 4196125	n:4340000
KS ci ratio: 1.083719e-01	ci left: 2.850470e-04	ci right 3.179298e-04	k: 1307	n:4340000
LLGL2   4340000 perm   8193 sec   (530 perm/sec)   p_kst 3.011521e-04   p_cons 9.668491e-01   p_joint 3.011521e-04

Joint ci ratio: 1.082478e-01	ci left: 2.850627e-04	ci right 3.179073e-04	k: 1310	n:4350000
Cons ci ratio: 3.479950e-04	ci left: 9.666861e-01	ci right 9.670227e-01	k: 4205818	n:4350000
KS ci ratio: 1.082478e-01	ci left: 2.850627e-04	ci right 3.179073e-04	k: 1310	n:4350000
LLGL2   4350000 perm   8228 sec   (529 perm/sec)   p_kst 3.011494e-04   p_cons 9.668547e-01   p_joint 3.011494e-04

Joint ci ratio: 1.081654e-01	ci left: 2.848552e-04	ci right 3.176493e-04	k: 1312	n:4360000
Cons ci ratio: 3.475927e-04	ci left: 9.666868e-01	ci right 9.670231e-01	k: 4215489	n:4360000
KS ci ratio: 1.081654e-01	ci left: 2.848552e-04	ci right 3.176493e-04	k: 1312	n:4360000
LLGL2   4360000 perm   8265 sec   (528 perm/sec)   p_kst 3.009174e-04   p_cons 9.668553e-01   p_joint 3.009174e-04

Joint ci ratio: 1.080010e-01	ci left: 2.850940e-04	ci right 3.178624e-04	k: 1316	n:4370000
Cons ci ratio: 3.472462e-04	ci left: 9.666775e-01	ci right 9.670134e-01	k: 4225116	n:4370000
KS ci ratio: 1.080010e-01	ci left: 2.850940e-04	ci right 3.178624e-04	k: 1316	n:4370000
LLGL2   4370000 perm   8301 sec   (526 perm/sec)   p_kst 3.011442e-04   p_cons 9.668458e-01   p_joint 3.011442e-04

Joint ci ratio: 1.078782e-01	ci left: 2.851095e-04	ci right 3.178401e-04	k: 1319	n:4380000
Cons ci ratio: 3.468662e-04	ci left: 9.666746e-01	ci right 9.670102e-01	k: 4234771	n:4380000
KS ci ratio: 1.078782e-01	ci left: 2.851095e-04	ci right 3.178401e-04	k: 1319	n:4380000
LLGL2   4380000 perm   8337 sec   (525 perm/sec)   p_kst 3.011416e-04   p_cons 9.668427e-01   p_joint 3.011416e-04

Joint ci ratio: 1.077558e-01	ci left: 2.851250e-04	ci right 3.178179e-04	k: 1322	n:4390000
Cons ci ratio: 3.465158e-04	ci left: 9.666665e-01	ci right 9.670017e-01	k: 4244403	n:4390000
KS ci ratio: 1.077558e-01	ci left: 2.851250e-04	ci right 3.178179e-04	k: 1322	n:4390000
LLGL2   4390000 perm   8373 sec   (524 perm/sec)   p_kst 3.011390e-04   p_cons 9.668344e-01   p_joint 3.011390e-04

Joint ci ratio: 1.075933e-01	ci left: 2.853616e-04	ci right 3.180292e-04	k: 1326	n:4400000
Cons ci ratio: 3.461026e-04	ci left: 9.666702e-01	ci right 9.670051e-01	k: 4254087	n:4400000
KS ci ratio: 1.075933e-01	ci left: 2.853616e-04	ci right 3.180292e-04	k: 1326	n:4400000
LLGL2   4400000 perm   8409 sec   (523 perm/sec)   p_kst 3.013636e-04   p_cons 9.668380e-01   p_joint 3.013636e-04

Joint ci ratio: 1.074718e-01	ci left: 2.853765e-04	ci right 3.180066e-04	k: 1329	n:4410000
Cons ci ratio: 3.456811e-04	ci left: 9.666758e-01	ci right 9.670102e-01	k: 4263779	n:4410000
KS ci ratio: 1.074718e-01	ci left: 2.853765e-04	ci right 3.180066e-04	k: 1329	n:4410000
LLGL2   4410000 perm   8445 sec   (522 perm/sec)   p_kst 3.013605e-04   p_cons 9.668433e-01   p_joint 3.013605e-04

Joint ci ratio: 1.074315e-01	ci left: 2.849510e-04	ci right 3.175194e-04	k: 1330	n:4420000
Cons ci ratio: 3.452586e-04	ci left: 9.666818e-01	ci right 9.670158e-01	k: 4273473	n:4420000
KS ci ratio: 1.074315e-01	ci left: 2.849510e-04	ci right 3.175194e-04	k: 1330	n:4420000
LLGL2   4420000 perm   8482 sec   (521 perm/sec)   p_kst 3.009050e-04   p_cons 9.668491e-01   p_joint 3.009050e-04

Joint ci ratio: 1.073912e-01	ci left: 2.845274e-04	ci right 3.170345e-04	k: 1331	n:4430000
Cons ci ratio: 3.448851e-04	ci left: 9.666789e-01	ci right 9.670126e-01	k: 4283128	n:4430000
KS ci ratio: 1.073912e-01	ci left: 2.845274e-04	ci right 3.170345e-04	k: 1331	n:4430000
LLGL2   4430000 perm   8519 sec   (520 perm/sec)   p_kst 3.004515e-04   p_cons 9.668460e-01   p_joint 3.004515e-04

Joint ci ratio: 1.072704e-01	ci left: 2.845442e-04	ci right 3.170142e-04	k: 1334	n:4440000
Cons ci ratio: 3.445140e-04	ci left: 9.666758e-01	ci right 9.670091e-01	k: 4292782	n:4440000
KS ci ratio: 1.072704e-01	ci left: 2.845442e-04	ci right 3.170142e-04	k: 1334	n:4440000
LLGL2   4440000 perm   8555 sec   (519 perm/sec)   p_kst 3.004505e-04   p_cons 9.668428e-01   p_joint 3.004505e-04

Joint ci ratio: 1.071902e-01	ci left: 2.843421e-04	ci right 3.167633e-04	k: 1336	n:4450000
Cons ci ratio: 3.441091e-04	ci left: 9.666793e-01	ci right 9.670122e-01	k: 4302465	n:4450000
KS ci ratio: 1.071902e-01	ci left: 2.843421e-04	ci right 3.167633e-04	k: 1336	n:4450000
LLGL2   4450000 perm   8592 sec   (518 perm/sec)   p_kst 3.002247e-04   p_cons 9.668461e-01   p_joint 3.002247e-04

Joint ci ratio: 1.071101e-01	ci left: 2.841410e-04	ci right 3.165135e-04	k: 1338	n:4460000
Cons ci ratio: 3.437177e-04	ci left: 9.666805e-01	ci right 9.670131e-01	k: 4312138	n:4460000
KS ci ratio: 1.071101e-01	ci left: 2.841410e-04	ci right 3.165135e-04	k: 1338	n:4460000
LLGL2   4460000 perm   8628 sec   (517 perm/sec)   p_kst 3.000000e-04   p_cons 9.668471e-01   p_joint 3.000000e-04

Joint ci ratio: 1.067915e-01	ci left: 2.852472e-04	ci right 3.176430e-04	k: 1346	n:4470000
Cons ci ratio: 3.433336e-04	ci left: 9.666806e-01	ci right 9.670128e-01	k: 4321806	n:4470000
KS ci ratio: 1.067915e-01	ci left: 2.852472e-04	ci right 3.176430e-04	k: 1346	n:4470000
LLGL2   4470000 perm   8665 sec   (516 perm/sec)   p_kst 3.011186e-04   p_cons 9.668470e-01   p_joint 3.011186e-04

Joint ci ratio: 1.067123e-01	ci left: 2.850450e-04	ci right 3.173923e-04	k: 1348	n:4480000
Cons ci ratio: 3.429507e-04	ci left: 9.666807e-01	ci right 9.670125e-01	k: 4331474	n:4480000
KS ci ratio: 1.067123e-01	ci left: 2.850450e-04	ci right 3.173923e-04	k: 1348	n:4480000
LLGL2   4480000 perm   8701 sec   (515 perm/sec)   p_kst 3.008929e-04   p_cons 9.668469e-01   p_joint 3.008929e-04

Joint ci ratio: 1.065545e-01	ci left: 2.852772e-04	ci right 3.176001e-04	k: 1352	n:4490000
Cons ci ratio: 3.425739e-04	ci left: 9.666799e-01	ci right 9.670113e-01	k: 4341138	n:4490000
KS ci ratio: 1.065545e-01	ci left: 2.852772e-04	ci right 3.176001e-04	k: 1352	n:4490000
LLGL2   4490000 perm   8739 sec   (514 perm/sec)   p_kst 3.011136e-04   p_cons 9.668459e-01   p_joint 3.011136e-04

Joint ci ratio: 1.064758e-01	ci left: 2.850759e-04	ci right 3.173506e-04	k: 1354	n:4500000
Cons ci ratio: 3.421628e-04	ci left: 9.666857e-01	ci right 9.670168e-01	k: 4350832	n:4500000
KS ci ratio: 1.064758e-01	ci left: 2.850759e-04	ci right 3.173506e-04	k: 1354	n:4500000
LLGL2   4500000 perm   8776 sec   (513 perm/sec)   p_kst 3.008889e-04   p_cons 9.668516e-01   p_joint 3.008889e-04

Joint ci ratio: 1.063973e-01	ci left: 2.848754e-04	ci right 3.171022e-04	k: 1356	n:4510000
Cons ci ratio: 3.418217e-04	ci left: 9.666787e-01	ci right 9.670094e-01	k: 4360468	n:4510000
KS ci ratio: 1.063973e-01	ci left: 2.848754e-04	ci right 3.171022e-04	k: 1356	n:4510000
LLGL2   4510000 perm   8814 sec   (512 perm/sec)   p_kst 3.006652e-04   p_cons 9.668443e-01   p_joint 3.006652e-04

Joint ci ratio: 1.063582e-01	ci left: 2.844605e-04	ci right 3.166277e-04	k: 1357	n:4520000
Cons ci ratio: 3.414462e-04	ci left: 9.666783e-01	ci right 9.670087e-01	k: 4370134	n:4520000
KS ci ratio: 1.063582e-01	ci left: 2.844605e-04	ci right 3.166277e-04	k: 1357	n:4520000
LLGL2   4520000 perm   8852 sec   (511 perm/sec)   p_kst 3.002212e-04   p_cons 9.668438e-01   p_joint 3.002212e-04

Joint ci ratio: 1.062800e-01	ci left: 2.842623e-04	ci right 3.163820e-04	k: 1359	n:4530000
Cons ci ratio: 3.410403e-04	ci left: 9.666840e-01	ci right 9.670139e-01	k: 4379827	n:4530000
KS ci ratio: 1.062800e-01	ci left: 2.842623e-04	ci right 3.163820e-04	k: 1359	n:4530000
LLGL2   4530000 perm   8889 sec   (510 perm/sec)   p_kst 3.000000e-04   p_cons 9.668492e-01   p_joint 3.000000e-04

Joint ci ratio: 1.060851e-01	ci left: 2.847083e-04	ci right 3.168157e-04	k: 1364	n:4540000
Cons ci ratio: 3.406826e-04	ci left: 9.666807e-01	ci right 9.670103e-01	k: 4389480	n:4540000
KS ci ratio: 1.060851e-01	ci left: 2.847083e-04	ci right 3.168157e-04	k: 1364	n:4540000
LLGL2   4540000 perm   8927 sec   (509 perm/sec)   p_kst 3.004405e-04   p_cons 9.668458e-01   p_joint 3.004405e-04

Joint ci ratio: 1.059300e-01	ci left: 2.849384e-04	ci right 3.170218e-04	k: 1368	n:4550000
Cons ci ratio: 3.403366e-04	ci left: 9.666755e-01	ci right 9.670048e-01	k: 4399124	n:4550000
KS ci ratio: 1.059300e-01	ci left: 2.849384e-04	ci right 3.170218e-04	k: 1368	n:4550000
LLGL2   4550000 perm   8966 sec   (507 perm/sec)   p_kst 3.006593e-04   p_cons 9.668404e-01   p_joint 3.006593e-04

Joint ci ratio: 1.058914e-01	ci left: 2.845270e-04	ci right 3.165517e-04	k: 1369	n:4560000
Cons ci ratio: 3.399532e-04	ci left: 9.666776e-01	ci right 9.670065e-01	k: 4408801	n:4560000
KS ci ratio: 1.058914e-01	ci left: 2.845270e-04	ci right 3.165517e-04	k: 1369	n:4560000
LLGL2   4560000 perm   9003 sec   (506 perm/sec)   p_kst 3.002193e-04   p_cons 9.668423e-01   p_joint 3.002193e-04

Joint ci ratio: 1.056986e-01	ci left: 2.849695e-04	ci right 3.169821e-04	k: 1374	n:4570000
Cons ci ratio: 3.395665e-04	ci left: 9.666805e-01	ci right 9.670090e-01	k: 4418482	n:4570000
KS ci ratio: 1.056986e-01	ci left: 2.849695e-04	ci right 3.169821e-04	k: 1374	n:4570000
LLGL2   4570000 perm   9042 sec   (505 perm/sec)   p_kst 3.006565e-04   p_cons 9.668451e-01   p_joint 3.006565e-04

Joint ci ratio: 1.055835e-01	ci left: 2.849851e-04	ci right 3.169623e-04	k: 1377	n:4580000
Cons ci ratio: 3.391903e-04	ci left: 9.666817e-01	ci right 9.670099e-01	k: 4428155	n:4580000
KS ci ratio: 1.055835e-01	ci left: 2.849851e-04	ci right 3.169623e-04	k: 1377	n:4580000
LLGL2   4580000 perm   9080 sec   (504 perm/sec)   p_kst 3.006550e-04   p_cons 9.668461e-01   p_joint 3.006550e-04

Joint ci ratio: 1.055452e-01	ci left: 2.845763e-04	ci right 3.164954e-04	k: 1378	n:4590000
Cons ci ratio: 3.387854e-04	ci left: 9.666885e-01	ci right 9.670163e-01	k: 4437854	n:4590000
KS ci ratio: 1.055452e-01	ci left: 2.845763e-04	ci right 3.164954e-04	k: 1378	n:4590000
LLGL2   4590000 perm   9118 sec   (503 perm/sec)   p_kst 3.002179e-04   p_cons 9.668527e-01   p_joint 3.002179e-04

Joint ci ratio: 1.052404e-01	ci left: 2.856509e-04	ci right 3.175923e-04	k: 1386	n:4600000
Cons ci ratio: 3.384222e-04	ci left: 9.666877e-01	ci right 9.670152e-01	k: 4447518	n:4600000
KS ci ratio: 1.052404e-01	ci left: 2.856509e-04	ci right 3.175923e-04	k: 1386	n:4600000
LLGL2   4600000 perm   9157 sec   (502 perm/sec)   p_kst 3.013043e-04   p_cons 9.668517e-01   p_joint 3.013043e-04

Joint ci ratio: 1.051267e-01	ci left: 2.856649e-04	ci right 3.175712e-04	k: 1389	n:4610000
Cons ci ratio: 3.380601e-04	ci left: 9.666869e-01	ci right 9.670140e-01	k: 4457182	n:4610000
KS ci ratio: 1.051267e-01	ci left: 2.856649e-04	ci right 3.175712e-04	k: 1389	n:4610000
LLGL2   4610000 perm   9196 sec   (501 perm/sec)   p_kst 3.013015e-04   p_cons 9.668508e-01   p_joint 3.013015e-04

Joint ci ratio: 1.050135e-01	ci left: 2.856789e-04	ci right 3.175502e-04	k: 1392	n:4620000
Cons ci ratio: 3.376878e-04	ci left: 9.666883e-01	ci right 9.670150e-01	k: 4466856	n:4620000
KS ci ratio: 1.050135e-01	ci left: 2.856789e-04	ci right 3.175502e-04	k: 1392	n:4620000
LLGL2   4620000 perm   9234 sec   (500 perm/sec)   p_kst 3.012987e-04   p_cons 9.668519e-01   p_joint 3.012987e-04

Joint ci ratio: 1.049006e-01	ci left: 2.856928e-04	ci right 3.175293e-04	k: 1395	n:4630000
Cons ci ratio: 3.373201e-04	ci left: 9.666890e-01	ci right 9.670154e-01	k: 4476527	n:4630000
KS ci ratio: 1.049006e-01	ci left: 2.856928e-04	ci right 3.175293e-04	k: 1395	n:4630000
LLGL2   4630000 perm   9272 sec   (499 perm/sec)   p_kst 3.012959e-04   p_cons 9.668525e-01   p_joint 3.012959e-04

Joint ci ratio: 1.047506e-01	ci left: 2.859166e-04	ci right 3.177297e-04	k: 1399	n:4640000
Cons ci ratio: 3.369592e-04	ci left: 9.666886e-01	ci right 9.670146e-01	k: 4486193	n:4640000
KS ci ratio: 1.047506e-01	ci left: 2.859166e-04	ci right 3.177297e-04	k: 1399	n:4640000
LLGL2   4640000 perm   9312 sec   (498 perm/sec)   p_kst 3.015086e-04   p_cons 9.668519e-01   p_joint 3.015086e-04

Joint ci ratio: 1.046013e-01	ci left: 2.861394e-04	ci right 3.179291e-04	k: 1403	n:4650000
Cons ci ratio: 3.366030e-04	ci left: 9.666876e-01	ci right 9.670133e-01	k: 4495856	n:4650000
KS ci ratio: 1.046013e-01	ci left: 2.861394e-04	ci right 3.179291e-04	k: 1403	n:4650000
LLGL2   4650000 perm   9350 sec   (497 perm/sec)   p_kst 3.017204e-04   p_cons 9.668508e-01   p_joint 3.017204e-04

Joint ci ratio: 1.044155e-01	ci left: 2.865703e-04	ci right 3.183479e-04	k: 1408	n:4660000
Cons ci ratio: 3.362242e-04	ci left: 9.666911e-01	ci right 9.670164e-01	k: 4505540	n:4660000
KS ci ratio: 1.044155e-01	ci left: 2.865703e-04	ci right 3.183479e-04	k: 1408	n:4660000
LLGL2   4660000 perm   9390 sec   (496 perm/sec)   p_kst 3.021459e-04   p_cons 9.668541e-01   p_joint 3.021459e-04

Joint ci ratio: 1.044155e-01	ci left: 2.859567e-04	ci right 3.176662e-04	k: 1408	n:4670000
Cons ci ratio: 3.358713e-04	ci left: 9.666899e-01	ci right 9.670149e-01	k: 4515202	n:4670000
KS ci ratio: 1.044155e-01	ci left: 2.859567e-04	ci right 3.176662e-04	k: 1408	n:4670000
LLGL2   4670000 perm   9429 sec   (495 perm/sec)   p_kst 3.014989e-04   p_cons 9.668527e-01   p_joint 3.014989e-04

Joint ci ratio: 1.043045e-01	ci left: 2.859699e-04	ci right 3.176451e-04	k: 1411	n:4680000
Cons ci ratio: 3.355028e-04	ci left: 9.666919e-01	ci right 9.670165e-01	k: 4524879	n:4680000
KS ci ratio: 1.043045e-01	ci left: 2.859699e-04	ci right 3.176451e-04	k: 1411	n:4680000
LLGL2   4680000 perm   9469 sec   (494 perm/sec)   p_kst 3.014957e-04   p_cons 9.668545e-01   p_joint 3.014957e-04

Joint ci ratio: 1.040469e-01	ci left: 2.868138e-04	ci right 3.184993e-04	k: 1418	n:4690000
Cons ci ratio: 3.350965e-04	ci left: 9.667014e-01	ci right 9.670256e-01	k: 4534591	n:4690000
KS ci ratio: 1.040469e-01	ci left: 2.868138e-04	ci right 3.184993e-04	k: 1418	n:4690000
LLGL2   4690000 perm   9508 sec   (493 perm/sec)   p_kst 3.023454e-04   p_cons 9.668638e-01   p_joint 3.023454e-04

Joint ci ratio: 1.040103e-01	ci left: 2.864108e-04	ci right 3.180399e-04	k: 1419	n:4700000
Cons ci ratio: 3.347516e-04	ci left: 9.666993e-01	ci right 9.670231e-01	k: 4544249	n:4700000
KS ci ratio: 1.040103e-01	ci left: 2.864108e-04	ci right 3.180399e-04	k: 1419	n:4700000
LLGL2   4700000 perm   9547 sec   (492 perm/sec)   p_kst 3.019149e-04   p_cons 9.668615e-01   p_joint 3.019149e-04

Joint ci ratio: 1.039006e-01	ci left: 2.864231e-04	ci right 3.180182e-04	k: 1422	n:4710000
Cons ci ratio: 3.344234e-04	ci left: 9.666942e-01	ci right 9.670177e-01	k: 4553893	n:4710000
KS ci ratio: 1.039006e-01	ci left: 2.864231e-04	ci right 3.180182e-04	k: 1422	n:4710000
LLGL2   4710000 perm   9586 sec   (491 perm/sec)   p_kst 3.019108e-04   p_cons 9.668563e-01   p_joint 3.019108e-04

Joint ci ratio: 1.038276e-01	ci left: 2.862290e-04	ci right 3.177791e-04	k: 1424	n:4720000
Cons ci ratio: 3.340750e-04	ci left: 9.666932e-01	ci right 9.670164e-01	k: 4563556	n:4720000
KS ci ratio: 1.038276e-01	ci left: 2.862290e-04	ci right 3.177791e-04	k: 1424	n:4720000
LLGL2   4720000 perm   9625 sec   (490 perm/sec)   p_kst 3.016949e-04   p_cons 9.668551e-01   p_joint 3.016949e-04

Joint ci ratio: 1.036822e-01	ci left: 2.864476e-04	ci right 3.179749e-04	k: 1428	n:4730000
Cons ci ratio: 3.337190e-04	ci left: 9.666939e-01	ci right 9.670167e-01	k: 4573227	n:4730000
KS ci ratio: 1.036822e-01	ci left: 2.864476e-04	ci right 3.179749e-04	k: 1428	n:4730000
LLGL2   4730000 perm   9665 sec   (489 perm/sec)   p_kst 3.019027e-04   p_cons 9.668556e-01   p_joint 3.019027e-04

Joint ci ratio: 1.035374e-01	ci left: 2.866653e-04	ci right 3.181698e-04	k: 1432	n:4740000
Cons ci ratio: 3.333520e-04	ci left: 9.666969e-01	ci right 9.670194e-01	k: 4582909	n:4740000
KS ci ratio: 1.035374e-01	ci left: 2.866653e-04	ci right 3.181698e-04	k: 1432	n:4740000
LLGL2   4740000 perm   9705 sec   (488 perm/sec)   p_kst 3.021097e-04   p_cons 9.668584e-01   p_joint 3.021097e-04

Joint ci ratio: 1.034652e-01	ci left: 2.864719e-04	ci right 3.179319e-04	k: 1434	n:4750000
Cons ci ratio: 3.329688e-04	ci left: 9.667033e-01	ci right 9.670254e-01	k: 4592607	n:4750000
KS ci ratio: 1.034652e-01	ci left: 2.864719e-04	ci right 3.179319e-04	k: 1434	n:4750000
LLGL2   4750000 perm   9744 sec   (487 perm/sec)   p_kst 3.018947e-04   p_cons 9.668646e-01   p_joint 3.018947e-04

Joint ci ratio: 1.032854e-01	ci left: 2.868934e-04	ci right 3.183416e-04	k: 1439	n:4760000
Cons ci ratio: 3.326065e-04	ci left: 9.667058e-01	ci right 9.670276e-01	k: 4602287	n:4760000
KS ci ratio: 1.032854e-01	ci left: 2.868934e-04	ci right 3.183416e-04	k: 1439	n:4760000
LLGL2   4760000 perm   9785 sec   (486 perm/sec)   p_kst 3.023109e-04   p_cons 9.668670e-01   p_joint 3.023109e-04

Joint ci ratio: 1.031780e-01	ci left: 2.869046e-04	ci right 3.183193e-04	k: 1442	n:4770000
Cons ci ratio: 3.322486e-04	ci left: 9.667078e-01	ci right 9.670292e-01	k: 4611964	n:4770000
KS ci ratio: 1.031780e-01	ci left: 2.869046e-04	ci right 3.183193e-04	k: 1442	n:4770000
LLGL2   4770000 perm   9825 sec   (486 perm/sec)   p_kst 3.023061e-04   p_cons 9.668688e-01   p_joint 3.023061e-04

Joint ci ratio: 1.031066e-01	ci left: 2.867120e-04	ci right 3.180826e-04	k: 1444	n:4780000
Cons ci ratio: 3.319059e-04	ci left: 9.667069e-01	ci right 9.670281e-01	k: 4621628	n:4780000
KS ci ratio: 1.031066e-01	ci left: 2.867120e-04	ci right 3.180826e-04	k: 1444	n:4780000
LLGL2   4780000 perm   9865 sec   (485 perm/sec)   p_kst 3.020921e-04   p_cons 9.668678e-01   p_joint 3.020921e-04

Joint ci ratio: 1.028932e-01	ci left: 2.873338e-04	ci right 3.187034e-04	k: 1450	n:4790000
Cons ci ratio: 3.315395e-04	ci left: 9.667109e-01	ci right 9.670317e-01	k: 4631315	n:4790000
KS ci ratio: 1.028932e-01	ci left: 2.873338e-04	ci right 3.187034e-04	k: 1450	n:4790000
LLGL2   4790000 perm   9905 sec   (484 perm/sec)   p_kst 3.027140e-04   p_cons 9.668716e-01   p_joint 3.027140e-04

Joint ci ratio: 1.027870e-01	ci left: 2.873441e-04	ci right 3.186805e-04	k: 1453	n:4800000
Cons ci ratio: 3.311872e-04	ci left: 9.667124e-01	ci right 9.670328e-01	k: 4640990	n:4800000
KS ci ratio: 1.027870e-01	ci left: 2.873441e-04	ci right 3.186805e-04	k: 1453	n:4800000
LLGL2   4800000 perm   9946 sec   (483 perm/sec)   p_kst 3.027083e-04   p_cons 9.668729e-01   p_joint 3.027083e-04

Joint ci ratio: 1.026459e-01	ci left: 2.875570e-04	ci right 3.188709e-04	k: 1457	n:4810000
Cons ci ratio: 3.308349e-04	ci left: 9.667141e-01	ci right 9.670342e-01	k: 4650666	n:4810000
KS ci ratio: 1.026459e-01	ci left: 2.875570e-04	ci right 3.188709e-04	k: 1457	n:4810000
LLGL2   4810000 perm   9986 sec   (482 perm/sec)   p_kst 3.029106e-04   p_cons 9.668744e-01   p_joint 3.029106e-04

Joint ci ratio: 1.025404e-01	ci left: 2.875668e-04	ci right 3.188477e-04	k: 1460	n:4820000
Cons ci ratio: 3.304784e-04	ci left: 9.667168e-01	ci right 9.670366e-01	k: 4660347	n:4820000
KS ci ratio: 1.025404e-01	ci left: 2.875668e-04	ci right 3.188477e-04	k: 1460	n:4820000
LLGL2   4820000 perm   10026 sec   (481 perm/sec)   p_kst 3.029046e-04   p_cons 9.668770e-01   p_joint 3.029046e-04

Joint ci ratio: 1.024353e-01	ci left: 2.875766e-04	ci right 3.188246e-04	k: 1463	n:4830000
Cons ci ratio: 3.301338e-04	ci left: 9.667175e-01	ci right 9.670369e-01	k: 4670018	n:4830000
KS ci ratio: 1.024353e-01	ci left: 2.875766e-04	ci right 3.188246e-04	k: 1463	n:4830000
LLGL2   4830000 perm   10067 sec   (480 perm/sec)   p_kst 3.028986e-04   p_cons 9.668774e-01   p_joint 3.028986e-04

Joint ci ratio: 1.024353e-01	ci left: 2.869825e-04	ci right 3.181659e-04	k: 1463	n:4840000
Cons ci ratio: 3.297955e-04	ci left: 9.667170e-01	ci right 9.670361e-01	k: 4679684	n:4840000
KS ci ratio: 1.024353e-01	ci left: 2.869825e-04	ci right 3.181659e-04	k: 1463	n:4840000
LLGL2   4840000 perm   10107 sec   (479 perm/sec)   p_kst 3.022727e-04   p_cons 9.668769e-01   p_joint 3.022727e-04

Joint ci ratio: 1.022608e-01	ci left: 2.873953e-04	ci right 3.185672e-04	k: 1468	n:4850000
Cons ci ratio: 3.294593e-04	ci left: 9.667164e-01	ci right 9.670352e-01	k: 4689349	n:4850000
KS ci ratio: 1.022608e-01	ci left: 2.873953e-04	ci right 3.185672e-04	k: 1468	n:4850000
LLGL2   4850000 perm   10148 sec   (478 perm/sec)   p_kst 3.026804e-04   p_cons 9.668761e-01   p_joint 3.026804e-04

Joint ci ratio: 1.020526e-01	ci left: 2.880070e-04	ci right 3.191778e-04	k: 1474	n:4860000
Cons ci ratio: 3.290999e-04	ci left: 9.667206e-01	ci right 9.670390e-01	k: 4699037	n:4860000
KS ci ratio: 1.020526e-01	ci left: 2.880070e-04	ci right 3.191778e-04	k: 1474	n:4860000
LLGL2   4860000 perm   10189 sec   (477 perm/sec)   p_kst 3.032922e-04   p_cons 9.668800e-01   p_joint 3.032922e-04

Joint ci ratio: 1.020526e-01	ci left: 2.874156e-04	ci right 3.185224e-04	k: 1474	n:4870000
Cons ci ratio: 3.287352e-04	ci left: 9.667259e-01	ci right 9.670440e-01	k: 4708731	n:4870000
KS ci ratio: 1.020526e-01	ci left: 2.874156e-04	ci right 3.185224e-04	k: 1474	n:4870000
LLGL2   4870000 perm   10229 sec   (476 perm/sec)   p_kst 3.026694e-04   p_cons 9.668852e-01   p_joint 3.026694e-04

Joint ci ratio: 1.018457e-01	ci left: 2.880248e-04	ci right 3.191305e-04	k: 1480	n:4880000
Cons ci ratio: 3.284233e-04	ci left: 9.667212e-01	ci right 9.670389e-01	k: 4718376	n:4880000
KS ci ratio: 1.018457e-01	ci left: 2.880248e-04	ci right 3.191305e-04	k: 1480	n:4880000
LLGL2   4880000 perm   10270 sec   (475 perm/sec)   p_kst 3.032787e-04   p_cons 9.668803e-01   p_joint 3.032787e-04

Joint ci ratio: 1.018113e-01	ci left: 2.876350e-04	ci right 3.186876e-04	k: 1481	n:4890000
Cons ci ratio: 3.280484e-04	ci left: 9.667290e-01	ci right 9.670463e-01	k: 4728082	n:4890000
KS ci ratio: 1.018113e-01	ci left: 2.876350e-04	ci right 3.186876e-04	k: 1481	n:4890000
LLGL2   4890000 perm   10311 sec   (474 perm/sec)   p_kst 3.028630e-04   p_cons 9.668879e-01   p_joint 3.028630e-04

Joint ci ratio: 1.017427e-01	ci left: 2.874458e-04	ci right 3.184558e-04	k: 1483	n:4900000
Cons ci ratio: 3.276997e-04	ci left: 9.667318e-01	ci right 9.670489e-01	k: 4737764	n:4900000
KS ci ratio: 1.017427e-01	ci left: 2.874458e-04	ci right 3.184558e-04	k: 1483	n:4900000
LLGL2   4900000 perm   10352 sec   (473 perm/sec)   p_kst 3.026531e-04   p_cons 9.668906e-01   p_joint 3.026531e-04

Joint ci ratio: 1.017085e-01	ci left: 2.870589e-04	ci right 3.180161e-04	k: 1484	n:4910000
Cons ci ratio: 3.273897e-04	ci left: 9.667273e-01	ci right 9.670440e-01	k: 4747410	n:4910000
KS ci ratio: 1.017085e-01	ci left: 2.870589e-04	ci right 3.180161e-04	k: 1484	n:4910000
LLGL2   4910000 perm   10393 sec   (472 perm/sec)   p_kst 3.022403e-04   p_cons 9.668859e-01   p_joint 3.022403e-04

Joint ci ratio: 1.016059e-01	ci left: 2.870697e-04	ci right 3.179949e-04	k: 1487	n:4920000
Cons ci ratio: 3.270961e-04	ci left: 9.667197e-01	ci right 9.670362e-01	k: 4757041	n:4920000
KS ci ratio: 1.016059e-01	ci left: 2.870697e-04	ci right 3.179949e-04	k: 1487	n:4920000
LLGL2   4920000 perm   10434 sec   (472 perm/sec)   p_kst 3.022358e-04   p_cons 9.668783e-01   p_joint 3.022358e-04

Joint ci ratio: 1.015718e-01	ci left: 2.866850e-04	ci right 3.175579e-04	k: 1488	n:4930000
Cons ci ratio: 3.267764e-04	ci left: 9.667175e-01	ci right 9.670337e-01	k: 4766698	n:4930000
KS ci ratio: 1.015718e-01	ci left: 2.866850e-04	ci right 3.175579e-04	k: 1488	n:4930000
LLGL2   4930000 perm   10475 sec   (471 perm/sec)   p_kst 3.018256e-04   p_cons 9.668759e-01   p_joint 3.018256e-04

Joint ci ratio: 1.014356e-01	ci left: 2.868939e-04	ci right 3.177454e-04	k: 1492	n:4940000
Cons ci ratio: 3.264432e-04	ci left: 9.667181e-01	ci right 9.670340e-01	k: 4776369	n:4940000
KS ci ratio: 1.014356e-01	ci left: 2.868939e-04	ci right 3.177454e-04	k: 1492	n:4940000
LLGL2   4940000 perm   10516 sec   (470 perm/sec)   p_kst 3.020243e-04   p_cons 9.668763e-01   p_joint 3.020243e-04

Joint ci ratio: 1.013000e-01	ci left: 2.871019e-04	ci right 3.179320e-04	k: 1496	n:4950000
Cons ci ratio: 3.260945e-04	ci left: 9.667220e-01	ci right 9.670375e-01	k: 4786056	n:4950000
KS ci ratio: 1.013000e-01	ci left: 2.871019e-04	ci right 3.179320e-04	k: 1496	n:4950000
LLGL2   4950000 perm   10557 sec   (469 perm/sec)   p_kst 3.022222e-04   p_cons 9.668800e-01   p_joint 3.022222e-04

Joint ci ratio: 1.012662e-01	ci left: 2.867196e-04	ci right 3.174977e-04	k: 1497	n:4960000
Cons ci ratio: 3.257787e-04	ci left: 9.667196e-01	ci right 9.670347e-01	k: 4795712	n:4960000
KS ci ratio: 1.012662e-01	ci left: 2.867196e-04	ci right 3.174977e-04	k: 1497	n:4960000
LLGL2   4960000 perm   10600 sec   (468 perm/sec)   p_kst 3.018145e-04   p_cons 9.668774e-01   p_joint 3.018145e-04

Joint ci ratio: 1.011987e-01	ci left: 2.865349e-04	ci right 3.172715e-04	k: 1499	n:4970000
Cons ci ratio: 3.254424e-04	ci left: 9.667214e-01	ci right 9.670362e-01	k: 4805389	n:4970000
KS ci ratio: 1.011987e-01	ci left: 2.865349e-04	ci right 3.172715e-04	k: 1499	n:4970000
LLGL2   4970000 perm   10643 sec   (467 perm/sec)   p_kst 3.016097e-04   p_cons 9.668791e-01   p_joint 3.016097e-04

Joint ci ratio: 1.010976e-01	ci left: 2.865467e-04	ci right 3.172521e-04	k: 1502	n:4980000
Cons ci ratio: 3.251387e-04	ci left: 9.667169e-01	ci right 9.670315e-01	k: 4815035	n:4980000
KS ci ratio: 1.010976e-01	ci left: 2.865467e-04	ci right 3.172521e-04	k: 1502	n:4980000
LLGL2   4980000 perm   10685 sec   (466 perm/sec)   p_kst 3.016064e-04   p_cons 9.668745e-01   p_joint 3.016064e-04

Joint ci ratio: 1.009969e-01	ci left: 2.865585e-04	ci right 3.172327e-04	k: 1505	n:4990000
Cons ci ratio: 3.248135e-04	ci left: 9.667170e-01	ci right 9.670312e-01	k: 4824703	n:4990000
KS ci ratio: 1.009969e-01	ci left: 2.865585e-04	ci right 3.172327e-04	k: 1505	n:4990000
LLGL2   4990000 perm   10726 sec   (465 perm/sec)   p_kst 3.016032e-04   p_cons 9.668743e-01   p_joint 3.016032e-04

Joint ci ratio: 1.009299e-01	ci left: 2.863752e-04	ci right 3.170083e-04	k: 1507	n:5000000
Cons ci ratio: 3.244792e-04	ci left: 9.667190e-01	ci right 9.670329e-01	k: 4834381	n:5000000
KS ci ratio: 1.009299e-01	ci left: 2.863752e-04	ci right 3.170083e-04	k: 1507	n:5000000
LLGL2   5000000 perm   10768 sec   (464 perm/sec)   p_kst 3.014000e-04   p_cons 9.668762e-01   p_joint 3.014000e-04

Outputting figure to mutsig2_images.part000000000097/LLGL2.2_3226_5000000_0.0003014_0.96688_0.0003014.png
                gene_name: LLGL2
               theta_stop: 0.10 
                    nperm: 5000000 
                     p_ks: 0.00030 
        ci_ks_bounds_left: 0.00029 
       ci_ks_bounds_right: 0.00032 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.00030 
     ci_joint_bounds_left: 0.00029 
    ci_joint_bounds_right: 0.00032 

Current progress: 50 percent done.
LMOD2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.302908e-01	ci left: 7.756782e-02	ci right 8.847654e-02	k: 829	n:10000
Cons ci ratio: 2.301068e-01	ci left: 2.494902e-02	ci right 3.152965e-02	k: 281	n:10000
KS ci ratio: 2.806431e-02	ci left: 6.517269e-01	ci right 6.703792e-01	k: 6611	n:10000
LMOD2   10000 perm   2 sec   (6591 perm/sec)   p_kst 6.611000e-01   p_cons 2.810000e-02   p_joint 8.290000e-02

Joint ci ratio: 4.401150e-02	ci left: 2.777075e-01	ci right 2.902553e-01	k: 5679	n:20000
Cons ci ratio: 1.596804e-01	ci left: 2.691024e-02	ci right 3.162794e-02	k: 584	n:20000
KS ci ratio: 1.993831e-02	ci left: 6.523824e-01	ci right 6.655713e-01	k: 13180	n:20000
LMOD2   20000 perm   3 sec   (5762 perm/sec)   p_kst 6.590000e-01   p_cons 2.920000e-02   p_joint 2.839500e-01

Joint ci ratio: 3.670136e-02	ci left: 2.704166e-01	ci right 2.805603e-01	k: 8264	n:30000
Cons ci ratio: 1.299606e-01	ci left: 2.751748e-02	ci right 3.137436e-02	k: 882	n:30000
KS ci ratio: 1.624598e-02	ci left: 6.545407e-01	ci right 6.652950e-01	k: 19798	n:30000
LMOD2   30000 perm   5 sec   (5464 perm/sec)   p_kst 6.599333e-01   p_cons 2.940000e-02   p_joint 2.754667e-01

Joint ci ratio: 3.387353e-02	ci left: 2.465577e-01	ci right 2.550785e-01	k: 10032	n:40000
Cons ci ratio: 1.116891e-01	ci left: 2.820403e-02	ci right 3.156468e-02	k: 1194	n:40000
KS ci ratio: 1.397821e-02	ci left: 6.581931e-01	ci right 6.674833e-01	k: 26514	n:40000
LMOD2   40000 perm   8 sec   (5268 perm/sec)   p_kst 6.628500e-01   p_cons 2.985000e-02   p_joint 2.508000e-01

Joint ci ratio: 3.167030e-02	ci left: 2.308117e-01	ci right 2.382592e-01	k: 11726	n:50000
Cons ci ratio: 1.004452e-01	ci left: 2.807328e-02	ci right 3.106167e-02	k: 1477	n:50000
KS ci ratio: 1.251905e-02	ci left: 6.580953e-01	ci right 6.664059e-01	k: 33113	n:50000
LMOD2   50000 perm   10 sec   (5118 perm/sec)   p_kst 6.622600e-01   p_cons 2.954000e-02   p_joint 2.345200e-01

Joint ci ratio: 1.362543e-02	ci left: 5.757717e-01	ci right 5.836873e-01	k: 34784	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: 1.147330e-02	ci left: 6.566949e-01	ci right 6.642895e-01	k: 39630	n:60000
LMOD2   60000 perm   12 sec   (4986 perm/sec)   p_kst 6.605000e-01   p_cons 2.935000e-02   p_joint 5.797333e-01

Outputting figure to mutsig2_images.part000000000097/LMOD2.2_1656_60000_0.6605_0.02935_0.57973.png
                gene_name: LMOD2
               theta_stop: 0.092 
                    nperm: 60000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.029 
      ci_cons_bounds_left: 0.028 
     ci_cons_bounds_right: 0.031 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.58 
    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.165.3896/
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/181708/iteration1/scatter.0000000097
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 97 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120047: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000098> was used as the working directory.
Started at Wed Oct 10 10:43:33 2012
Results reported at Wed Oct 10 10:48:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000098.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000098.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 98  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    338.94 sec.
    Max Memory :      1476 MB
    Max Swap   :      3872 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.165.3896/
-whichjob
98
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 98: processing genes 8777 - 8866
Calculating significance of each gene.
Using projection method.
8777	LOC642587	5.330745e-02
8778	LOC645961	1
8779	LOC646498	1
8780	LOC649330	1
8781	LOC653486	1
8782	LOC728819	1
8783	LOC729020	5.442412e-02
8784	LOC729991-MEF2B	1
8785	LOC81691	1
8786	LOH12CR1	1
8787	LONP1	1
8788	LONP2	1
8789	LONRF1	1
8790	LONRF2	1
8791	LONRF3	1
8792	LOX	1
8793	LOXL1	1
8794	LOXL2	1
8795	LOXL3	1
8796	LOXL4	1
8797	LPA	1.828735e-01
8798	LPAR1	1
8799	LPAR2	1
8800	LPAR3	1.106024e-01
8801	LPAR4	1
8802	LPAR5	1
8803	LPAR6	3.584519e-02
8804	LPCAT1	1
8805	LPCAT2	1
8806	LPCAT3	1
8807	LPCAT4	1
8808	LPGAT1	1
8809	LPHN1	5.210935e-01
8810	LPHN2	3.208237e-02
8811	LPHN3	1
8812	LPIN1	3.038017e-01
8813	LPIN2	1
8814	LPIN3	1
8815	LPL	1
8816	LPO	1
8817	LPP	1
8818	LPPR1	1
8819	LPPR2	1
8820	LPPR3	1
8821	LPPR4	1
8822	LPPR5	9.989588e-02
8823	LPXN	1.784419e-01
8824	LRAT	1
8825	LRBA	5.455203e-01
8826	LRCH1	1
8827	LRCH2	1
8828	LRCH3	2.642222e-01
8829	LRCH4	2.142249e-01
8830	LRDD	3.428570e-01
8831	LRFN1	8.139480e-02
8832	LRFN2	3.079289e-01
8833	LRFN3	6.223538e-02
8834	LRFN4	1
8835	LRFN5	2.733885e-01
8836	LRG1	1
8837	LRGUK	9.114533e-02
8838	LRIG1	1.398796e-01
8839	LRIG2	4.130883e-01
8840	LRIG3	3.827583e-02
8841	LRIT1	1
8842	LRIT2	5.288867e-02
8843	LRIT3	1
8844	LRMP	1
8845	LRP1	1.633841e-01
8846	LRP10	2.820147e-01
8847	LRP11	1
8848	LRP12	1
8849	LRP1B	5.401264e-02
8850	LRP2	1.640719e-01
8851	LRP2BP	1
8852	LRP3	1
8853	LRP4	1
8854	LRP5	1
8855	LRP5L	1
8856	LRP6	3.849747e-01
8857	LRP8	1
8858	LRPAP1	1
8859	LRPPRC	1
8860	LRRC1	1
8861	LRRC10	1
8862	LRRC14	1
8863	LRRC14B	1
8864	LRRC15	1.060366e-01
8865	LRRC16A	1
8866	LRRC16B	1
Done

Running MutSig 2:
Scatter job 98: processing genes 8777 - 8866
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
LRP1
Processing conservation and coverage...
71% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.989652e-01	ci left: 1.437251e-02	ci right 1.951444e-02	k: 168	n:10000
Cons ci ratio: 2.684594e-02	ci left: 6.714609e-01	ci right 6.898338e-01	k: 6807	n:10000
KS ci ratio: 4.364913e-01	ci left: 6.259350e-03	ci right 9.836166e-03	k: 79	n:10000
LRP1   10000 perm   4 sec   (2269 perm/sec)   p_kst 7.900000e-03   p_cons 6.807000e-01   p_joint 1.680000e-02

Joint ci ratio: 2.205424e-01	ci left: 1.383370e-02	ci right 1.730922e-02	k: 310	n:20000
Cons ci ratio: 1.836183e-02	ci left: 6.885662e-01	ci right 7.013771e-01	k: 13900	n:20000
KS ci ratio: 3.096304e-01	ci left: 6.720018e-03	ci right 9.226206e-03	k: 158	n:20000
LRP1   20000 perm   12 sec   (1616 perm/sec)   p_kst 7.900000e-03   p_cons 6.950000e-01   p_joint 1.550000e-02

Joint ci ratio: 2.053554e-01	ci left: 1.076700e-02	ci right 1.326218e-02	k: 359	n:30000
Cons ci ratio: 1.511758e-02	ci left: 6.862050e-01	ci right 6.966912e-01	k: 20744	n:30000
KS ci ratio: 2.478852e-01	ci left: 7.241974e-03	ci right 9.321610e-03	k: 247	n:30000
LRP1   30000 perm   17 sec   (1718 perm/sec)   p_kst 8.233333e-03   p_cons 6.914667e-01   p_joint 1.196667e-02

Joint ci ratio: 1.543189e-01	ci left: 1.464879e-02	ci right 1.712221e-02	k: 634	n:40000
Cons ci ratio: 1.308588e-02	ci left: 6.871231e-01	ci right 6.961990e-01	k: 27667	n:40000
KS ci ratio: 2.142406e-01	ci left: 7.410577e-03	ci right 9.211899e-03	k: 331	n:40000
LRP1   40000 perm   23 sec   (1756 perm/sec)   p_kst 8.275000e-03   p_cons 6.916750e-01   p_joint 1.585000e-02

Joint ci ratio: 1.341919e-01	ci left: 1.565292e-02	ci right 1.792368e-02	k: 838	n:50000
Cons ci ratio: 1.203359e-02	ci left: 6.756099e-01	ci right 6.838092e-01	k: 33986	n:50000
KS ci ratio: 1.906986e-01	ci left: 7.580572e-03	ci right 9.197284e-03	k: 418	n:50000
LRP1   50000 perm   29 sec   (1720 perm/sec)   p_kst 8.360000e-03   p_cons 6.797200e-01   p_joint 1.676000e-02

Joint ci ratio: 1.156653e-01	ci left: 1.769585e-02	ci right 1.988438e-02	k: 1126	n:60000
Cons ci ratio: 1.101382e-02	ci left: 6.748296e-01	ci right 6.823198e-01	k: 40715	n:60000
KS ci ratio: 1.885800e-01	ci left: 6.475540e-03	ci right 7.839451e-03	k: 428	n:60000
LRP1   60000 perm   35 sec   (1709 perm/sec)   p_kst 7.133333e-03   p_cons 6.785833e-01   p_joint 1.876667e-02

Joint ci ratio: 1.302636e-01	ci left: 1.193889e-02	ci right 1.361615e-02	k: 893	n:70000
Cons ci ratio: 1.023554e-02	ci left: 6.734498e-01	ci right 6.803927e-01	k: 47385	n:70000
KS ci ratio: 1.755656e-01	ci left: 6.450383e-03	ci right 7.705285e-03	k: 494	n:70000
LRP1   70000 perm   41 sec   (1709 perm/sec)   p_kst 7.057143e-03   p_cons 6.769286e-01   p_joint 1.275714e-02

Joint ci ratio: 1.323289e-01	ci left: 1.013157e-02	ci right 1.157924e-02	k: 867	n:80000
Cons ci ratio: 9.569633e-03	ci left: 6.738974e-01	ci right 6.803898e-01	k: 54172	n:80000
KS ci ratio: 1.661172e-01	ci left: 6.338070e-03	ci right 7.498122e-03	k: 552	n:80000
LRP1   80000 perm   46 sec   (1722 perm/sec)   p_kst 6.900000e-03   p_cons 6.771500e-01   p_joint 1.083750e-02

Joint ci ratio: 1.303038e-01	ci left: 9.306465e-03	ci right 1.061430e-02	k: 895	n:90000
Cons ci ratio: 9.024294e-03	ci left: 6.739894e-01	ci right 6.801103e-01	k: 60935	n:90000
KS ci ratio: 1.585696e-01	ci left: 6.209438e-03	ci right 7.289389e-03	k: 606	n:90000
LRP1   90000 perm   52 sec   (1725 perm/sec)   p_kst 6.733333e-03   p_cons 6.770556e-01   p_joint 9.944444e-03

Joint ci ratio: 1.273217e-01	ci left: 8.791812e-03	ci right 9.996902e-03	k: 938	n:100000
Cons ci ratio: 8.571690e-03	ci left: 6.736105e-01	ci right 6.794193e-01	k: 67652	n:100000
KS ci ratio: 1.511612e-01	ci left: 6.174855e-03	ci right 7.194075e-03	k: 667	n:100000
LRP1   100000 perm   58 sec   (1714 perm/sec)   p_kst 6.670000e-03   p_cons 6.765200e-01   p_joint 9.380000e-03

Joint ci ratio: 1.161158e-01	ci left: 9.658761e-03	ci right 1.085818e-02	k: 1127	n:110000
Cons ci ratio: 8.179276e-03	ci left: 6.733983e-01	ci right 6.789379e-01	k: 74379	n:110000
KS ci ratio: 1.429368e-01	ci left: 6.305307e-03	ci right 7.284605e-03	k: 746	n:110000
LRP1   110000 perm   64 sec   (1715 perm/sec)   p_kst 6.781818e-03   p_cons 6.761727e-01   p_joint 1.024545e-02

Joint ci ratio: 1.062459e-01	ci left: 1.062037e-02	ci right 1.182010e-02	k: 1345	n:120000
Cons ci ratio: 7.827299e-03	ci left: 6.737278e-01	ci right 6.790303e-01	k: 81166	n:120000
KS ci ratio: 1.373539e-01	ci left: 6.278413e-03	ci right 7.212331e-03	k: 808	n:120000
LRP1   120000 perm   70 sec   (1713 perm/sec)   p_kst 6.733333e-03   p_cons 6.763833e-01   p_joint 1.120833e-02

Joint ci ratio: 1.047310e-01	ci left: 1.010285e-02	ci right 1.122683e-02	k: 1385	n:130000
Cons ci ratio: 7.521793e-03	ci left: 6.737411e-01	ci right 6.788356e-01	k: 87918	n:130000
KS ci ratio: 1.326850e-01	ci left: 6.226532e-03	ci right 7.118765e-03	k: 866	n:130000
LRP1   130000 perm   76 sec   (1713 perm/sec)   p_kst 6.661538e-03   p_cons 6.762923e-01   p_joint 1.065385e-02

Joint ci ratio: 9.427035e-02	ci left: 1.162453e-02	ci right 1.278152e-02	k: 1707	n:140000
Cons ci ratio: 7.252786e-03	ci left: 6.735556e-01	ci right 6.784657e-01	k: 94642	n:140000
KS ci ratio: 1.190986e-01	ci left: 7.221041e-03	ci right 8.142382e-03	k: 1074	n:140000
LRP1   140000 perm   82 sec   (1702 perm/sec)   p_kst 7.671429e-03   p_cons 6.760143e-01   p_joint 1.219286e-02

Joint ci ratio: 9.132678e-02	ci left: 1.157889e-02	ci right 1.269342e-02	k: 1819	n:150000
Cons ci ratio: 7.006342e-03	ci left: 6.736717e-01	ci right 6.784149e-01	k: 101407	n:150000
KS ci ratio: 1.150494e-01	ci left: 7.237944e-03	ci right 8.127911e-03	k: 1151	n:150000
LRP1   150000 perm   89 sec   (1693 perm/sec)   p_kst 7.673333e-03   p_cons 6.760467e-01   p_joint 1.212667e-02

Joint ci ratio: 8.697203e-02	ci left: 1.199191e-02	ci right 1.308836e-02	k: 2005	n:160000
Cons ci ratio: 6.783231e-03	ci left: 6.737882e-01	ci right 6.783804e-01	k: 108174	n:160000
KS ci ratio: 1.117541e-01	ci left: 7.204584e-03	ci right 8.063402e-03	k: 1220	n:160000
LRP1   160000 perm   95 sec   (1690 perm/sec)   p_kst 7.625000e-03   p_cons 6.760875e-01   p_joint 1.253125e-02

Joint ci ratio: 8.605447e-02	ci left: 1.153961e-02	ci right 1.258301e-02	k: 2049	n:170000
Cons ci ratio: 6.578923e-03	ci left: 6.739756e-01	ci right 6.784301e-01	k: 114955	n:170000
KS ci ratio: 1.086418e-01	ci left: 7.186917e-03	ci right 8.018243e-03	k: 1291	n:170000
LRP1   170000 perm   101 sec   (1684 perm/sec)   p_kst 7.594118e-03   p_cons 6.762059e-01   p_joint 1.205294e-02

Joint ci ratio: 8.844876e-02	ci left: 1.031675e-02	ci right 1.127688e-02	k: 1942	n:180000
Cons ci ratio: 6.388786e-03	ci left: 6.743666e-01	ci right 6.786943e-01	k: 121776	n:180000
KS ci ratio: 1.056587e-01	ci left: 7.187738e-03	ci right 7.994909e-03	k: 1365	n:180000
LRP1   180000 perm   107 sec   (1678 perm/sec)   p_kst 7.583333e-03   p_cons 6.765333e-01   p_joint 1.078889e-02

Joint ci ratio: 8.425941e-02	ci left: 1.078833e-02	ci right 1.174245e-02	k: 2139	n:190000
Cons ci ratio: 6.220208e-03	ci left: 6.742963e-01	ci right 6.785089e-01	k: 128517	n:190000
KS ci ratio: 1.066676e-01	ci left: 6.681257e-03	ci right 7.439163e-03	k: 1340	n:190000
LRP1   190000 perm   114 sec   (1671 perm/sec)   p_kst 7.052632e-03   p_cons 6.764053e-01   p_joint 1.125789e-02

Joint ci ratio: 8.202713e-02	ci left: 1.082666e-02	ci right 1.175759e-02	k: 2257	n:200000
Cons ci ratio: 6.065068e-03	ci left: 6.741793e-01	ci right 6.782856e-01	k: 135247	n:200000
KS ci ratio: 1.036191e-01	ci left: 6.736686e-03	ci right 7.477708e-03	k: 1420	n:200000
LRP1   200000 perm   120 sec   (1660 perm/sec)   p_kst 7.100000e-03   p_cons 6.762350e-01   p_joint 1.128500e-02

Joint ci ratio: 7.977677e-02	ci left: 1.091298e-02	ci right 1.182439e-02	k: 2386	n:210000
Cons ci ratio: 5.922722e-03	ci left: 6.739459e-01	ci right 6.779540e-01	k: 141950	n:210000
KS ci ratio: 1.008516e-01	ci left: 6.782471e-03	ci right 7.507424e-03	k: 1499	n:210000
LRP1   210000 perm   127 sec   (1651 perm/sec)   p_kst 7.138095e-03   p_cons 6.759524e-01   p_joint 1.136190e-02

Joint ci ratio: 7.778020e-02	ci left: 1.096948e-02	ci right 1.186164e-02	k: 2510	n:220000
Cons ci ratio: 5.783700e-03	ci left: 6.742083e-01	ci right 6.781235e-01	k: 148757	n:220000
KS ci ratio: 9.845178e-02	ci left: 6.802161e-03	ci right 7.510918e-03	k: 1573	n:220000
LRP1   220000 perm   134 sec   (1643 perm/sec)   p_kst 7.150000e-03   p_cons 6.761682e-01   p_joint 1.140909e-02

Outputting figure to mutsig2_images.part000000000098/LRP1.4_13991_220000_0.00715_0.67617_0.011409.png
                gene_name: LRP1
               theta_stop: 0.098 
                    nperm: 220000 
                     p_ks: 0.0072 
        ci_ks_bounds_left: 0.0068 
       ci_ks_bounds_right: 0.0075 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.011 
     ci_joint_bounds_left: 0.011 
    ci_joint_bounds_right: 0.012 

Current progress: 20 percent done.
LRP1B
Processing conservation and coverage...
70% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.705195e-02	ci left: 1.976171e-01	ci right 2.135548e-01	k: 2055	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: 1.217655e-01	ci left: 8.815461e-02	ci right 9.968320e-02	k: 938	n:10000
LRP1B   10000 perm   4 sec   (2226 perm/sec)   p_kst 9.380000e-02   p_cons 9.033000e-01   p_joint 2.055000e-01

Joint ci ratio: 6.905766e-02	ci left: 1.339376e-01	ci right 1.435677e-01	k: 2774	n:20000
Cons ci ratio: 9.078381e-03	ci left: 8.989673e-01	ci right 9.072150e-01	k: 18063	n:20000
KS ci ratio: 8.689668e-02	ci left: 8.832299e-02	ci right 9.639598e-02	k: 1846	n:20000
LRP1B   20000 perm   10 sec   (2079 perm/sec)   p_kst 9.230000e-02   p_cons 9.031500e-01   p_joint 1.387000e-01

Outputting figure to mutsig2_images.part000000000098/LRP1B.4_14164_20000_0.0923_0.90315_0.1387.png
                gene_name: LRP1B
               theta_stop: 0.087 
                    nperm: 20000 
                     p_ks: 0.092 
        ci_ks_bounds_left: 0.088 
       ci_ks_bounds_right: 0.096 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.90 
     ci_cons_bounds_right: 0.91 
                  p_joint: 0.14 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 40 percent done.
LPHN2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.617042e-01	ci left: 5.099641e-02	ci right 6.006470e-02	k: 554	n:10000
Cons ci ratio: 2.437784e-02	ci left: 7.121969e-01	ci right 7.298742e-01	k: 7211	n:10000
KS ci ratio: 1.874410e-01	ci left: 3.796147e-02	ci right 4.590818e-02	k: 418	n:10000
LPHN2   10000 perm   2 sec   (4492 perm/sec)   p_kst 4.180000e-02   p_cons 7.211000e-01   p_joint 5.540000e-02

Joint ci ratio: 1.227707e-01	ci left: 4.551508e-02	ci right 5.151706e-02	k: 969	n:20000
Cons ci ratio: 1.714812e-02	ci left: 7.169421e-01	ci right 7.293930e-01	k: 14464	n:20000
KS ci ratio: 1.288943e-01	ci left: 4.134441e-02	ci right 4.708905e-02	k: 883	n:20000
LPHN2   20000 perm   5 sec   (4130 perm/sec)   p_kst 4.415000e-02   p_cons 7.232000e-01   p_joint 4.845000e-02

Joint ci ratio: 8.887230e-02	ci left: 5.818716e-02	ci right 6.363159e-02	k: 1826	n:30000
Cons ci ratio: 1.410992e-02	ci left: 7.149819e-01	ci right 7.251754e-01	k: 21603	n:30000
KS ci ratio: 1.057862e-01	ci left: 4.144684e-02	ci right 4.610870e-02	k: 1312	n:30000
LPHN2   30000 perm   8 sec   (3978 perm/sec)   p_kst 4.373333e-02   p_cons 7.201000e-01   p_joint 6.086667e-02

Joint ci ratio: 7.701646e-02	ci left: 5.847765e-02	ci right 6.318635e-02	k: 2432	n:40000
Cons ci ratio: 1.226886e-02	ci left: 7.140394e-01	ci right 7.228789e-01	k: 28739	n:40000
KS ci ratio: 9.210094e-02	ci left: 4.132614e-02	ci right 4.534049e-02	k: 1732	n:40000
LPHN2   40000 perm   10 sec   (3875 perm/sec)   p_kst 4.330000e-02   p_cons 7.184750e-01   p_joint 6.080000e-02

Outputting figure to mutsig2_images.part000000000098/LPHN2.3_4288_40000_0.0433_0.71847_0.0608.png
                gene_name: LPHN2
               theta_stop: 0.092 
                    nperm: 40000 
                     p_ks: 0.043 
        ci_ks_bounds_left: 0.041 
       ci_ks_bounds_right: 0.045 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.061 
     ci_joint_bounds_left: 0.058 
    ci_joint_bounds_right: 0.063 

Current progress: 60 percent done.
LRP2
Processing conservation and coverage...
70% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.105514e-02	ci left: 7.678000e-01	ci right 7.842389e-01	k: 7761	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: 1.391793e-02	ci left: 8.817580e-01	ci right 8.942150e-01	k: 8881	n:10000
LRP2   10000 perm   5 sec   (2204 perm/sec)   p_kst 8.881000e-01   p_cons 4.494000e-01   p_joint 7.761000e-01

Outputting figure to mutsig2_images.part000000000098/LRP2.3_14284_10000_0.8881_0.4494_0.7761.png
                gene_name: LRP2
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.78 

Current progress: 80 percent done.
LRIG3
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: 1.410433e-01	ci left: 6.662205e-02	ci right 7.682914e-02	k: 716	n:10000
KS ci ratio: 7.172305e-02	ci left: 2.216827e-01	ci right 2.382749e-01	k: 2299	n:10000
LRIG3   10000 perm   2 sec   (5192 perm/sec)   p_kst 2.299000e-01   p_cons 7.160000e-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: 9.906657e-02	ci left: 6.899234e-02	ci right 7.623250e-02	k: 1451	n:20000
KS ci ratio: 5.050963e-02	ci left: 2.255696e-01	ci right 2.373085e-01	k: 4628	n:20000
LRIG3   20000 perm   4 sec   (4619 perm/sec)   p_kst 2.314000e-01   p_cons 7.255000e-02   p_joint 1

Outputting figure to mutsig2_images.part000000000098/LRIG3.2_3496_20000_0.2314_0.07255_1.png
                gene_name: LRIG3
               theta_stop: 0.099 
                    nperm: 20000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.073 
      ci_cons_bounds_left: 0.069 
     ci_cons_bounds_right: 0.076 
                  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.165.3896/
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/181708/iteration1/scatter.0000000098
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 98 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1648>
Subject: Job 1120051: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000099> was used as the working directory.
Started at Wed Oct 10 10:43:39 2012
Results reported at Wed Oct 10 10:45:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000099.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000099.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 99  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    104.13 sec.
    Max Memory :       613 MB
    Max Swap   :      3452 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.165.3896/
-whichjob
99
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 99: processing genes 8867 - 8957
Calculating significance of each gene.
Using projection method.
8867	LRRC17	1.226063e-01
8868	LRRC18	1
8869	LRRC19	1
8870	LRRC2	1
8871	LRRC20	2.776216e-02
8872	LRRC23	1
8873	LRRC24	1
8874	LRRC25	1
8875	LRRC27	1
8876	LRRC28	1
8877	LRRC29	1
8878	LRRC3	8.041387e-02
8879	LRRC30	1
8880	LRRC31	1
8881	LRRC32	1
8882	LRRC33	1
8883	LRRC34	1
8884	LRRC36	1
8885	LRRC37A2	1
8886	LRRC37A3	1
8887	LRRC37B	1
8888	LRRC39	1
8889	LRRC3B	1
8890	LRRC4	1
8891	LRRC40	1
8892	LRRC41	7.695255e-02
8893	LRRC42	1
8894	LRRC43	1
8895	LRRC45	1
8896	LRRC46	1
8897	LRRC47	3.205640e-02
8898	LRRC48	2.379622e-01
8899	LRRC49	1
8900	LRRC4B	1
8901	LRRC4C	2.707341e-01
8902	LRRC50	1.710834e-01
8903	LRRC52	1
8904	LRRC55	1
8905	LRRC56	1
8906	LRRC57	1
8907	LRRC58	1
8908	LRRC59	1
8909	LRRC6	1.550333e-02
8910	LRRC61	1
8911	LRRC66	1
8912	LRRC67	1
8913	LRRC7	8.888713e-02
8914	LRRC8A	1
8915	LRRC8B	3.521706e-01
8916	LRRC8C	2.182587e-01
8917	LRRC8D	1
8918	LRRC8E	1
8919	LRRCC1	1
8920	LRRFIP1	1
8921	LRRFIP2	1
8922	LRRIQ1	1
8923	LRRIQ3	1
8924	LRRIQ4	1
8925	LRRK1	1
8926	LRRK2	7.441072e-01
8927	LRRN1	6.553227e-02
8928	LRRN2	1
8929	LRRN3	2.826499e-01
8930	LRRN4	2.224015e-01
8931	LRRN4CL	1
8932	LRRTM1	1.441065e-01
8933	LRRTM2	1.026350e-01
8934	LRRTM3	1
8935	LRRTM4	1
8936	LRSAM1	1
8937	LRTM1	1
8938	LRTM2	1
8939	LRTOMT	1
8940	LRWD1	1
8941	LSAMP	1
8942	LSG1	1
8943	LSM1	1
8944	LSM10	1
8945	LSM11	1
8946	LSM12	1
8947	LSM14A	1
8948	LSM14B	1
8949	LSM2	1
8950	LSM3	1
8951	LSM4	1
8952	LSM5	1
8953	LSM6	1
8954	LSM7	1
8955	LSMD1	1
8956	LSP1	1
8957	LSR	1.239102e-01
Done

Running MutSig 2:
Scatter job 99: processing genes 8867 - 8957
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
LRRC6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.091423e-02	ci left: 6.068871e-01	ci right 6.260450e-01	k: 6165	n:10000
Cons ci ratio: 2.589946e-02	ci left: 6.869792e-01	ci right 7.051065e-01	k: 6961	n:10000
KS ci ratio: 5.307046e-02	ci left: 3.435278e-01	ci right 3.623579e-01	k: 3529	n:10000
LRRC6   10000 perm   2 sec   (5523 perm/sec)   p_kst 3.529000e-01   p_cons 6.961000e-01   p_joint 6.165000e-01

Outputting figure to mutsig2_images.part000000000099/LRRC6.2_1449_10000_0.3529_0.6961_0.6165.png
                gene_name: LRRC6
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.34 
       ci_ks_bounds_right: 0.36 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.62 
     ci_joint_bounds_left: 0.61 
    ci_joint_bounds_right: 0.63 

Current progress: 50 percent done.
LRRC7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.564741e-02	ci left: 8.556968e-01	ci right 8.692912e-01	k: 8626	n:10000
Cons ci ratio: 3.215005e-02	ci left: 5.881121e-01	ci right 6.074309e-01	k: 5978	n:10000
KS ci ratio: 1.901106e-02	ci left: 8.017651e-01	ci right 8.172541e-01	k: 8096	n:10000
LRRC7   10000 perm   2 sec   (5201 perm/sec)   p_kst 8.096000e-01   p_cons 5.978000e-01   p_joint 8.626000e-01

Outputting figure to mutsig2_images.part000000000099/LRRC7.2_4714_10000_0.8096_0.5978_0.8626.png
                gene_name: LRRC7
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.81 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

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.165.3896/
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/181708/iteration1/scatter.0000000099
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 99 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120054: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000100> was used as the working directory.
Started at Wed Oct 10 10:43:39 2012
Results reported at Wed Oct 10 10:45:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000100.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000100.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 100  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    126.52 sec.
    Max Memory :      1199 MB
    Max Swap   :      3899 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.165.3896/
-whichjob
100
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 100: processing genes 8958 - 9047
Calculating significance of each gene.
Using projection method.
8958	LSS	1.290130e-01
8959	LST-3TM12	2.689687e-01
8960	LST1	1
8961	LTA	1
8962	LTA4H	1
8963	LTB	1
8964	LTB4R	1
8965	LTB4R2	1
8966	LTBP1	1
8967	LTBP2	1.393529e-01
8968	LTBP3	1
8969	LTBP4	1
8970	LTBR	1
8971	LTC4S	1
8972	LTF	1
8973	LTK	2.837301e-01
8974	LTV1	1
8975	LUC7L	1
8976	LUC7L2	4.648489e-02
8977	LUC7L3	1
8978	LUM	1
8979	LUZP1	1
8980	LUZP2	1
8981	LUZP4	1
8982	LXN	1
8983	LY6D	1
8984	LY6E	1
8985	LY6G5B	1
8986	LY6G5C	1
8987	LY6G6C	1
8988	LY6G6D	1
8989	LY6G6F	3.043423e-02
8990	LY6H	1
8991	LY6K	1
8992	LY75	4.834143e-01
8993	LY86	1
8994	LY9	1
8995	LY96	1
8996	LYAR	1
8997	LYG1	1
8998	LYG2	1
8999	LYN	1
9000/18094 9000	LYNX1	1
9001	LYPD1	1
9002	LYPD2	1
9003	LYPD3	1
9004	LYPD4	1
9005	LYPD5	1.065848e-01
9006	LYPD6	1
9007	LYPD6B	1
9008	LYPLA1	1
9009	LYPLA2	1
9010	LYPLAL1	1
9011	LYRM1	1
9012	LYRM2	1
9013	LYRM4	1
9014	LYRM5	1
9015	LYRM7	1
9016	LYSMD1	1
9017	LYSMD2	1
9018	LYSMD3	1.161869e-01
9019	LYSMD4	1
9020	LYST	5.990534e-01
9021	LYVE1	1
9022	LYZ	1
9023	LYZL1	1
9024	LYZL2	1
9025	LYZL4	1
9026	LYZL6	1
9027	LZIC	1
9028	LZTFL1	1
9029	LZTR1	1
9030	LZTS1	1
9031	LZTS2	1
9032	M6PR	1
9033	MAB21L1	1
9034	MAB21L2	1
9035	MACC1	1
9036	MACF1	1.127857e-01
9037	MACROD1	1
9038	MACROD2	1
9039	MAD1L1	1
9040	MAD2L1	1
9041	MAD2L1BP	1
9042	MAD2L2	1
9043	MADCAM1	3.217613e-02
9044	MADD	1
9045	MAEA	1
9046	MAEL	1
9047	MAF	1
Done

Running MutSig 2:
Scatter job 100: processing genes 8958 - 9047
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MACF1
Processing conservation and coverage...
43% 87% 
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: 1.513557e-02	ci left: 8.635571e-01	ci right 8.768264e-01	k: 8703	n:10000
KS ci ratio: 1.368725e-01	ci left: 7.058968e-02	ci right 8.105902e-02	k: 757	n:10000
MACF1   10000 perm   4 sec   (2337 perm/sec)   p_kst 7.570000e-02   p_cons 8.703000e-01   p_joint 2.088000e-01

Joint ci ratio: 5.073069e-02	ci left: 2.240336e-01	ci right 2.357450e-01	k: 4597	n:20000
Cons ci ratio: 1.072046e-02	ci left: 8.651588e-01	ci right 8.745334e-01	k: 17398	n:20000
KS ci ratio: 9.833821e-02	ci left: 6.996946e-02	ci right 7.725509e-02	k: 1471	n:20000
MACF1   20000 perm   11 sec   (1810 perm/sec)   p_kst 7.355000e-02   p_cons 8.699000e-01   p_joint 2.298500e-01

Outputting figure to mutsig2_images.part000000000100/MACF1.9_22842_20000_0.07355_0.8699_0.22985.png
                gene_name: MACF1
               theta_stop: 0.098 
                    nperm: 20000 
                     p_ks: 0.074 
        ci_ks_bounds_left: 0.070 
       ci_ks_bounds_right: 0.077 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.87 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.24 

Current progress: 50 percent done.
LTBP2
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: 2.012596e-02	ci left: 7.833022e-01	ci right 7.993277e-01	k: 7914	n:10000
KS ci ratio: 4.997652e-02	ci left: 3.712686e-01	ci right 3.904009e-01	k: 3808	n:10000
LTBP2   10000 perm   2 sec   (4998 perm/sec)   p_kst 3.808000e-01   p_cons 7.914000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000100/LTBP2.2_5610_10000_0.3808_0.7914_1.png
                gene_name: LTBP2
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.79 
      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.165.3896/
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/181708/iteration1/scatter.0000000100
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 100 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120061: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000101> was used as the working directory.
Started at Wed Oct 10 10:43:39 2012
Results reported at Wed Oct 10 10:45:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000101.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000101.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 101  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    139.49 sec.
    Max Memory :      1251 MB
    Max Swap   :      3879 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.165.3896/
-whichjob
101
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 101: processing genes 9048 - 9137
Calculating significance of each gene.
Using projection method.
9048	MAF1	1.096013e-02
9049	MAFB	1
9050	MAFF	1
9051	MAFG	1
9052	MAFK	1
9053	MAG	1
9054	MAGEA1	1
9055	MAGEA10	1
9056	MAGEA11	1
9057	MAGEA12	1
9058	MAGEA3	1
9059	MAGEA4	1
9060	MAGEA5	1
9061	MAGEA6	1.058100e-01
9062	MAGEA8	1
9063	MAGEB1	1
9064	MAGEB10	1
9065	MAGEB16	1
9066	MAGEB18	1
9067	MAGEB2	1
9068	MAGEB3	1
9069	MAGEB4	4.530336e-02
9070	MAGEB6	1
9071	MAGEC1	2.232868e-01
9072	MAGEC2	1
9073	MAGEC3	1.108707e-01
9074	MAGED1	1
9075	MAGED2	5.493207e-02
9076	MAGEE1	2.515846e-01
9077	MAGEE2	5.334863e-02
9078	MAGEF1	1
9079	MAGEH1	1
9080	MAGEL2	1
9081	MAGI1	1
9082	MAGI2	7.407548e-02
9083	MAGI3	1
9084	MAGIX	1
9085	MAGOH	5.915352e-02
9086	MAGOHB	1
9087	MAGT1	1
9088	MAK	1
9089	MAK16	1
9090	MAL	1
9091	MAL2	1
9092	MALL	1.822055e-02
9093	MALT1	1.083072e-02
9094	MAMDC2	1
9095	MAMDC4	1
9096	MAML1	1
9097	MAML2	1
9098	MAML3	1.178416e-01
9099	MAMLD1	1
9100	MAMSTR	1
9101	MAN1A1	1
9102	MAN1A2	2.092491e-01
9103	MAN1B1	1
9104	MAN1C1	1
9105	MAN2A1	2.636736e-01
9106	MAN2A2	2.396549e-01
9107	MAN2B1	2.155022e-01
9108	MAN2B2	2.885776e-01
9109	MAN2C1	1
9110	MANBA	2.696975e-01
9111	MANBAL	1
9112	MANEA	1
9113	MANEAL	1
9114	MANF	1
9115	MANSC1	1
9116	MAOA	1
9117	MAOB	1
9118	MAP1A	7.485673e-01
9119	MAP1B	1
9120	MAP1D	1
9121	MAP1LC3A	1
9122	MAP1LC3B	1
9123	MAP1LC3B2	1
9124	MAP1LC3C	1
9125	MAP1S	1
9126	MAP2	6.616564e-01
9127	MAP2K1	3.707653e-02
9128	MAP2K2	1
9129	MAP2K3	1
9130	MAP2K4	1
9131	MAP2K5	1
9132	MAP2K6	1
9133	MAP2K7	1
9134	MAP3K1	5.917840e-02
9135	MAP3K10	1
9136	MAP3K11	1
9137	MAP3K12	1
Done

Running MutSig 2:
Scatter job 101: processing genes 9048 - 9137
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MAGI2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.890521e-02	ci left: 4.938506e-01	ci right 5.135473e-01	k: 5037	n:10000
Cons ci ratio: 1.991394e-01	ci left: 3.357607e-02	ci right 4.109654e-02	k: 372	n:10000
KS ci ratio: 1.140181e-01	ci left: 9.964203e-02	ci right 1.117887e-01	k: 1056	n:10000
MAGI2   10000 perm   2 sec   (4353 perm/sec)   p_kst 1.056000e-01   p_cons 3.720000e-02   p_joint 5.037000e-01

Joint ci ratio: 2.549655e-02	ci left: 5.347139e-01	ci right 5.485740e-01	k: 10833	n:20000
Cons ci ratio: 1.382379e-01	ci left: 3.597246e-02	ci right 4.136272e-02	k: 772	n:20000
KS ci ratio: 8.222091e-02	ci left: 9.783865e-02	ci right 1.062774e-01	k: 2040	n:20000
MAGI2   20000 perm   8 sec   (2494 perm/sec)   p_kst 1.020000e-01   p_cons 3.860000e-02   p_joint 5.416500e-01

Joint ci ratio: 1.049357e-02	ci left: 8.187005e-01	ci right 8.273702e-01	k: 24692	n:30000
Cons ci ratio: 1.137677e-01	ci left: 3.589704e-02	ci right 4.025967e-02	k: 1141	n:30000
KS ci ratio: 6.770759e-02	ci left: 9.708702e-02	ci right 1.039239e-01	k: 3014	n:30000
MAGI2   30000 perm   11 sec   (2797 perm/sec)   p_kst 1.004667e-01   p_cons 3.803333e-02   p_joint 8.230667e-01

Joint ci ratio: 2.260441e-02	ci left: 4.242923e-01	ci right 4.340180e-01	k: 17166	n:40000
Cons ci ratio: 9.858217e-02	ci left: 3.614741e-02	ci right 3.992003e-02	k: 1520	n:40000
KS ci ratio: 5.853960e-02	ci left: 9.784151e-02	ci right 1.037666e-01	k: 4031	n:40000
MAGI2   40000 perm   13 sec   (2965 perm/sec)   p_kst 1.007750e-01   p_cons 3.800000e-02   p_joint 4.291500e-01

Outputting figure to mutsig2_images.part000000000101/MAGI2.2_4456_40000_0.10078_0.038_0.42915.png
                gene_name: MAGI2
               theta_stop: 0.099 
                    nperm: 40000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.098 
       ci_ks_bounds_right: 0.10 
                   p_cons: 0.038 
      ci_cons_bounds_left: 0.036 
     ci_cons_bounds_right: 0.040 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.43 

Current progress: 33 percent done.
MALT1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.466887e-02	ci left: 7.073525e-01	ci right 7.251214e-01	k: 7163	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: 5.536657e-02	ci left: 3.245569e-01	ci right 3.431400e-01	k: 3338	n:10000
MALT1   10000 perm   2 sec   (5644 perm/sec)   p_kst 3.338000e-01   p_cons 1.333000e-01   p_joint 7.163000e-01

Outputting figure to mutsig2_images.part000000000101/MALT1.2_2543_10000_0.3338_0.1333_0.7163.png
                gene_name: MALT1
               theta_stop: 0.100 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.72 
     ci_joint_bounds_left: 0.71 
    ci_joint_bounds_right: 0.73 

Current progress: 67 percent done.
MAP3K1
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: 5.040300e-02	ci left: 3.672894e-01	ci right 3.863825e-01	k: 3768	n:10000
KS ci ratio: 2.011987e-02	ci left: 7.834036e-01	ci right 7.994263e-01	k: 7915	n:10000
MAP3K1   10000 perm   2 sec   (4617 perm/sec)   p_kst 7.915000e-01   p_cons 3.768000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000101/MAP3K1.2_4619_10000_0.7915_0.3768_1.png
                gene_name: MAP3K1
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.80 
                   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.165.3896/
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/181708/iteration1/scatter.0000000101
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 101 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120064: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000102> was used as the working directory.
Started at Wed Oct 10 10:43:39 2012
Results reported at Wed Oct 10 10:46:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000102.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000102.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 102  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    173.47 sec.
    Max Memory :      1414 MB
    Max Swap   :      3792 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.165.3896/
-whichjob
102
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 102: processing genes 9138 - 9228
Calculating significance of each gene.
Using projection method.
9138	MAP3K13	1
9139	MAP3K14	1
9140	MAP3K15	1
9141	MAP3K2	1.114384e-01
9142	MAP3K3	1
9143	MAP3K4	1
9144	MAP3K5	1.156535e-01
9145	MAP3K6	1
9146	MAP3K7	1
9147	MAP3K8	1
9148	MAP3K9	1
9149	MAP4	1
9150	MAP4K1	8.253775e-02
9151	MAP4K2	4.827183e-02
9152	MAP4K3	2.729293e-01
9153	MAP4K4	1
9154	MAP4K5	1
9155	MAP6	2.099054e-01
9156	MAP7	1
9157	MAP7D1	4.017369e-02
9158	MAP7D2	1
9159	MAP7D3	1
9160	MAP9	1
9161	MAPK1	1
9162	MAPK10	1
9163	MAPK11	1
9164	MAPK12	1
9165	MAPK13	1
9166	MAPK14	1
9167	MAPK15	1
9168	MAPK1IP1L	1
9169	MAPK3	1
9170	MAPK4	1
9171	MAPK6	1
9172	MAPK7	1
9173	MAPK8	1.293836e-01
9174	MAPK8IP1	1
9175	MAPK8IP2	1
9176	MAPK8IP3	1.690774e-01
9177	MAPK9	1
9178	MAPKAP1	1
9179	MAPKAPK2	1
9180	MAPKAPK3	1
9181	MAPKAPK5	1
9182	MAPKBP1	5.437163e-01
9183	MAPKSP1	1
9184	MAPRE1	1
9185	MAPRE2	1
9186	MAPRE3	1
9187	MAPT	1
9188	MARCH1	1
9189	MARCH10	1
9190	MARCH11	1.126607e-01
9191	MARCH2	1
9192	MARCH3	1
9193	MARCH4	1
9194	MARCH5	6.850895e-02
9195	MARCH6	6.727219e-02
9196	MARCH7	1
9197	MARCH8	1
9198	MARCH9	1
9199	MARCKS	1
9200	MARCKSL1	1
9201	MARCO	4.324719e-02
9202	MARK1	2.665914e-01
9203	MARK2	1
9204	MARK3	1
9205	MARK4	1
9206	MARS	1
9207	MARS2	1
9208	MARVELD2	4.665675e-02
9209	MARVELD3	1
9210	MAS1	1
9211	MAS1L	1
9212	MASP1	2.540536e-01
9213	MASP2	9.624276e-02
9214	MAST1	1
9215	MAST2	1
9216	MAST3	1
9217	MAST4	1
9218	MASTL	1
9219	MAT1A	1
9220	MAT2A	1
9221	MAT2B	1
9222	MATK	1.114132e-01
9223	MATN1	1
9224	MATN2	2.898697e-01
9225	MATN3	1
9226	MATN4	7.638417e-02
9227	MATR3	1
9228	MAVS	1
Done

Running MutSig 2:
Scatter job 102: processing genes 9138 - 9228
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MAP3K5
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: 1.784267e-02	ci left: 8.208650e-01	ci right 8.357433e-01	k: 8284	n:10000
KS ci ratio: 1.517575e-02	ci left: 8.629443e-01	ci right 8.762395e-01	k: 8697	n:10000
MAP3K5   10000 perm   4 sec   (2669 perm/sec)   p_kst 8.697000e-01   p_cons 8.284000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000102/MAP3K5.2_4245_10000_0.8697_0.8284_1.png
                gene_name: MAP3K5
               theta_stop: 0.018 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.88 
                   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: 20 percent done.
MAP4K2
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: 2.662392e-02	ci left: 6.750875e-01	ci right 6.934051e-01	k: 6843	n:10000
KS ci ratio: 3.151877e-02	ci left: 5.976484e-01	ci right 6.168891e-01	k: 6073	n:10000
MAP4K2   10000 perm   2 sec   (4443 perm/sec)   p_kst 6.073000e-01   p_cons 6.843000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000102/MAP4K2.2_2591_10000_0.6073_0.6843_1.png
                gene_name: MAP4K2
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.68 
      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: 40 percent done.
MAPK8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.647702e-02	ci left: 2.493471e-01	ci right 2.665941e-01	k: 2579	n:10000
Cons ci ratio: 5.681654e-02	ci left: 3.132420e-01	ci right 3.316615e-01	k: 3224	n:10000
KS ci ratio: 9.349504e-02	ci left: 1.424659e-01	ci right 1.565389e-01	k: 1494	n:10000
MAPK8   10000 perm   2 sec   (6351 perm/sec)   p_kst 1.494000e-01   p_cons 3.224000e-01   p_joint 2.579000e-01

Outputting figure to mutsig2_images.part000000000102/MAPK8.2_1409_10000_0.1494_0.3224_0.2579.png
                gene_name: MAPK8
               theta_stop: 0.093 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.26 
     ci_joint_bounds_left: 0.25 
    ci_joint_bounds_right: 0.27 

Current progress: 60 percent done.
MAPK8IP3
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: 2.434149e-02	ci left: 7.128025e-01	ci right 7.304682e-01	k: 7217	n:10000
KS ci ratio: 7.496648e-03	ci left: 9.610001e-01	ci right 9.683260e-01	k: 9648	n:10000
MAPK8IP3   10000 perm   2 sec   (5095 perm/sec)   p_kst 9.648000e-01   p_cons 7.217000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000102/MAPK8IP3.2_4155_10000_0.9648_0.7217_1.png
                gene_name: MAPK8IP3
               theta_stop: 0.024 
                    nperm: 10000 
                     p_ks: 0.96 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   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: 80 percent done.
MARCH6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.389164e-01	ci left: 1.096414e-02	ci right 1.552595e-02	k: 131	n:10000
Cons ci ratio: 4.388548e-02	ci left: 4.339301e-01	ci right 4.535027e-01	k: 4437	n:10000
KS ci ratio: 3.389164e-01	ci left: 1.096414e-02	ci right 1.552595e-02	k: 131	n:10000
MARCH6   10000 perm   2 sec   (5448 perm/sec)   p_kst 1.310000e-02   p_cons 4.437000e-01   p_joint 1.310000e-02

Joint ci ratio: 1.779009e-01	ci left: 2.158850e-02	ci right 2.585152e-02	k: 473	n:20000
Cons ci ratio: 3.096222e-02	ci left: 4.379462e-01	ci right 4.517698e-01	k: 8897	n:20000
KS ci ratio: 2.330359e-01	ci left: 1.232340e-02	ci right 1.562013e-02	k: 278	n:20000
MARCH6   20000 perm   4 sec   (4735 perm/sec)   p_kst 1.390000e-02   p_cons 4.448500e-01   p_joint 2.365000e-02

Joint ci ratio: 1.910866e-01	ci left: 1.251047e-02	ci right 1.518490e-02	k: 414	n:30000
Cons ci ratio: 2.530602e-02	ci left: 4.387328e-01	ci right 4.500113e-01	k: 13331	n:30000
KS ci ratio: 1.910866e-01	ci left: 1.251047e-02	ci right 1.518490e-02	k: 414	n:30000
MARCH6   30000 perm   7 sec   (4109 perm/sec)   p_kst 1.380000e-02   p_cons 4.443667e-01   p_joint 1.380000e-02

Joint ci ratio: 1.666096e-01	ci left: 1.251184e-02	ci right 1.480957e-02	k: 545	n:40000
Cons ci ratio: 2.194225e-02	ci left: 4.388979e-01	ci right 4.486603e-01	k: 17751	n:40000
KS ci ratio: 1.666096e-01	ci left: 1.251184e-02	ci right 1.480957e-02	k: 545	n:40000
MARCH6   40000 perm   10 sec   (4103 perm/sec)   p_kst 1.362500e-02   p_cons 4.437750e-01   p_joint 1.362500e-02

Joint ci ratio: 1.513417e-01	ci left: 1.223721e-02	ci right 1.425989e-02	k: 661	n:50000
Cons ci ratio: 1.966313e-02	ci left: 4.384795e-01	ci right 4.472071e-01	k: 22142	n:50000
KS ci ratio: 1.513417e-01	ci left: 1.223721e-02	ci right 1.425989e-02	k: 661	n:50000
MARCH6   50000 perm   12 sec   (4043 perm/sec)   p_kst 1.322000e-02   p_cons 4.428400e-01   p_joint 1.322000e-02

Joint ci ratio: 1.380149e-01	ci left: 1.235035e-02	ci right 1.419718e-02	k: 795	n:60000
Cons ci ratio: 1.794236e-02	ci left: 4.390698e-01	ci right 4.470357e-01	k: 26583	n:60000
KS ci ratio: 1.380149e-01	ci left: 1.235035e-02	ci right 1.419718e-02	k: 795	n:60000
MARCH6   60000 perm   15 sec   (3972 perm/sec)   p_kst 1.325000e-02   p_cons 4.430500e-01   p_joint 1.325000e-02

Joint ci ratio: 1.279634e-01	ci left: 1.238144e-02	ci right 1.408783e-02	k: 925	n:70000
Cons ci ratio: 1.662374e-02	ci left: 4.390014e-01	ci right 4.463747e-01	k: 30988	n:70000
KS ci ratio: 1.279634e-01	ci left: 1.238144e-02	ci right 1.408783e-02	k: 925	n:70000
MARCH6   70000 perm   18 sec   (3965 perm/sec)   p_kst 1.321429e-02   p_cons 4.426857e-01   p_joint 1.321429e-02

Joint ci ratio: 1.191460e-01	ci left: 1.255401e-02	ci right 1.415657e-02	k: 1067	n:80000
Cons ci ratio: 1.553354e-02	ci left: 4.397660e-01	ci right 4.466631e-01	k: 35457	n:80000
KS ci ratio: 1.191460e-01	ci left: 1.255401e-02	ci right 1.415657e-02	k: 1067	n:80000
MARCH6   80000 perm   20 sec   (3943 perm/sec)   p_kst 1.333750e-02   p_cons 4.432125e-01   p_joint 1.333750e-02

Joint ci ratio: 1.121665e-01	ci left: 1.263736e-02	ci right 1.414980e-02	k: 1204	n:90000
Cons ci ratio: 1.463173e-02	ci left: 4.404172e-01	ci right 4.469198e-01	k: 39930	n:90000
KS ci ratio: 1.121665e-01	ci left: 1.263736e-02	ci right 1.414980e-02	k: 1204	n:90000
MARCH6   90000 perm   23 sec   (3915 perm/sec)   p_kst 1.337778e-02   p_cons 4.436667e-01   p_joint 1.337778e-02

Joint ci ratio: 1.064867e-01	ci left: 1.265755e-02	ci right 1.409088e-02	k: 1336	n:100000
Cons ci ratio: 1.383395e-02	ci left: 4.422562e-01	ci right 4.484270e-01	k: 44534	n:100000
KS ci ratio: 1.064867e-01	ci left: 1.265755e-02	ci right 1.409088e-02	k: 1336	n:100000
MARCH6   100000 perm   26 sec   (3867 perm/sec)   p_kst 1.336000e-02   p_cons 4.453400e-01   p_joint 1.336000e-02

Joint ci ratio: 1.014857e-01	ci left: 1.270224e-02	ci right 1.406905e-02	k: 1471	n:110000
Cons ci ratio: 1.318202e-02	ci left: 4.427051e-01	ci right 4.485886e-01	k: 49021	n:110000
KS ci ratio: 1.014857e-01	ci left: 1.270224e-02	ci right 1.406905e-02	k: 1471	n:110000
MARCH6   110000 perm   30 sec   (3673 perm/sec)   p_kst 1.337273e-02   p_cons 4.456455e-01   p_joint 1.337273e-02

Joint ci ratio: 9.737493e-02	ci left: 1.267573e-02	ci right 1.398128e-02	k: 1598	n:120000
Cons ci ratio: 1.262158e-02	ci left: 4.428017e-01	ci right 4.484343e-01	k: 53474	n:120000
KS ci ratio: 9.737493e-02	ci left: 1.267573e-02	ci right 1.398128e-02	k: 1598	n:120000
MARCH6   120000 perm   35 sec   (3402 perm/sec)   p_kst 1.331667e-02   p_cons 4.456167e-01   p_joint 1.331667e-02

Outputting figure to mutsig2_images.part000000000102/MARCH6.2_2837_120000_0.013317_0.44562_0.013317.png
                gene_name: MARCH6
               theta_stop: 0.097 
                    nperm: 120000 
                     p_ks: 0.013 
        ci_ks_bounds_left: 0.013 
       ci_ks_bounds_right: 0.014 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.45 
                  p_joint: 0.013 
     ci_joint_bounds_left: 0.013 
    ci_joint_bounds_right: 0.014 

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.165.3896/
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/181708/iteration1/scatter.0000000102
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 102 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120068: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000103> was used as the working directory.
Started at Wed Oct 10 10:43:39 2012
Results reported at Wed Oct 10 10:45:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000103.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000103.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 103  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    124.39 sec.
    Max Memory :      1313 MB
    Max Swap   :      3823 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.165.3896/
-whichjob
103
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 103: processing genes 9229 - 9318
Calculating significance of each gene.
Using projection method.
9229	MAX	1
9230	MAZ	1
9231	MB	1
9232	MBD1	1
9233	MBD2	1
9234	MBD3	1
9235	MBD3L1	1
9236	MBD4	1
9237	MBD5	1
9238	MBD6	2.646516e-01
9239	MBIP	1
9240	MBL2	1
9241	MBLAC1	1
9242	MBLAC2	1
9243	MBNL1	8.204446e-02
9244	MBNL2	1
9245	MBNL3	1
9246	MBOAT1	1
9247	MBOAT2	1
9248	MBOAT7	1
9249	MBP	1
9250	MBTD1	1.696743e-01
9251	MBTPS1	6.216399e-02
9252	MBTPS2	1
9253	MC1R	1
9254	MC2R	1
9255	MC3R	1
9256	MC4R	1
9257	MC5R	1
9258	MCAM	1
9259	MCART1	1
9260	MCART2	1
9261	MCART6	1
9262	MCAT	1.540997e-01
9263	MCC	3.514947e-01
9264	MCCC1	1
9265	MCCC2	1.655358e-01
9266	MCCD1	1
9267	MCEE	1
9268	MCF2	1
9269	MCF2L	3.062958e-01
9270	MCF2L2	3.572428e-01
9271	MCFD2	1
9272	MCHR1	1.013857e-01
9273	MCHR2	1
9274	MCL1	1
9275	MCM10	1
9276	MCM2	3.821007e-01
9277	MCM3	1
9278	MCM3AP	1
9279	MCM4	6.646260e-02
9280	MCM5	1
9281	MCM6	1
9282	MCM7	1
9283	MCM8	1
9284	MCM9	1
9285	MCOLN1	1.526619e-01
9286	MCOLN2	1
9287	MCOLN3	1
9288	MCPH1	2.956824e-02
9289	MCRS1	1
9290	MCTP1	1
9291	MCTP2	1
9292	MCTS1	6.584469e-02
9293	MDC1	1
9294	MDFI	1
9295	MDFIC	1
9296	MDGA1	2.319579e-01
9297	MDGA2	1
9298	MDH1	1
9299	MDH1B	1
9300	MDH2	1
9301	MDK	1
9302	MDM1	1
9303	MDM2	1
9304	MDM4	1
9305	MDN1	7.046709e-01
9306	MDP1	1
9307	ME1	9.313852e-02
9308	ME2	7.276060e-02
9309	ME3	2.800426e-01
9310	MEA1	1
9311	MEAF6	1
9312	MECOM	3.537177e-02
9313	MECP2	1
9314	MECR	1
9315	MED1	1
9316	MED10	1
9317	MED11	1
9318	MED12	1.265261e-01
Done

Running MutSig 2:
Scatter job 103: processing genes 9229 - 9318
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MBD6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.625207e-02	ci left: 2.506326e-01	ci right 2.679078e-01	k: 2592	n:10000
Cons ci ratio: 9.487959e-02	ci left: 1.388391e-01	ci right 1.527680e-01	k: 1457	n:10000
KS ci ratio: 6.582365e-02	ci left: 2.531052e-01	ci right 2.704338e-01	k: 2617	n:10000
MBD6   10000 perm   2 sec   (4807 perm/sec)   p_kst 2.617000e-01   p_cons 1.457000e-01   p_joint 2.592000e-01

Outputting figure to mutsig2_images.part000000000103/MBD6.2_3056_10000_0.2617_0.1457_0.2592.png
                gene_name: MBD6
               theta_stop: 0.095 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.15 
                  p_joint: 0.26 
     ci_joint_bounds_left: 0.25 
    ci_joint_bounds_right: 0.27 

Current progress: 14 percent done.
MBTPS1
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: 29 percent done.
MCM4
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: 3.204321e-02	ci left: 5.897180e-01	ci right 6.090241e-01	k: 5994	n:10000
KS ci ratio: 3.797060e-03	ci left: 9.887288e-01	ci right 9.925772e-01	k: 9908	n:10000
MCM4   10000 perm   2 sec   (4923 perm/sec)   p_kst 9.908000e-01   p_cons 5.994000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000103/MCM4.2_2656_10000_0.9908_0.5994_1.png
                gene_name: MCM4
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.99 
        ci_ks_bounds_left: 0.99 
       ci_ks_bounds_right: 0.99 
                   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: 43 percent done.
MCPH1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.415671e-02	ci left: 3.343879e-01	ci right 3.531032e-01	k: 3437	n:10000
Cons ci ratio: 2.703135e-02	ci left: 6.684392e-01	ci right 6.868572e-01	k: 6777	n:10000
KS ci ratio: 7.698126e-02	ci left: 1.979127e-01	ci right 2.138590e-01	k: 2058	n:10000
MCPH1   10000 perm   2 sec   (4651 perm/sec)   p_kst 2.058000e-01   p_cons 6.777000e-01   p_joint 3.437000e-01

Outputting figure to mutsig2_images.part000000000103/MCPH1.2_2572_10000_0.2058_0.6777_0.3437.png
                gene_name: MCPH1
               theta_stop: 0.077 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.34 
     ci_joint_bounds_left: 0.33 
    ci_joint_bounds_right: 0.35 

Current progress: 57 percent done.
MDN1
Processing conservation and coverage...
58% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.495916e-02	ci left: 4.220628e-01	ci right 4.415769e-01	k: 4318	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: 7.228335e-03	ci left: 9.635202e-01	ci right 9.706043e-01	k: 9672	n:10000
MDN1   10000 perm   4 sec   (2681 perm/sec)   p_kst 9.672000e-01   p_cons 4.114000e-01   p_joint 4.318000e-01

Outputting figure to mutsig2_images.part000000000103/MDN1.2_17199_10000_0.9672_0.4114_0.4318.png
                gene_name: MDN1
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 71 percent done.
MECOM
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: 9.874809e-03	ci left: 9.355802e-01	ci right 9.449613e-01	k: 9404	n:10000
KS ci ratio: 1.319350e-02	ci left: 8.922095e-01	ci right 9.041574e-01	k: 8983	n:10000
MECOM   10000 perm   2 sec   (4930 perm/sec)   p_kst 8.983000e-01   p_cons 9.404000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000103/MECOM.2_3798_10000_0.8983_0.9404_1.png
                gene_name: MECOM
               theta_stop: 0.013 
                    nperm: 10000 
                     p_ks: 0.90 
        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: 0.94 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 86 percent done.
MED12
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: 3.669516e-02	ci left: 5.230630e-01	ci right 5.427178e-01	k: 5329	n:10000
KS ci ratio: 4.161190e-02	ci left: 4.602776e-01	ci right 4.799398e-01	k: 4701	n:10000
MED12   10000 perm   2 sec   (4439 perm/sec)   p_kst 4.701000e-01   p_cons 5.329000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000103/MED12.2_6714_10000_0.4701_0.5329_1.png
                gene_name: MED12
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.53 
      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.165.3896/
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/181708/iteration1/scatter.0000000103
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 103 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120071: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000104> was used as the working directory.
Started at Wed Oct 10 10:43:49 2012
Results reported at Wed Oct 10 10:45:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000104.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000104.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 104  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     82.83 sec.
    Max Memory :      1246 MB
    Max Swap   :      3874 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.165.3896/
-whichjob
104
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 104: processing genes 9319 - 9409
Calculating significance of each gene.
Using projection method.
9319	MED12L	5.211405e-01
9320	MED13	6.871873e-01
9321	MED13L	3.628026e-01
9322	MED14	1
9323	MED15	1.489796e-01
9324	MED16	1
9325	MED17	1
9326	MED18	1
9327	MED19	1
9328	MED20	1
9329	MED21	1
9330	MED22	1
9331	MED23	1
9332	MED24	3.197686e-01
9333	MED25	2.088505e-01
9334	MED26	1
9335	MED27	1.427268e-01
9336	MED28	1
9337	MED29	1
9338	MED30	1
9339	MED31	1
9340	MED4	1
9341	MED6	1
9342	MED7	8.661138e-02
9343	MED8	1
9344	MED9	2.361168e-02
9345	MEF2A	1
9346	MEF2B	1
9347	MEF2C	1.251435e-01
9348	MEF2D	1.944824e-01
9349	MEFV	1
9350	MEGF10	3.504769e-01
9351	MEGF11	1
9352	MEGF6	1
9353	MEGF8	3.239146e-01
9354	MEGF9	1
9355	MEI1	2.459951e-01
9356	MEIG1	1
9357	MEIS1	1.097525e-01
9358	MEIS2	1.398457e-01
9359	MEIS3	1
9360	MELK	1
9361	MEMO1	1
9362	MEN1	1
9363	MEOX1	1
9364	MEOX2	1
9365	MEP1A	5.106571e-02
9366	MEP1B	3.113882e-01
9367	MEPCE	1
9368	MEPE	1
9369	MERTK	1
9370	MESDC1	1
9371	MESDC2	7.463289e-02
9372	MESP2	1
9373	MEST	1
9374	MET	1.454372e-01
9375	METAP1	5.422044e-02
9376	METAP2	1
9377	METRN	1
9378	METRNL	1
9379	METT10D	1
9380	METT11D1	1
9381	METT5D1	1
9382	METTL1	1
9383	METTL10	1
9384	METTL11A	1
9385	METTL12	7.672626e-02
9386	METTL13	1
9387	METTL14	1
9388	METTL2A	1
9389	METTL2B	1
9390	METTL3	1
9391	METTL4	2.157890e-01
9392	METTL5	1
9393	METTL6	1
9394	METTL7A	1
9395	METTL7B	1
9396	METTL8	1
9397	METTL9	1
9398	MEX3A	1
9399	MEX3B	1
9400	MEX3C	1
9401	MEX3D	1
9402	MFAP1	1
9403	MFAP2	1
9404	MFAP3	1
9405	MFAP3L	1
9406	MFAP4	1
9407	MFAP5	1
9408	MFF	1
9409	MFGE8	1
Done

Running MutSig 2:
Scatter job 104: processing genes 9319 - 9409
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MERTK
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.982851e-02	ci left: 3.726615e-01	ci right 3.918072e-01	k: 3822	n:10000
Cons ci ratio: 4.261065e-02	ci left: 4.484977e-01	ci right 4.681266e-01	k: 4583	n:10000
KS ci ratio: 6.067200e-02	ci left: 2.854779e-01	ci right 3.034419e-01	k: 2944	n:10000
MERTK   10000 perm   2 sec   (5372 perm/sec)   p_kst 2.944000e-01   p_cons 4.583000e-01   p_joint 3.822000e-01

Outputting figure to mutsig2_images.part000000000104/MERTK.3_3076_10000_0.2944_0.4583_0.3822.png
                gene_name: MERTK
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 25 percent done.
MED13L
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: 1.053537e-01	ci left: 1.151575e-01	ci right 1.280638e-01	k: 1215	n:10000
KS ci ratio: 1.154861e-02	ci left: 9.147155e-01	ci right 9.254382e-01	k: 9202	n:10000
MED13L   10000 perm   2 sec   (4736 perm/sec)   p_kst 9.202000e-01   p_cons 1.215000e-01   p_joint 1

Joint ci ratio: 4.456139e-03	ci left: 9.725847e-01	ci right 9.769758e-01	k: 19497	n:20000
Cons ci ratio: 7.265587e-02	ci left: 1.224148e-01	ci right 1.316940e-01	k: 2540	n:20000
KS ci ratio: 8.169932e-03	ci left: 9.162559e-01	ci right 9.238215e-01	k: 18402	n:20000
MED13L   20000 perm   5 sec   (4259 perm/sec)   p_kst 9.201000e-01   p_cons 1.270000e-01   p_joint 9.748500e-01

Outputting figure to mutsig2_images.part000000000104/MED13L.2_6757_20000_0.9201_0.127_0.97485.png
                gene_name: MED13L
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.92 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.98 

Current progress: 50 percent done.
MEP1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.442662e-02	ci left: 5.547144e-01	ci right 5.742480e-01	k: 5645	n:10000
Cons ci ratio: 1.445804e-02	ci left: 8.737768e-01	ci right 8.866008e-01	k: 8803	n:10000
KS ci ratio: 5.058591e-02	ci left: 3.655984e-01	ci right 3.846744e-01	k: 3751	n:10000
MEP1A   10000 perm   2 sec   (5966 perm/sec)   p_kst 3.751000e-01   p_cons 8.803000e-01   p_joint 5.645000e-01

Outputting figure to mutsig2_images.part000000000104/MEP1A.2_2297_10000_0.3751_0.8803_0.5645.png
                gene_name: MEP1A
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.56 
     ci_joint_bounds_left: 0.55 
    ci_joint_bounds_right: 0.57 

Current progress: 75 percent done.
MET
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.133002e-01	ci left: 1.008116e-01	ci right 1.130184e-01	k: 1068	n:10000
Cons ci ratio: 1.231710e-02	ci left: 9.044264e-01	ci right 9.157334e-01	k: 9102	n:10000
KS ci ratio: 1.615502e-01	ci left: 5.109258e-02	ci right 6.016847e-02	k: 555	n:10000
MET   10000 perm   2 sec   (5498 perm/sec)   p_kst 5.550000e-02   p_cons 9.102000e-01   p_joint 1.068000e-01

Joint ci ratio: 8.485175e-03	ci left: 9.103861e-01	ci right 9.181930e-01	k: 18287	n:20000
Cons ci ratio: 8.638583e-03	ci left: 9.074787e-01	ci right 9.154012e-01	k: 18230	n:20000
KS ci ratio: 1.153940e-01	ci left: 5.139392e-02	ci right 5.773637e-02	k: 1090	n:20000
MET   20000 perm   4 sec   (4910 perm/sec)   p_kst 5.450000e-02   p_cons 9.115000e-01   p_joint 9.143500e-01

Joint ci ratio: 8.730545e-02	ci left: 6.021111e-02	ci right 6.574056e-02	k: 1888	n:30000
Cons ci ratio: 6.994526e-03	ci left: 9.095846e-01	ci right 9.160019e-01	k: 27385	n:30000
KS ci ratio: 9.512983e-02	ci left: 5.101286e-02	ci right 5.614069e-02	k: 1606	n:30000
MET   30000 perm   6 sec   (4699 perm/sec)   p_kst 5.353333e-02   p_cons 9.128333e-01   p_joint 6.293333e-02

Outputting figure to mutsig2_images.part000000000104/MET.2_4307_30000_0.053533_0.91283_0.062933.png
                gene_name: MET
               theta_stop: 0.095 
                    nperm: 30000 
                     p_ks: 0.054 
        ci_ks_bounds_left: 0.051 
       ci_ks_bounds_right: 0.056 
                   p_cons: 0.91 
      ci_cons_bounds_left: 0.91 
     ci_cons_bounds_right: 0.92 
                  p_joint: 0.063 
     ci_joint_bounds_left: 0.060 
    ci_joint_bounds_right: 0.066 

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.165.3896/
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/181708/iteration1/scatter.0000000104
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 104 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120074: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000105> was used as the working directory.
Started at Wed Oct 10 10:43:49 2012
Results reported at Wed Oct 10 10:48:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000105.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000105.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 105  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    285.40 sec.
    Max Memory :      1278 MB
    Max Swap   :      3920 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.165.3896/
-whichjob
105
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 105: processing genes 9410 - 9499
Calculating significance of each gene.
Using projection method.
9410	MFHAS1	1
9411	MFI2	1
9412	MFN1	2.053593e-01
9413	MFN2	1
9414	MFNG	1
9415	MFRP	2.290064e-01
9416	MFSD1	1
9417	MFSD10	1
9418	MFSD11	1
9419	MFSD2A	1
9420	MFSD2B	1
9421	MFSD3	1
9422	MFSD4	1
9423	MFSD5	1.380771e-01
9424	MFSD6	1
9425	MFSD6L	1
9426	MFSD7	1.219586e-01
9427	MFSD8	1
9428	MFSD9	1
9429	MGA	3.369813e-01
9430	MGAM	1
9431	MGAT1	1
9432	MGAT2	1
9433	MGAT3	1
9434	MGAT4A	1
9435	MGAT4B	1
9436	MGAT4C	1
9437	MGAT5	1
9438	MGAT5B	2.353606e-01
9439	MGC26647	1
9440	MGC29506	1
9441	MGC42105	1
9442	MGC70857	2.555628e-02
9443	MGC87042	1
9444	MGEA5	1.109110e-01
9445	MGLL	1
9446	MGMT	6.803859e-02
9447	MGP	9.779461e-03
9448	MGRN1	1
9449	MGST1	1
9450	MGST2	1
9451	MGST3	1
9452	MIA	1
9453	MIA2	1
9454	MIA3	5.072035e-01
9455	MIB1	1
9456	MIB2	1
9457	MICA	1
9458	MICAL1	3.696591e-01
9459	MICAL2	8.862520e-02
9460	MICAL3	3.779979e-01
9461	MICALCL	1
9462	MICALL1	1
9463	MICALL2	1
9464	MICB	1
9465	MID1	1
9466	MID1IP1	1
9467	MID2	1
9468	MIDN	1
9469	MIER1	1.740120e-01
9470	MIER2	1
9471	MIER3	5.144541e-02
9472	MIF	1
9473	MIF4GD	1
9474	MIIP	1
9475	MINA	1
9476	MINK1	1
9477	MINPP1	1.462430e-01
9478	MIOS	3.190881e-01
9479	MIOX	1
9480	MIP	1.303812e-01
9481	MIPEP	1
9482	MIPOL1	3.982885e-02
9483	MIS12	1
9484	MITD1	1
9485	MITF	1
9486	MIXL1	1
9487	MKI67	4.031717e-01
9488	MKI67IP	1.132436e-01
9489	MKKS	1
9490	MKL1	3.701251e-01
9491	MKL2	3.587971e-01
9492	MKLN1	1
9493	MKNK1	1
9494	MKNK2	1
9495	MKRN1	1
9496	MKRN2	1
9497	MKRN3	1.588972e-01
9498	MKS1	1
9499	MKX	1
Done

Running MutSig 2:
Scatter job 105: processing genes 9410 - 9499
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MICAL2
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: 3.592106e-02	ci left: 5.336759e-01	ci right 5.532988e-01	k: 5435	n:10000
KS ci ratio: 3.541838e-01	ci left: 9.958933e-03	ci right 1.433217e-02	k: 120	n:10000
MICAL2   10000 perm   2 sec   (4955 perm/sec)   p_kst 1.200000e-02   p_cons 5.435000e-01   p_joint 1.360000e-02

Joint ci ratio: 1.071685e-01	ci left: 5.933027e-02	ci right 6.609755e-02	k: 1253	n:20000
Cons ci ratio: 2.524344e-02	ci left: 5.396693e-01	ci right 5.535172e-01	k: 10932	n:20000
KS ci ratio: 2.382876e-01	ci left: 1.175842e-02	ci right 1.498535e-02	k: 266	n:20000
MICAL2   20000 perm   7 sec   (3025 perm/sec)   p_kst 1.330000e-02   p_cons 5.466000e-01   p_joint 6.265000e-02

Joint ci ratio: 1.232207e-01	ci left: 3.061915e-02	ci right 3.467202e-02	k: 978	n:30000
Cons ci ratio: 2.022645e-02	ci left: 5.502891e-01	ci right 5.615668e-01	k: 16678	n:30000
KS ci ratio: 1.937065e-01	ci left: 1.216125e-02	ci right 1.480087e-02	k: 403	n:30000
MICAL2   30000 perm   9 sec   (3326 perm/sec)   p_kst 1.343333e-02   p_cons 5.559333e-01   p_joint 3.260000e-02

Joint ci ratio: 1.215923e-01	ci left: 2.378312e-02	ci right 2.688631e-02	k: 1012	n:40000
Cons ci ratio: 1.749140e-02	ci left: 5.517652e-01	ci right 5.615266e-01	k: 22266	n:40000
KS ci ratio: 1.666096e-01	ci left: 1.251184e-02	ci right 1.480957e-02	k: 545	n:40000
MICAL2   40000 perm   11 sec   (3505 perm/sec)   p_kst 1.362500e-02   p_cons 5.566500e-01   p_joint 2.530000e-02

Joint ci ratio: 9.824089e-02	ci left: 2.934192e-02	ci right 3.239287e-02	k: 1542	n:50000
Cons ci ratio: 1.610498e-02	ci left: 5.379207e-01	ci right 5.466743e-01	k: 27115	n:50000
KS ci ratio: 1.483061e-01	ci left: 1.275721e-02	ci right 1.481980e-02	k: 688	n:50000
MICAL2   50000 perm   14 sec   (3598 perm/sec)   p_kst 1.376000e-02   p_cons 5.423000e-01   p_joint 3.084000e-02

Joint ci ratio: 1.323187e-01	ci left: 1.346197e-02	ci right 1.538542e-02	k: 864	n:60000
Cons ci ratio: 1.471566e-02	ci left: 5.378363e-01	ci right 5.458263e-01	k: 32510	n:60000
KS ci ratio: 1.362054e-01	ci left: 1.268849e-02	ci right 1.455899e-02	k: 816	n:60000
MICAL2   60000 perm   16 sec   (3645 perm/sec)   p_kst 1.360000e-02   p_cons 5.418333e-01   p_joint 1.440000e-02

Joint ci ratio: 9.127709e-02	ci left: 2.449842e-02	ci right 2.685541e-02	k: 1796	n:70000
Cons ci ratio: 1.327322e-02	ci left: 5.510661e-01	ci right 5.584437e-01	k: 38833	n:70000
KS ci ratio: 1.249876e-01	ci left: 1.299037e-02	ci right 1.473598e-02	k: 969	n:70000
MICAL2   70000 perm   19 sec   (3655 perm/sec)   p_kst 1.384286e-02   p_cons 5.547571e-01   p_joint 2.565714e-02

Joint ci ratio: 1.312628e-01	ci left: 1.030085e-02	ci right 1.175993e-02	k: 881	n:80000
Cons ci ratio: 1.243786e-02	ci left: 5.504348e-01	ci right 5.573363e-01	k: 44311	n:80000
KS ci ratio: 1.171605e-01	ci left: 1.299088e-02	ci right 1.461966e-02	k: 1103	n:80000
MICAL2   80000 perm   22 sec   (3655 perm/sec)   p_kst 1.378750e-02   p_cons 5.538875e-01   p_joint 1.101250e-02

Joint ci ratio: 1.121194e-01	ci left: 1.264817e-02	ci right 1.416122e-02	k: 1205	n:90000
Cons ci ratio: 1.174102e-02	ci left: 5.500225e-01	ci right 5.565296e-01	k: 49795	n:90000
KS ci ratio: 1.109594e-01	ci left: 1.291829e-02	ci right 1.444662e-02	k: 1230	n:90000
MICAL2   90000 perm   25 sec   (3647 perm/sec)   p_kst 1.366667e-02   p_cons 5.532778e-01   p_joint 1.338889e-02

Joint ci ratio: 1.052567e-01	ci left: 1.295945e-02	ci right 1.440896e-02	k: 1367	n:100000
Cons ci ratio: 1.140669e-02	ci left: 5.383955e-01	ci right 5.445820e-01	k: 54149	n:100000
KS ci ratio: 1.058070e-01	ci left: 1.282309e-02	ci right 1.426533e-02	k: 1353	n:100000
MICAL2   100000 perm   28 sec   (3630 perm/sec)   p_kst 1.353000e-02   p_cons 5.414900e-01   p_joint 1.367000e-02

Joint ci ratio: 9.383273e-02	ci left: 1.488481e-02	ci right 1.635907e-02	k: 1717	n:110000
Cons ci ratio: 1.087146e-02	ci left: 5.387408e-01	ci right 5.446388e-01	k: 59586	n:110000
KS ci ratio: 9.984834e-02	ci left: 1.312776e-02	ci right 1.451623e-02	k: 1519	n:110000
MICAL2   110000 perm   30 sec   (3608 perm/sec)   p_kst 1.380909e-02   p_cons 5.416909e-01   p_joint 1.560909e-02

Outputting figure to mutsig2_images.part000000000105/MICAL2.3_3475_110000_0.013809_0.54169_0.015609.png
                gene_name: MICAL2
               theta_stop: 0.100 
                    nperm: 110000 
                     p_ks: 0.014 
        ci_ks_bounds_left: 0.013 
       ci_ks_bounds_right: 0.015 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.016 
     ci_joint_bounds_left: 0.015 
    ci_joint_bounds_right: 0.016 

Current progress: 25 percent done.
MGA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.247955e-01	ci left: 8.416945e-02	ci right 9.547082e-02	k: 897	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: 2.006502e-02	ci left: 7.843160e-01	ci right 8.003134e-01	k: 7924	n:10000
MGA   10000 perm   2 sec   (4109 perm/sec)   p_kst 7.924000e-01   p_cons 2.500000e-03   p_joint 8.970000e-02

Joint ci ratio: 1.212672e-01	ci left: 4.663162e-02	ci right 5.270016e-02	k: 992	n:20000
Cons ci ratio: 4.373811e-01	ci left: 3.128462e-03	ci right 4.920482e-03	k: 79	n:20000
KS ci ratio: 1.417929e-02	ci left: 7.869136e-01	ci right 7.982012e-01	k: 15852	n:20000
MGA   20000 perm   5 sec   (3735 perm/sec)   p_kst 7.926000e-01   p_cons 3.950000e-03   p_joint 4.960000e-02

Joint ci ratio: 1.611854e-01	ci left: 1.777321e-02	ci right 2.092085e-02	k: 579	n:30000
Cons ci ratio: 3.713748e-01	ci left: 3.014489e-03	ci right 4.417661e-03	k: 110	n:30000
KS ci ratio: 1.172853e-02	ci left: 7.836328e-01	ci right 7.929113e-01	k: 23649	n:30000
MGA   30000 perm   8 sec   (3589 perm/sec)   p_kst 7.883000e-01   p_cons 3.666667e-03   p_joint 1.930000e-02

Joint ci ratio: 1.105968e-01	ci left: 2.876350e-02	ci right 3.215512e-02	k: 1217	n:40000
Cons ci ratio: 3.216214e-01	ci left: 3.105786e-03	ci right 4.318021e-03	k: 147	n:40000
KS ci ratio: 1.022333e-02	ci left: 7.820735e-01	ci right 7.901349e-01	k: 31445	n:40000
MGA   40000 perm   11 sec   (3496 perm/sec)   p_kst 7.861250e-01   p_cons 3.675000e-03   p_joint 3.042500e-02

Joint ci ratio: 1.025744e-01	ci left: 2.692241e-02	ci right 2.985269e-02	k: 1418	n:50000
Cons ci ratio: 2.853546e-01	ci left: 3.223947e-03	ci right 4.314914e-03	k: 187	n:50000
KS ci ratio: 9.130012e-03	ci left: 7.830225e-01	ci right 7.902242e-01	k: 39332	n:50000
MGA   50000 perm   15 sec   (3424 perm/sec)   p_kst 7.866400e-01   p_cons 3.740000e-03   p_joint 2.836000e-02

Joint ci ratio: 2.354110e-01	ci left: 4.058617e-03	ci right 5.156815e-03	k: 275	n:60000
Cons ci ratio: 2.585439e-01	ci left: 3.323490e-03	ci right 4.325446e-03	k: 228	n:60000
KS ci ratio: 8.311091e-03	ci left: 7.842884e-01	ci right 7.908505e-01	k: 47255	n:60000
MGA   60000 perm   18 sec   (3358 perm/sec)   p_kst 7.875833e-01   p_cons 3.800000e-03   p_joint 4.583333e-03

Joint ci ratio: 2.166010e-01	ci left: 4.152744e-03	ci right 5.174697e-03	k: 325	n:70000
Cons ci ratio: 2.359184e-01	ci left: 3.465243e-03	ci right 4.405185e-03	k: 274	n:70000
KS ci ratio: 7.680389e-03	ci left: 7.851542e-01	ci right 7.912219e-01	k: 55174	n:70000
MGA   70000 perm   21 sec   (3300 perm/sec)   p_kst 7.882000e-01   p_cons 3.914286e-03   p_joint 4.642857e-03

Joint ci ratio: 1.992992e-01	ci left: 4.332844e-03	ci right 5.303603e-03	k: 384	n:80000
Cons ci ratio: 2.176725e-01	ci left: 3.598075e-03	ci right 4.488484e-03	k: 322	n:80000
KS ci ratio: 7.189991e-03	ci left: 7.850883e-01	ci right 7.907658e-01	k: 63035	n:80000
MGA   80000 perm   25 sec   (3228 perm/sec)   p_kst 7.879375e-01   p_cons 4.025000e-03   p_joint 4.800000e-03

Joint ci ratio: 1.849476e-01	ci left: 4.507247e-03	ci right 5.436212e-03	k: 446	n:90000
Cons ci ratio: 2.039248e-01	ci left: 3.671932e-03	ci right 4.516081e-03	k: 367	n:90000
KS ci ratio: 6.779998e-03	ci left: 7.851921e-01	ci right 7.905449e-01	k: 70909	n:90000
MGA   90000 perm   28 sec   (3184 perm/sec)   p_kst 7.878778e-01   p_cons 4.077778e-03   p_joint 4.955556e-03

Joint ci ratio: 1.731365e-01	ci left: 4.658344e-03	ci right 5.550732e-03	k: 509	n:100000
Cons ci ratio: 1.917927e-01	ci left: 3.760994e-03	ci right 4.568183e-03	k: 415	n:100000
KS ci ratio: 6.438953e-03	ci left: 7.849713e-01	ci right 7.900520e-01	k: 78752	n:100000
MGA   100000 perm   32 sec   (3141 perm/sec)   p_kst 7.875200e-01   p_cons 4.150000e-03   p_joint 5.090000e-03

Joint ci ratio: 1.671891e-01	ci left: 4.556878e-03	ci right 5.396821e-03	k: 546	n:110000
Cons ci ratio: 1.842060e-01	ci left: 3.722289e-03	ci right 4.486040e-03	k: 450	n:110000
KS ci ratio: 6.126323e-03	ci left: 7.858007e-01	ci right 7.906386e-01	k: 86705	n:110000
MGA   110000 perm   35 sec   (3101 perm/sec)   p_kst 7.882273e-01   p_cons 4.090909e-03   p_joint 4.963636e-03

Joint ci ratio: 1.599001e-01	ci left: 4.584755e-03	ci right 5.389454e-03	k: 597	n:120000
Cons ci ratio: 1.756483e-01	ci left: 3.770224e-03	ci right 4.504058e-03	k: 495	n:120000
KS ci ratio: 5.859397e-03	ci left: 7.862536e-01	ci right 7.908824e-01	k: 94629	n:120000
MGA   120000 perm   39 sec   (3062 perm/sec)   p_kst 7.885750e-01   p_cons 4.125000e-03   p_joint 4.975000e-03

Joint ci ratio: 1.533696e-01	ci left: 4.616413e-03	ci right 5.390536e-03	k: 649	n:130000
Cons ci ratio: 1.683386e-01	ci left: 3.804108e-03	ci right 4.510599e-03	k: 539	n:130000
KS ci ratio: 5.637284e-03	ci left: 7.858838e-01	ci right 7.903342e-01	k: 102455	n:130000
MGA   130000 perm   43 sec   (3012 perm/sec)   p_kst 7.881154e-01   p_cons 4.146154e-03   p_joint 4.992308e-03

Joint ci ratio: 1.470535e-01	ci left: 4.678524e-03	ci right 5.427915e-03	k: 706	n:140000
Cons ci ratio: 1.614556e-01	ci left: 3.854258e-03	ci right 4.537956e-03	k: 586	n:140000
KS ci ratio: 5.435609e-03	ci left: 7.857563e-01	ci right 7.900461e-01	k: 110307	n:140000
MGA   140000 perm   47 sec   (2968 perm/sec)   p_kst 7.879071e-01   p_cons 4.185714e-03   p_joint 5.042857e-03

Joint ci ratio: 1.408116e-01	ci left: 4.777946e-03	ci right 5.508050e-03	k: 770	n:150000
Cons ci ratio: 1.551077e-01	ci left: 3.911048e-03	ci right 4.575007e-03	k: 635	n:150000
KS ci ratio: 5.250152e-03	ci left: 7.859026e-01	ci right 7.900462e-01	k: 118197	n:150000
MGA   150000 perm   51 sec   (2925 perm/sec)   p_kst 7.879800e-01   p_cons 4.233333e-03   p_joint 5.133333e-03

Joint ci ratio: 1.368766e-01	ci left: 4.750800e-03	ci right 5.454816e-03	k: 815	n:160000
Cons ci ratio: 1.513519e-01	ci left: 3.858931e-03	ci right 4.496742e-03	k: 667	n:160000
KS ci ratio: 5.083609e-03	ci left: 7.859576e-01	ci right 7.899695e-01	k: 126075	n:160000
MGA   160000 perm   55 sec   (2893 perm/sec)   p_kst 7.879687e-01   p_cons 4.168750e-03   p_joint 5.093750e-03

Joint ci ratio: 1.329441e-01	ci left: 4.749849e-03	ci right 5.431903e-03	k: 864	n:170000
Cons ci ratio: 1.470151e-01	ci left: 3.858447e-03	ci right 4.476298e-03	k: 707	n:170000
KS ci ratio: 4.937006e-03	ci left: 7.856656e-01	ci right 7.895599e-01	k: 133895	n:170000
MGA   170000 perm   59 sec   (2860 perm/sec)   p_kst 7.876176e-01   p_cons 4.158824e-03   p_joint 5.082353e-03

Joint ci ratio: 1.289075e-01	ci left: 4.781522e-03	ci right 5.445682e-03	k: 919	n:180000
Cons ci ratio: 1.428393e-01	ci left: 3.868963e-03	ci right 4.469401e-03	k: 749	n:180000
KS ci ratio: 4.794894e-03	ci left: 7.859316e-01	ci right 7.897146e-01	k: 141809	n:180000
MGA   180000 perm   64 sec   (2828 perm/sec)   p_kst 7.878278e-01   p_cons 4.161111e-03   p_joint 5.105556e-03

Joint ci ratio: 1.256719e-01	ci left: 4.774449e-03	ci right 5.419740e-03	k: 967	n:190000
Cons ci ratio: 1.393540e-01	ci left: 3.858272e-03	ci right 4.441227e-03	k: 787	n:190000
KS ci ratio: 4.665484e-03	ci left: 7.860918e-01	ci right 7.897731e-01	k: 149708	n:190000
MGA   190000 perm   68 sec   (2797 perm/sec)   p_kst 7.879368e-01   p_cons 4.142105e-03   p_joint 5.089474e-03

Joint ci ratio: 1.221857e-01	ci left: 4.807052e-03	ci right 5.437423e-03	k: 1023	n:200000
Cons ci ratio: 1.354549e-01	ci left: 3.887457e-03	ci right 4.457062e-03	k: 833	n:200000
KS ci ratio: 4.547784e-03	ci left: 7.861068e-01	ci right 7.896949e-01	k: 157581	n:200000
MGA   200000 perm   72 sec   (2766 perm/sec)   p_kst 7.879050e-01   p_cons 4.165000e-03   p_joint 5.115000e-03

Joint ci ratio: 1.194198e-01	ci left: 4.799808e-03	ci right 5.413974e-03	k: 1071	n:210000
Cons ci ratio: 1.325481e-01	ci left: 3.872622e-03	ci right 4.426917e-03	k: 870	n:210000
KS ci ratio: 4.437048e-03	ci left: 7.862360e-01	ci right 7.897370e-01	k: 165478	n:210000
MGA   210000 perm   77 sec   (2737 perm/sec)   p_kst 7.879905e-01   p_cons 4.142857e-03   p_joint 5.100000e-03

Joint ci ratio: 1.170439e-01	ci left: 4.775717e-03	ci right 5.373801e-03	k: 1115	n:220000
Cons ci ratio: 1.295346e-01	ci left: 3.876848e-03	ci right 4.418163e-03	k: 911	n:220000
KS ci ratio: 4.334083e-03	ci left: 7.863498e-01	ci right 7.897698e-01	k: 173374	n:220000
MGA   220000 perm   81 sec   (2705 perm/sec)   p_kst 7.880636e-01   p_cons 4.140909e-03   p_joint 5.068182e-03

Joint ci ratio: 1.176944e-01	ci left: 4.517399e-03	ci right 5.086495e-03	k: 1103	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: 4.237804e-03	ci left: 7.864677e-01	ci right 7.898120e-01	k: 181273	n:230000
MGA   230000 perm   86 sec   (2676 perm/sec)   p_kst 7.881435e-01   p_cons 4.182609e-03   p_joint 4.795652e-03

Joint ci ratio: 1.156712e-01	ci left: 4.486927e-03	ci right 5.041804e-03	k: 1142	n:240000
Cons ci ratio: 1.237647e-01	ci left: 3.904801e-03	ci right 4.423953e-03	k: 998	n:240000
KS ci ratio: 4.152015e-03	ci left: 7.862255e-01	ci right 7.895009e-01	k: 189088	n:240000
MGA   240000 perm   91 sec   (2647 perm/sec)   p_kst 7.878667e-01   p_cons 4.158333e-03   p_joint 4.758333e-03

Joint ci ratio: 1.137489e-01	ci left: 4.458970e-03	ci right 5.000610e-03	k: 1181	n:250000
Cons ci ratio: 1.216536e-01	ci left: 3.884309e-03	ci right 4.391293e-03	k: 1033	n:250000
KS ci ratio: 4.067040e-03	ci left: 7.863484e-01	ci right 7.895569e-01	k: 196989	n:250000
MGA   250000 perm   95 sec   (2619 perm/sec)   p_kst 7.879560e-01   p_cons 4.132000e-03   p_joint 4.724000e-03

Joint ci ratio: 1.116441e-01	ci left: 4.455669e-03	ci right 4.986233e-03	k: 1226	n:260000
Cons ci ratio: 1.194228e-01	ci left: 3.880389e-03	ci right 4.376919e-03	k: 1072	n:260000
KS ci ratio: 3.984460e-03	ci left: 7.866822e-01	ci right 7.898268e-01	k: 204947	n:260000
MGA   260000 perm   100 sec   (2591 perm/sec)   p_kst 7.882577e-01   p_cons 4.123077e-03   p_joint 4.715385e-03

Joint ci ratio: 1.100000e-01	ci left: 4.423879e-03	ci right 4.942397e-03	k: 1263	n:270000
Cons ci ratio: 1.178437e-01	ci left: 3.840886e-03	ci right 4.325410e-03	k: 1101	n:270000
KS ci ratio: 3.910393e-03	ci left: 7.866762e-01	ci right 7.897621e-01	k: 212820	n:270000
MGA   270000 perm   105 sec   (2564 perm/sec)   p_kst 7.882222e-01   p_cons 4.077778e-03   p_joint 4.677778e-03

Joint ci ratio: 1.076396e-01	ci left: 4.460444e-03	ci right 4.971319e-03	k: 1319	n:280000
Cons ci ratio: 1.151557e-01	ci left: 3.884020e-03	ci right 4.362048e-03	k: 1153	n:280000
KS ci ratio: 3.835666e-03	ci left: 7.870757e-01	ci right 7.901040e-01	k: 220806	n:280000
MGA   280000 perm   110 sec   (2538 perm/sec)   p_kst 7.885929e-01   p_cons 4.117857e-03   p_joint 4.710714e-03

Joint ci ratio: 1.055406e-01	ci left: 4.484525e-03	ci right 4.987520e-03	k: 1372	n:290000
Cons ci ratio: 1.132106e-01	ci left: 3.884079e-03	ci right 4.353502e-03	k: 1193	n:290000
KS ci ratio: 3.770510e-03	ci left: 7.869642e-01	ci right 7.899404e-01	k: 228652	n:290000
MGA   290000 perm   115 sec   (2512 perm/sec)   p_kst 7.884552e-01   p_cons 4.113793e-03   p_joint 4.731034e-03

Joint ci ratio: 1.034505e-01	ci left: 4.516833e-03	ci right 5.012808e-03	k: 1428	n:300000
Cons ci ratio: 1.111801e-01	ci left: 3.897162e-03	ci right 4.359164e-03	k: 1237	n:300000
KS ci ratio: 3.706860e-03	ci left: 7.870142e-01	ci right 7.899402e-01	k: 236544	n:300000
MGA   300000 perm   121 sec   (2485 perm/sec)   p_kst 7.884800e-01   p_cons 4.123333e-03   p_joint 4.760000e-03

Joint ci ratio: 1.017209e-01	ci left: 4.525138e-03	ci right 5.013223e-03	k: 1477	n:310000
Cons ci ratio: 1.092979e-01	ci left: 3.906333e-03	ci right 4.361078e-03	k: 1280	n:310000
KS ci ratio: 3.649219e-03	ci left: 7.867962e-01	ci right 7.896758e-01	k: 244354	n:310000
MGA   310000 perm   126 sec   (2456 perm/sec)   p_kst 7.882387e-01   p_cons 4.129032e-03   p_joint 4.764516e-03

Joint ci ratio: 1.005062e-01	ci left: 4.493379e-03	ci right 4.971908e-03	k: 1513	n:320000
Cons ci ratio: 1.078769e-01	ci left: 3.887623e-03	ci right 4.333931e-03	k: 1314	n:320000
KS ci ratio: 3.593038e-03	ci left: 7.866987e-01	ci right 7.895335e-01	k: 252198	n:320000
MGA   320000 perm   132 sec   (2432 perm/sec)   p_kst 7.881187e-01   p_cons 4.106250e-03   p_joint 4.728125e-03

Joint ci ratio: 9.866454e-02	ci left: 4.525645e-03	ci right 4.998268e-03	k: 1570	n:330000
Cons ci ratio: 1.058812e-01	ci left: 3.917284e-03	ci right 4.358160e-03	k: 1364	n:330000
KS ci ratio: 3.537383e-03	ci left: 7.867959e-01	ci right 7.895870e-01	k: 260104	n:330000
MGA   330000 perm   137 sec   (2408 perm/sec)   p_kst 7.881939e-01   p_cons 4.133333e-03   p_joint 4.757576e-03

Joint ci ratio: 9.698045e-02	ci left: 4.550348e-03	ci right 5.016978e-03	k: 1625	n:340000
Cons ci ratio: 1.036619e-01	ci left: 3.971058e-03	ci right 4.408047e-03	k: 1423	n:340000
KS ci ratio: 3.483713e-03	ci left: 7.869377e-01	ci right 7.896868e-01	k: 268027	n:340000
MGA   340000 perm   143 sec   (2386 perm/sec)   p_kst 7.883147e-01   p_cons 4.185294e-03   p_joint 4.779412e-03

Joint ci ratio: 9.518082e-02	ci left: 4.593229e-03	ci right 5.055028e-03	k: 1687	n:350000
Cons ci ratio: 1.016453e-01	ci left: 4.016280e-03	ci right 4.449135e-03	k: 1480	n:350000
KS ci ratio: 3.432826e-03	ci left: 7.870316e-01	ci right 7.897408e-01	k: 275936	n:350000
MGA   350000 perm   148 sec   (2364 perm/sec)   p_kst 7.883886e-01   p_cons 4.228571e-03   p_joint 4.820000e-03

Joint ci ratio: 9.372024e-02	ci left: 4.609386e-03	ci right 5.065308e-03	k: 1740	n:360000
Cons ci ratio: 1.001679e-01	ci left: 4.023855e-03	ci right 4.450853e-03	k: 1524	n:360000
KS ci ratio: 3.387232e-03	ci left: 7.868115e-01	ci right 7.894839e-01	k: 283734	n:360000
MGA   360000 perm   154 sec   (2341 perm/sec)   p_kst 7.881500e-01   p_cons 4.233333e-03   p_joint 4.833333e-03

Joint ci ratio: 9.255849e-02	ci left: 4.600955e-03	ci right 5.050097e-03	k: 1784	n:370000
Cons ci ratio: 9.894338e-02	ci left: 4.015247e-03	ci right 4.435819e-03	k: 1562	n:370000
KS ci ratio: 3.340509e-03	ci left: 7.868934e-01	ci right 7.895291e-01	k: 291639	n:370000
MGA   370000 perm   160 sec   (2320 perm/sec)   p_kst 7.882135e-01   p_cons 4.221622e-03   p_joint 4.821622e-03

Outputting figure to mutsig2_images.part000000000105/MGA.2_9290_370000_0.78821_0.0042216_0.0048216.png
                gene_name: MGA
               theta_stop: 0.099 
                    nperm: 370000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.79 
       ci_ks_bounds_right: 0.79 
                   p_cons: 0.0042 
      ci_cons_bounds_left: 0.0040 
     ci_cons_bounds_right: 0.0044 
                  p_joint: 0.0048 
     ci_joint_bounds_left: 0.0046 
    ci_joint_bounds_right: 0.0051 

Current progress: 50 percent done.
MICAL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.889536e-02	ci left: 6.384467e-01	ci right 6.572671e-01	k: 6479	n:10000
Cons ci ratio: 7.905421e-03	ci left: 9.570190e-01	ci right 9.647096e-01	k: 9610	n:10000
KS ci ratio: 2.437940e-01	ci left: 2.212298e-02	ci right 2.835777e-02	k: 251	n:10000
MICAL1   10000 perm   2 sec   (5955 perm/sec)   p_kst 2.510000e-02   p_cons 9.610000e-01   p_joint 6.479000e-01

Joint ci ratio: 3.555302e-02	ci left: 3.712731e-01	ci right 3.847624e-01	k: 7560	n:20000
Cons ci ratio: 5.723288e-03	ci left: 9.563142e-01	ci right 9.618514e-01	k: 19183	n:20000
KS ci ratio: 1.756369e-01	ci left: 2.216252e-02	ci right 2.647729e-02	k: 485	n:20000
MICAL1   20000 perm   4 sec   (5281 perm/sec)   p_kst 2.425000e-02   p_cons 9.591500e-01   p_joint 3.780000e-01

Joint ci ratio: 2.545860e-02	ci left: 4.357703e-01	ci right 4.470411e-01	k: 13242	n:30000
Cons ci ratio: 4.748192e-03	ci left: 9.555320e-01	ci right 9.601122e-01	k: 28736	n:30000
KS ci ratio: 1.409503e-01	ci left: 2.335931e-02	ci right 2.693346e-02	k: 753	n:30000
MICAL1   30000 perm   6 sec   (5025 perm/sec)   p_kst 2.510000e-02   p_cons 9.578667e-01   p_joint 4.414000e-01

Joint ci ratio: 1.499205e-02	ci left: 6.261241e-01	ci right 6.356069e-01	k: 25235	n:40000
Cons ci ratio: 4.113839e-03	ci left: 9.558093e-01	ci right 9.597738e-01	k: 38313	n:40000
KS ci ratio: 1.233527e-01	ci left: 2.310407e-02	ci right 2.616548e-02	k: 984	n:40000
MICAL1   40000 perm   8 sec   (4857 perm/sec)   p_kst 2.460000e-02   p_cons 9.578250e-01   p_joint 6.308750e-01

Joint ci ratio: 2.323002e-02	ci left: 3.586236e-01	ci right 3.670724e-01	k: 18142	n:50000
Cons ci ratio: 3.681396e-03	ci left: 9.559806e-01	ci right 9.595260e-01	k: 47889	n:50000
KS ci ratio: 1.104798e-01	ci left: 2.320152e-02	ci right 2.593406e-02	k: 1227	n:50000
MICAL1   50000 perm   11 sec   (4721 perm/sec)   p_kst 2.454000e-02   p_cons 9.577800e-01   p_joint 3.628400e-01

Joint ci ratio: 2.322542e-02	ci left: 3.181786e-01	ci right 3.256719e-01	k: 19315	n:60000
Cons ci ratio: 3.402404e-03	ci left: 9.551087e-01	ci right 9.583802e-01	k: 57406	n:60000
KS ci ratio: 1.007699e-01	ci left: 2.335899e-02	ci right 2.585395e-02	k: 1475	n:60000
MICAL1   60000 perm   13 sec   (4608 perm/sec)   p_kst 2.458333e-02   p_cons 9.567667e-01   p_joint 3.219167e-01

Joint ci ratio: 1.964399e-02	ci left: 3.590230e-01	ci right 3.661599e-01	k: 25381	n:70000
Cons ci ratio: 3.152479e-03	ci left: 9.551661e-01	ci right 9.581959e-01	k: 66969	n:70000
KS ci ratio: 9.425326e-02	ci left: 2.297653e-02	ci right 2.526315e-02	k: 1687	n:70000
MICAL1   70000 perm   16 sec   (4506 perm/sec)   p_kst 2.410000e-02   p_cons 9.567000e-01   p_joint 3.625857e-01

Outputting figure to mutsig2_images.part000000000105/MICAL1.2_3300_70000_0.0241_0.9567_0.36259.png
                gene_name: MICAL1
               theta_stop: 0.094 
                    nperm: 70000 
                     p_ks: 0.024 
        ci_ks_bounds_left: 0.023 
       ci_ks_bounds_right: 0.025 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.96 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.37 

Current progress: 75 percent done.
MKI67
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: 2.367603e-02	ci left: 7.239092e-01	ci right 7.413551e-01	k: 7327	n:10000
KS ci ratio: 6.844577e-03	ci left: 9.669936e-01	ci right 9.737287e-01	k: 9705	n:10000
MKI67   10000 perm   3 sec   (3935 perm/sec)   p_kst 9.705000e-01   p_cons 7.327000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000105/MKI67.2_9827_10000_0.9705_0.7327_1.png
                gene_name: MKI67
               theta_stop: 0.024 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.74 
                  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.165.3896/
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/181708/iteration1/scatter.0000000105
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 105 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120078: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000106> was used as the working directory.
Started at Wed Oct 10 10:43:49 2012
Results reported at Wed Oct 10 10:50:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000106.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000106.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 106  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    454.94 sec.
    Max Memory :      1335 MB
    Max Swap   :      3837 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.165.3896/
-whichjob
106
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 106: processing genes 9500 - 9590
Calculating significance of each gene.
Using projection method.
9500	MLANA	1
9501	MLC1	1
9502	MLEC	1
9503	MLF1	6.791075e-02
9504	MLF1IP	1
9505	MLF2	1
9506	MLH1	2.437121e-01
9507	MLH3	1
9508	MLKL	1
9509	MLL	3.114929e-03
9510	MLL2	4.773981e-03
9511	MLL3	9.775860e-03
9512	MLL4	1.075164e-01
9513	MLL5	1
9514	MLLT1	1
9515	MLLT10	1
9516	MLLT11	1
9517	MLLT3	6.100921e-02
9518	MLLT4	6.308109e-01
9519	MLLT6	1
9520	MLN	1
9521	MLNR	1
9522	MLPH	1
9523	MLST8	1
9524	MLX	1.246921e-01
9525	MLXIP	1
9526	MLXIPL	1
9527	MLYCD	1
9528	MMAA	1
9529	MMAB	1
9530	MMACHC	1
9531	MMADHC	1
9532	MMD	1
9533	MMD2	1
9534	MME	1
9535	MMEL1	2.220080e-01
9536	MMGT1	1
9537	MMP1	1
9538	MMP10	1
9539	MMP11	1
9540	MMP12	5.421801e-02
9541	MMP13	1
9542	MMP14	4.633330e-02
9543	MMP15	1.891081e-01
9544	MMP16	2.581846e-02
9545	MMP17	1
9546	MMP19	1
9547	MMP2	1
9548	MMP20	1
9549	MMP21	7.066149e-02
9550	MMP24	5.008637e-02
9551	MMP25	1
9552	MMP26	1
9553	MMP27	2.022642e-01
9554	MMP28	1
9555	MMP3	1
9556	MMP7	1
9557	MMP8	1.964761e-01
9558	MMP9	4.700100e-03
9559	MMRN1	2.193753e-01
9560	MMRN2	1
9561	MMS19	1
9562	MN1	1
9563	MNAT1	1
9564	MND1	1
9565	MNDA	1.578661e-01
9566	MNS1	1
9567	MNT	1
9568	MNX1	1
9569	MOAP1	1
9570	MOB2	1
9571	MOBKL1A	1
9572	MOBKL1B	1
9573	MOBKL2A	1
9574	MOBKL2B	1
9575	MOBKL2C	1
9576	MOBKL3	1
9577	MOBP	1
9578	MOCOS	3.323311e-01
9579	MOCS1	1
9580	MOCS2	1
9581	MOCS3	1
9582	MOG	1
9583	MOGAT1	4.181686e-02
9584	MOGAT2	1
9585	MOGAT3	1
9586	MOGS	4.846567e-02
9587	MON1A	1
9588	MON1B	1
9589	MON2	1
9590	MORC1	2.765171e-01
Done

Running MutSig 2:
Scatter job 106: processing genes 9500 - 9590
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MLL
Processing conservation and coverage...
82% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.479208e-01	ci left: 5.903663e-03	ci right 9.392367e-03	k: 75	n:10000
Cons ci ratio: 3.430079e-02	ci left: 5.565186e-01	ci right 5.760428e-01	k: 5663	n:10000
KS ci ratio: 6.918207e-01	ci left: 2.107242e-03	ci right 4.397341e-03	k: 31	n:10000
MLL   10000 perm   4 sec   (2665 perm/sec)   p_kst 3.100000e-03   p_cons 5.663000e-01   p_joint 7.500000e-03

Joint ci ratio: 1.925569e-01	ci left: 1.834288e-02	ci right 2.229831e-02	k: 405	n:20000
Cons ci ratio: 2.416459e-02	ci left: 5.612507e-01	ci right 5.750295e-01	k: 11363	n:20000
KS ci ratio: 4.745492e-01	ci left: 2.597119e-03	ci right 4.252457e-03	k: 67	n:20000
MLL   20000 perm   9 sec   (2161 perm/sec)   p_kst 3.350000e-03   p_cons 5.681500e-01   p_joint 2.025000e-02

Joint ci ratio: 1.917907e-01	ci left: 1.241520e-02	ci right 1.508019e-02	k: 411	n:30000
Cons ci ratio: 1.970191e-02	ci left: 5.632396e-01	ci right 5.744804e-01	k: 17066	n:30000
KS ci ratio: 3.994361e-01	ci left: 2.562755e-03	ci right 3.869722e-03	k: 95	n:30000
MLL   30000 perm   13 sec   (2248 perm/sec)   p_kst 3.166667e-03   p_cons 5.688667e-01   p_joint 1.370000e-02

Joint ci ratio: 1.569776e-01	ci left: 1.414395e-02	ci right 1.657714e-02	k: 613	n:40000
Cons ci ratio: 1.705181e-02	ci left: 5.643048e-01	ci right 5.740351e-01	k: 22767	n:40000
KS ci ratio: 3.588064e-01	ci left: 2.442383e-03	ci right 3.531758e-03	k: 118	n:40000
MLL   40000 perm   19 sec   (2057 perm/sec)   p_kst 2.950000e-03   p_cons 5.691750e-01   p_joint 1.532500e-02

Joint ci ratio: 1.626742e-01	ci left: 1.054551e-02	ci right 1.243185e-02	k: 573	n:50000
Cons ci ratio: 1.455869e-02	ci left: 5.874967e-01	ci right 5.961326e-01	k: 29591	n:50000
KS ci ratio: 3.164248e-01	ci left: 2.576504e-03	ci right 3.562591e-03	k: 152	n:50000
MLL   50000 perm   24 sec   (2121 perm/sec)   p_kst 3.040000e-03   p_cons 5.918200e-01   p_joint 1.146000e-02

Joint ci ratio: 1.625461e-01	ci left: 8.819250e-03	ci right 1.039540e-02	k: 575	n:60000
Cons ci ratio: 1.328989e-02	ci left: 5.878879e-01	ci right 5.957698e-01	k: 35510	n:60000
KS ci ratio: 2.885404e-01	ci left: 2.624630e-03	ci right 3.524501e-03	k: 183	n:60000
MLL   60000 perm   27 sec   (2195 perm/sec)   p_kst 3.050000e-03   p_cons 5.918333e-01   p_joint 9.583333e-03

Joint ci ratio: 1.300428e-01	ci left: 1.198036e-02	ci right 1.366038e-02	k: 896	n:70000
Cons ci ratio: 1.228856e-02	ci left: 5.887918e-01	ci right 5.960862e-01	k: 41471	n:70000
KS ci ratio: 2.663085e-01	ci left: 2.675081e-03	ci right 3.509809e-03	k: 215	n:70000
MLL   70000 perm   31 sec   (2245 perm/sec)   p_kst 3.071429e-03   p_cons 5.924429e-01   p_joint 1.280000e-02

Joint ci ratio: 1.372919e-01	ci left: 9.394529e-03	ci right 1.079134e-02	k: 806	n:80000
Cons ci ratio: 1.147869e-02	ci left: 5.897113e-01	ci right 5.965320e-01	k: 47450	n:80000
KS ci ratio: 2.485326e-01	ci left: 2.714922e-03	ci right 3.496801e-03	k: 247	n:80000
MLL   80000 perm   35 sec   (2273 perm/sec)   p_kst 3.087500e-03   p_cons 5.931250e-01   p_joint 1.007500e-02

Joint ci ratio: 1.175214e-01	ci left: 1.149300e-02	ci right 1.293870e-02	k: 1098	n:90000
Cons ci ratio: 1.081731e-02	ci left: 5.901267e-01	ci right 5.965561e-01	k: 53401	n:90000
KS ci ratio: 2.330653e-01	ci left: 2.768278e-03	ci right 3.508765e-03	k: 281	n:90000
MLL   90000 perm   39 sec   (2295 perm/sec)   p_kst 3.122222e-03   p_cons 5.933444e-01   p_joint 1.220000e-02

Joint ci ratio: 1.165267e-01	ci left: 1.053754e-02	ci right 1.185104e-02	k: 1118	n:100000
Cons ci ratio: 1.025699e-02	ci left: 5.905381e-01	ci right 5.966365e-01	k: 59359	n:100000
KS ci ratio: 2.208697e-01	ci left: 2.793271e-03	ci right 3.496037e-03	k: 313	n:100000
MLL   100000 perm   43 sec   (2302 perm/sec)   p_kst 3.130000e-03   p_cons 5.935900e-01   p_joint 1.118000e-02

Joint ci ratio: 1.208603e-01	ci left: 8.899895e-03	ci right 1.005346e-02	k: 1041	n:110000
Cons ci ratio: 9.779100e-03	ci left: 5.907087e-01	ci right 5.965227e-01	k: 65298	n:110000
KS ci ratio: 2.091983e-01	ci left: 2.849004e-03	ci right 3.523066e-03	k: 349	n:110000
MLL   110000 perm   48 sec   (2311 perm/sec)   p_kst 3.172727e-03   p_cons 5.936182e-01   p_joint 9.463636e-03

Joint ci ratio: 1.199255e-01	ci left: 8.295481e-03	ci right 9.361793e-03	k: 1058	n:120000
Cons ci ratio: 9.372842e-03	ci left: 5.903141e-01	ci right 5.958814e-01	k: 71172	n:120000
KS ci ratio: 2.029264e-01	ci left: 2.785452e-03	ci right 3.422270e-03	k: 371	n:120000
MLL   120000 perm   53 sec   (2247 perm/sec)   p_kst 3.091667e-03   p_cons 5.931000e-01   p_joint 8.816667e-03

Joint ci ratio: 1.218962e-01	ci left: 7.410990e-03	ci right 8.380385e-03	k: 1025	n:130000
Cons ci ratio: 9.005285e-03	ci left: 5.904160e-01	ci right 5.957645e-01	k: 77102	n:130000
KS ci ratio: 1.954526e-01	ci left: 2.783140e-03	ci right 3.393205e-03	k: 400	n:130000
MLL   130000 perm   59 sec   (2206 perm/sec)   p_kst 3.076923e-03   p_cons 5.930923e-01   p_joint 7.884615e-03

Joint ci ratio: 1.208090e-01	ci left: 7.013140e-03	ci right 7.921724e-03	k: 1044	n:140000
Cons ci ratio: 8.681687e-03	ci left: 5.902924e-01	ci right 5.954466e-01	k: 83002	n:140000
KS ci ratio: 1.889685e-01	ci left: 2.774720e-03	ci right 3.360447e-03	k: 428	n:140000
MLL   140000 perm   64 sec   (2204 perm/sec)   p_kst 3.057143e-03   p_cons 5.928714e-01   p_joint 7.457143e-03

Joint ci ratio: 1.198047e-01	ci left: 6.661913e-03	ci right 7.517306e-03	k: 1062	n:150000
Cons ci ratio: 8.532508e-03	ci left: 5.820612e-01	ci right 5.870555e-01	k: 87684	n:150000
KS ci ratio: 1.822912e-01	ci left: 2.793163e-03	ci right 3.359648e-03	k: 460	n:150000
MLL   150000 perm   68 sec   (2205 perm/sec)   p_kst 3.066667e-03   p_cons 5.845600e-01   p_joint 7.080000e-03

Joint ci ratio: 1.173029e-01	ci left: 6.524490e-03	ci right 7.343530e-03	k: 1108	n:160000
Cons ci ratio: 8.260995e-03	ci left: 5.821745e-01	ci right 5.870100e-01	k: 93535	n:160000
KS ci ratio: 1.755622e-01	ci left: 2.833521e-03	ci right 3.384728e-03	k: 496	n:160000
MLL   160000 perm   73 sec   (2199 perm/sec)   p_kst 3.100000e-03   p_cons 5.845938e-01   p_joint 6.925000e-03

Joint ci ratio: 1.190129e-01	ci left: 5.963630e-03	ci right 6.723941e-03	k: 1077	n:170000
Cons ci ratio: 8.005898e-03	ci left: 5.827594e-01	ci right 5.874495e-01	k: 99468	n:170000
KS ci ratio: 1.709814e-01	ci left: 2.818778e-03	ci right 3.351333e-03	k: 523	n:170000
MLL   170000 perm   78 sec   (2187 perm/sec)   p_kst 3.076471e-03   p_cons 5.851059e-01   p_joint 6.335294e-03

Joint ci ratio: 1.187573e-01	ci left: 5.659216e-03	ci right 6.379056e-03	k: 1082	n:180000
Cons ci ratio: 7.779542e-03	ci left: 5.828753e-01	ci right 5.874330e-01	k: 105328	n:180000
KS ci ratio: 1.667414e-01	ci left: 2.805838e-03	ci right 3.321483e-03	k: 550	n:180000
MLL   180000 perm   82 sec   (2183 perm/sec)   p_kst 3.055556e-03   p_cons 5.851556e-01   p_joint 6.011111e-03

Joint ci ratio: 1.186661e-01	ci left: 5.371529e-03	ci right 6.054211e-03	k: 1084	n:190000
Cons ci ratio: 7.571688e-03	ci left: 5.829597e-01	ci right 5.873956e-01	k: 111184	n:190000
KS ci ratio: 1.635128e-01	ci left: 2.769163e-03	ci right 3.267245e-03	k: 572	n:190000
MLL   190000 perm   87 sec   (2177 perm/sec)   p_kst 3.010526e-03   p_cons 5.851789e-01   p_joint 5.705263e-03

Joint ci ratio: 1.164903e-01	ci left: 5.301912e-03	ci right 5.962541e-03	k: 1125	n:200000
Cons ci ratio: 7.376459e-03	ci left: 5.832472e-01	ci right 5.875703e-01	k: 117082	n:200000
KS ci ratio: 1.592611e-01	ci left: 2.779446e-03	ci right 3.265135e-03	k: 603	n:200000
MLL   200000 perm   92 sec   (2167 perm/sec)   p_kst 3.015000e-03   p_cons 5.854100e-01   p_joint 5.625000e-03

Joint ci ratio: 1.148762e-01	ci left: 5.197395e-03	ci right 5.835419e-03	k: 1157	n:210000
Cons ci ratio: 7.200885e-03	ci left: 5.831512e-01	ci right 5.873703e-01	k: 122905	n:210000
KS ci ratio: 1.558177e-01	ci left: 2.770594e-03	ci right 3.243290e-03	k: 630	n:210000
MLL   210000 perm   97 sec   (2159 perm/sec)   p_kst 3.000000e-03   p_cons 5.852619e-01   p_joint 5.509524e-03

Joint ci ratio: 1.048856e-01	ci left: 5.978048e-03	ci right 6.644151e-03	k: 1387	n:220000
Cons ci ratio: 7.037608e-03	ci left: 5.830423e-01	ci right 5.871645e-01	k: 128723	n:220000
KS ci ratio: 1.513250e-01	ci left: 2.810753e-03	ci right 3.275221e-03	k: 668	n:220000
MLL   220000 perm   102 sec   (2149 perm/sec)   p_kst 3.036364e-03   p_cons 5.851045e-01   p_joint 6.304545e-03

Joint ci ratio: 9.686888e-02	ci left: 6.726967e-03	ci right 7.415978e-03	k: 1625	n:230000
Cons ci ratio: 6.881565e-03	ci left: 5.831832e-01	ci right 5.872146e-01	k: 134596	n:230000
KS ci ratio: 1.447555e-01	ci left: 2.948145e-03	ci right 3.412341e-03	k: 730	n:230000
MLL   230000 perm   108 sec   (2138 perm/sec)   p_kst 3.173913e-03   p_cons 5.852000e-01   p_joint 7.065217e-03

Joint ci ratio: 9.462440e-02	ci left: 6.763900e-03	ci right 7.439752e-03	k: 1703	n:240000
Cons ci ratio: 6.736559e-03	ci left: 5.832341e-01	ci right 5.871805e-01	k: 140450	n:240000
KS ci ratio: 1.421555e-01	ci left: 2.933766e-03	ci right 3.386698e-03	k: 757	n:240000
MLL   240000 perm   113 sec   (2129 perm/sec)   p_kst 3.154167e-03   p_cons 5.852083e-01   p_joint 7.095833e-03

Joint ci ratio: 9.683655e-02	ci left: 6.196533e-03	ci right 6.830989e-03	k: 1627	n:250000
Cons ci ratio: 6.602526e-03	ci left: 5.831216e-01	ci right 5.869884e-01	k: 146264	n:250000
KS ci ratio: 1.380250e-01	ci left: 2.993974e-03	ci right 3.441666e-03	k: 803	n:250000
MLL   250000 perm   118 sec   (2119 perm/sec)   p_kst 3.212000e-03   p_cons 5.850560e-01   p_joint 6.508000e-03

Joint ci ratio: 9.708911e-02	ci left: 5.928142e-03	ci right 6.536789e-03	k: 1619	n:260000
Cons ci ratio: 6.472134e-03	ci left: 5.833226e-01	ci right 5.871140e-01	k: 152157	n:260000
KS ci ratio: 1.356019e-01	ci left: 2.986541e-03	ci right 3.424649e-03	k: 832	n:260000
MLL   260000 perm   123 sec   (2108 perm/sec)   p_kst 3.200000e-03   p_cons 5.852192e-01   p_joint 6.226923e-03

Joint ci ratio: 9.719096e-02	ci left: 5.697708e-03	ci right 6.283343e-03	k: 1616	n:270000
Cons ci ratio: 6.349560e-03	ci left: 5.834797e-01	ci right 5.872000e-01	k: 158042	n:270000
KS ci ratio: 1.335355e-01	ci left: 2.968981e-03	ci right 3.397349e-03	k: 858	n:270000
MLL   270000 perm   129 sec   (2093 perm/sec)   p_kst 3.177778e-03   p_cons 5.853407e-01   p_joint 5.985185e-03

Joint ci ratio: 8.908389e-02	ci left: 6.561789e-03	ci right 7.177056e-03	k: 1922	n:280000
Cons ci ratio: 6.234980e-03	ci left: 5.835261e-01	ci right 5.871793e-01	k: 163899	n:280000
KS ci ratio: 1.306019e-01	ci left: 2.997632e-03	ci right 3.419897e-03	k: 897	n:280000
MLL   280000 perm   134 sec   (2082 perm/sec)   p_kst 3.203571e-03   p_cons 5.853536e-01   p_joint 6.864286e-03

Joint ci ratio: 8.774943e-02	ci left: 6.534466e-03	ci right 7.137522e-03	k: 1981	n:290000
Cons ci ratio: 6.127694e-03	ci left: 5.834664e-01	ci right 5.870561e-01	k: 169726	n:290000
KS ci ratio: 1.286131e-01	ci left: 2.987686e-03	ci right 3.401651e-03	k: 925	n:290000
MLL   290000 perm   140 sec   (2071 perm/sec)   p_kst 3.189655e-03   p_cons 5.852621e-01   p_joint 6.831034e-03

Joint ci ratio: 8.685967e-02	ci left: 6.450321e-03	ci right 7.039268e-03	k: 2022	n:300000
Cons ci ratio: 6.130289e-03	ci left: 5.750330e-01	ci right 5.785722e-01	k: 173041	n:300000
KS ci ratio: 1.270470e-01	ci left: 2.962309e-03	ci right 3.367383e-03	k: 948	n:300000
MLL   300000 perm   146 sec   (2059 perm/sec)   p_kst 3.160000e-03   p_cons 5.768033e-01   p_joint 6.740000e-03

Joint ci ratio: 8.646143e-02	ci left: 6.302187e-03	ci right 6.874837e-03	k: 2041	n:310000
Cons ci ratio: 6.029609e-03	ci left: 5.751424e-01	ci right 5.786239e-01	k: 178834	n:310000
KS ci ratio: 1.250856e-01	ci left: 2.960473e-03	ci right 3.358582e-03	k: 978	n:310000
MLL   310000 perm   151 sec   (2048 perm/sec)   p_kst 3.154839e-03   p_cons 5.768839e-01   p_joint 6.583871e-03

Joint ci ratio: 8.737938e-02	ci left: 5.976803e-03	ci right 6.525946e-03	k: 1999	n:320000
Cons ci ratio: 5.931453e-03	ci left: 5.754330e-01	ci right 5.788594e-01	k: 184687	n:320000
KS ci ratio: 1.225440e-01	ci left: 2.992118e-03	ci right 3.385714e-03	k: 1019	n:320000
MLL   320000 perm   157 sec   (2033 perm/sec)   p_kst 3.184375e-03   p_cons 5.771469e-01   p_joint 6.246875e-03

Joint ci ratio: 8.580488e-02	ci left: 6.015080e-03	ci right 6.557282e-03	k: 2073	n:330000
Cons ci ratio: 5.841162e-03	ci left: 5.754365e-01	ci right 5.788106e-01	k: 190451	n:330000
KS ci ratio: 1.206658e-01	ci left: 2.995468e-03	ci right 3.383035e-03	k: 1051	n:330000
MLL   330000 perm   164 sec   (2017 perm/sec)   p_kst 3.184848e-03   p_cons 5.771242e-01   p_joint 6.281818e-03

Joint ci ratio: 8.467028e-02	ci left: 5.999358e-03	ci right 6.532639e-03	k: 2129	n:340000
Cons ci ratio: 5.752239e-03	ci left: 5.756639e-01	ci right 5.789877e-01	k: 196291	n:340000
KS ci ratio: 1.184338e-01	ci left: 3.021497e-03	ci right 3.404694e-03	k: 1091	n:340000
MLL   340000 perm   170 sec   (2005 perm/sec)   p_kst 3.208824e-03   p_cons 5.773265e-01   p_joint 6.261765e-03

Joint ci ratio: 7.990954e-02	ci left: 6.555602e-03	ci right 7.104039e-03	k: 2389	n:350000
Cons ci ratio: 5.669278e-03	ci left: 5.757043e-01	ci right 5.789802e-01	k: 202070	n:350000
KS ci ratio: 1.170496e-01	ci left: 3.007265e-03	ci right 3.383892e-03	k: 1117	n:350000
MLL   350000 perm   176 sec   (1993 perm/sec)   p_kst 3.191429e-03   p_cons 5.773429e-01   p_joint 6.825714e-03

Joint ci ratio: 7.913758e-02	ci left: 6.501454e-03	ci right 7.039864e-03	k: 2436	n:360000
Cons ci ratio: 5.592321e-03	ci left: 5.755231e-01	ci right 5.787534e-01	k: 207770	n:360000
KS ci ratio: 1.153593e-01	ci left: 3.012733e-03	ci right 3.384224e-03	k: 1150	n:360000
MLL   360000 perm   182 sec   (1980 perm/sec)   p_kst 3.194444e-03   p_cons 5.771389e-01   p_joint 6.766667e-03

Joint ci ratio: 7.821337e-02	ci left: 6.479409e-03	ci right 7.009441e-03	k: 2494	n:370000
Cons ci ratio: 5.517405e-03	ci left: 5.754413e-01	ci right 5.786277e-01	k: 213503	n:370000
KS ci ratio: 1.137883e-01	ci left: 3.015316e-03	ci right 3.381722e-03	k: 1182	n:370000
MLL   370000 perm   188 sec   (1967 perm/sec)   p_kst 3.194595e-03   p_cons 5.770351e-01   p_joint 6.740541e-03

Joint ci ratio: 7.742773e-02	ci left: 6.440492e-03	ci right 6.961810e-03	k: 2545	n:380000
Cons ci ratio: 5.440754e-03	ci left: 5.757828e-01	ci right 5.789266e-01	k: 219395	n:380000
KS ci ratio: 1.124192e-01	ci left: 3.010122e-03	ci right 3.371204e-03	k: 1211	n:380000
MLL   380000 perm   194 sec   (1956 perm/sec)   p_kst 3.186842e-03   p_cons 5.773553e-01   p_joint 6.697368e-03

Joint ci ratio: 7.326310e-02	ci left: 7.020110e-03	ci right 7.556481e-03	k: 2841	n:390000
Cons ci ratio: 5.370846e-03	ci left: 5.757760e-01	ci right 5.788793e-01	k: 225158	n:390000
KS ci ratio: 1.113687e-01	ci left: 2.990261e-03	ci right 3.345389e-03	k: 1234	n:390000
MLL   390000 perm   201 sec   (1944 perm/sec)   p_kst 3.164103e-03   p_cons 5.773282e-01   p_joint 7.284615e-03

Joint ci ratio: 7.269243e-02	ci left: 6.955045e-03	ci right 7.482131e-03	k: 2886	n:400000
Cons ci ratio: 5.300523e-03	ci left: 5.760500e-01	ci right 5.791139e-01	k: 231033	n:400000
KS ci ratio: 1.100841e-01	ci left: 2.985996e-03	ci right 3.336262e-03	k: 1263	n:400000
MLL   400000 perm   207 sec   (1932 perm/sec)   p_kst 3.157500e-03   p_cons 5.775825e-01   p_joint 7.215000e-03

Joint ci ratio: 7.035610e-02	ci left: 7.250158e-03	ci right 7.781228e-03	k: 3080	n:410000
Cons ci ratio: 5.234040e-03	ci left: 5.762034e-01	ci right 5.792296e-01	k: 236864	n:410000
KS ci ratio: 1.087165e-01	ci left: 2.989080e-03	ci right 3.335073e-03	k: 1295	n:410000
MLL   410000 perm   214 sec   (1920 perm/sec)   p_kst 3.158537e-03   p_cons 5.777171e-01   p_joint 7.512195e-03

Joint ci ratio: 7.044310e-02	ci left: 7.061137e-03	ci right 7.579028e-03	k: 3073	n:420000
Cons ci ratio: 5.173151e-03	ci left: 5.760521e-01	ci right 5.790421e-01	k: 242570	n:420000
KS ci ratio: 1.072772e-01	ci left: 2.998995e-03	ci right 3.341249e-03	k: 1330	n:420000
MLL   420000 perm   220 sec   (1907 perm/sec)   p_kst 3.166667e-03   p_cons 5.775476e-01   p_joint 7.316667e-03

Joint ci ratio: 7.183920e-02	ci left: 6.629619e-03	ci right 7.125898e-03	k: 2956	n:430000
Cons ci ratio: 5.114021e-03	ci left: 5.759382e-01	ci right 5.788934e-01	k: 248289	n:430000
KS ci ratio: 1.059714e-01	ci left: 3.003949e-03	ci right 3.342335e-03	k: 1363	n:430000
MLL   430000 perm   227 sec   (1895 perm/sec)   p_kst 3.169767e-03   p_cons 5.774163e-01   p_joint 6.874419e-03

Joint ci ratio: 7.114573e-02	ci left: 6.608405e-03	ci right 7.098123e-03	k: 3014	n:440000
Cons ci ratio: 5.053741e-03	ci left: 5.761321e-01	ci right 5.790533e-01	k: 254141	n:440000
KS ci ratio: 1.050142e-01	ci left: 2.990995e-03	ci right 3.324691e-03	k: 1388	n:440000
MLL   440000 perm   234 sec   (1883 perm/sec)   p_kst 3.154545e-03   p_cons 5.775932e-01   p_joint 6.850000e-03

Joint ci ratio: 7.055291e-02	ci left: 6.572873e-03	ci right 7.055733e-03	k: 3065	n:450000
Cons ci ratio: 4.996794e-03	ci left: 5.761952e-01	ci right 5.790838e-01	k: 259938	n:450000
KS ci ratio: 1.040087e-01	ci left: 2.982960e-03	ci right 3.312378e-03	k: 1415	n:450000
MLL   450000 perm   241 sec   (1871 perm/sec)   p_kst 3.144444e-03   p_cons 5.776400e-01   p_joint 6.811111e-03

Joint ci ratio: 7.011066e-02	ci left: 6.513268e-03	ci right 6.988628e-03	k: 3104	n:460000
Cons ci ratio: 4.942742e-03	ci left: 5.761558e-01	ci right 5.790128e-01	k: 265689	n:460000
KS ci ratio: 1.026753e-01	ci left: 2.996470e-03	ci right 3.322882e-03	k: 1452	n:460000
MLL   460000 perm   247 sec   (1859 perm/sec)   p_kst 3.156522e-03   p_cons 5.775848e-01   p_joint 6.747826e-03

Joint ci ratio: 6.963201e-02	ci left: 6.464574e-03	ci right 6.933028e-03	k: 3147	n:470000
Cons ci ratio: 4.889469e-03	ci left: 5.762119e-01	ci right 5.790382e-01	k: 271484	n:470000
KS ci ratio: 1.014944e-01	ci left: 3.003209e-03	ci right 3.326368e-03	k: 1486	n:470000
MLL   470000 perm   254 sec   (1847 perm/sec)   p_kst 3.161702e-03   p_cons 5.776255e-01   p_joint 6.695745e-03

Joint ci ratio: 6.948155e-02	ci left: 6.358542e-03	ci right 6.818277e-03	k: 3161	n:480000
Cons ci ratio: 4.837097e-03	ci left: 5.763450e-01	ci right 5.791416e-01	k: 277317	n:480000
KS ci ratio: 1.001883e-01	ci left: 3.019844e-03	ci right 3.340366e-03	k: 1525	n:480000
MLL   480000 perm   261 sec   (1836 perm/sec)   p_kst 3.177083e-03   p_cons 5.777438e-01   p_joint 6.585417e-03

Joint ci ratio: 6.892896e-02	ci left: 6.331053e-03	ci right 6.785015e-03	k: 3212	n:490000
Cons ci ratio: 4.786452e-03	ci left: 5.764646e-01	ci right 5.792324e-01	k: 283146	n:490000
KS ci ratio: 9.912212e-02	ci left: 3.023883e-03	ci right 3.341220e-03	k: 1558	n:490000
MLL   490000 perm   269 sec   (1825 perm/sec)   p_kst 3.179592e-03   p_cons 5.778490e-01   p_joint 6.555102e-03

Outputting figure to mutsig2_images.part000000000106/MLL.9_12054_490000_0.0031796_0.57785_0.0065551.png
                gene_name: MLL
               theta_stop: 0.099 
                    nperm: 490000 
                     p_ks: 0.0032 
        ci_ks_bounds_left: 0.0030 
       ci_ks_bounds_right: 0.0033 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.58 
                  p_joint: 0.0066 
     ci_joint_bounds_left: 0.0063 
    ci_joint_bounds_right: 0.0068 

Current progress: 14 percent done.
MLL3
Processing conservation and coverage...
66% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.161806e-01	ci left: 9.623212e-02	ci right 1.082007e-01	k: 1021	n:10000
Cons ci ratio: 3.346348e-02	ci left: 5.686497e-01	ci right 5.881046e-01	k: 5784	n:10000
KS ci ratio: 1.447756e-01	ci left: 6.333545e-02	ci right 7.331780e-02	k: 682	n:10000
MLL3   10000 perm   3 sec   (2874 perm/sec)   p_kst 6.820000e-02   p_cons 5.784000e-01   p_joint 1.021000e-01

Joint ci ratio: 6.223004e-02	ci left: 1.603734e-01	ci right 1.707240e-01	k: 3310	n:20000
Cons ci ratio: 2.362243e-02	ci left: 5.723720e-01	ci right 5.861050e-01	k: 11585	n:20000
KS ci ratio: 1.026161e-01	ci left: 6.450023e-02	ci right 7.152600e-02	k: 1359	n:20000
MLL3   20000 perm   8 sec   (2496 perm/sec)   p_kst 6.795000e-02   p_cons 5.792500e-01   p_joint 1.655000e-01

Joint ci ratio: 5.051558e-02	ci left: 1.629272e-01	ci right 1.714041e-01	k: 5014	n:30000
Cons ci ratio: 1.928735e-02	ci left: 5.736562e-01	ci right 5.848618e-01	k: 17378	n:30000
KS ci ratio: 8.394088e-02	ci left: 6.491509e-02	ci right 7.063563e-02	k: 2032	n:30000
MLL3   30000 perm   12 sec   (2501 perm/sec)   p_kst 6.773333e-02   p_cons 5.792667e-01   p_joint 1.671333e-01

Outputting figure to mutsig2_images.part000000000106/MLL3.6_14972_30000_0.067733_0.57927_0.16713.png
                gene_name: MLL3
               theta_stop: 0.084 
                    nperm: 30000 
                     p_ks: 0.068 
        ci_ks_bounds_left: 0.065 
       ci_ks_bounds_right: 0.071 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.58 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.16 
    ci_joint_bounds_right: 0.17 

Current progress: 29 percent done.
MLL2
Processing conservation and coverage...
59% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.019906e-02	ci left: 7.820857e-01	ci right 7.981449e-01	k: 7902	n:10000
Cons ci ratio: 5.900626e-02	ci left: 2.970746e-01	ci right 3.152384e-01	k: 3061	n:10000
KS ci ratio: 1.551522e-02	ci left: 8.577378e-01	ci right 8.712491e-01	k: 8646	n:10000
MLL2   10000 perm   4 sec   (2748 perm/sec)   p_kst 8.646000e-01   p_cons 3.061000e-01   p_joint 7.902000e-01

Outputting figure to mutsig2_images.part000000000106/MLL2.5_16830_10000_0.8646_0.3061_0.7902.png
                gene_name: MLL2
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.87 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.80 

Current progress: 43 percent done.
MLL4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.199832e-03	ci left: 9.800565e-01	ci right 9.852569e-01	k: 9828	n:10000
Cons ci ratio: 4.099081e-02	ci left: 4.677677e-01	ci right 4.874453e-01	k: 4776	n:10000
KS ci ratio: 2.621199e-02	ci left: 6.818387e-01	ci right 7.000499e-01	k: 6910	n:10000
MLL4   10000 perm   2 sec   (4203 perm/sec)   p_kst 6.910000e-01   p_cons 4.776000e-01   p_joint 9.828000e-01

Outputting figure to mutsig2_images.part000000000106/MLL4.2_8296_10000_0.691_0.4776_0.9828.png
                gene_name: MLL4
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 0.69 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.70 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.99 

Current progress: 57 percent done.
MMP16
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.307221e-02	ci left: 7.340122e-01	ci right 7.512462e-01	k: 7427	n:10000
Cons ci ratio: 2.182909e-02	ci left: 7.548431e-01	ci right 7.716033e-01	k: 7633	n:10000
KS ci ratio: 6.429240e-02	ci left: 2.622072e-01	ci right 2.797264e-01	k: 2709	n:10000
MMP16   10000 perm   2 sec   (6098 perm/sec)   p_kst 2.709000e-01   p_cons 7.633000e-01   p_joint 7.427000e-01

Outputting figure to mutsig2_images.part000000000106/MMP16.2_2020_10000_0.2709_0.7633_0.7427.png
                gene_name: MMP16
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.27 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.28 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.74 
     ci_joint_bounds_left: 0.73 
    ci_joint_bounds_right: 0.75 

Current progress: 71 percent done.
MMP9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.133002e-01	ci left: 1.008116e-01	ci right 1.130184e-01	k: 1068	n:10000
Cons ci ratio: 2.541083e-02	ci left: 6.950453e-01	ci right 7.130357e-01	k: 7041	n:10000
KS ci ratio: 2.723101e-01	ci left: 1.753307e-02	ci right 2.315124e-02	k: 202	n:10000
MMP9   10000 perm   2 sec   (5953 perm/sec)   p_kst 2.020000e-02   p_cons 7.041000e-01   p_joint 1.068000e-01

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 1.844199e-02	ci left: 6.867057e-01	ci right 6.995382e-01	k: 13863	n:20000
KS ci ratio: 1.878865e-01	ci left: 1.929613e-02	ci right 2.334471e-02	k: 425	n:20000
MMP9   20000 perm   4 sec   (5338 perm/sec)   p_kst 2.125000e-02   p_cons 6.931500e-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: 1.457997e-02	ci left: 7.015117e-01	ci right 7.118483e-01	k: 21201	n:30000
KS ci ratio: 1.529216e-01	ci left: 1.979225e-02	ci right 2.310134e-02	k: 642	n:30000
MMP9   30000 perm   6 sec   (5083 perm/sec)   p_kst 2.140000e-02   p_cons 7.067000e-01   p_joint 1

Joint ci ratio: 1.645433e-02	ci left: 5.817305e-01	ci right 5.914070e-01	k: 23463	n:40000
Cons ci ratio: 1.268381e-02	ci left: 7.003278e-01	ci right 7.092924e-01	k: 28193	n:40000
KS ci ratio: 1.316779e-01	ci left: 2.024606e-02	ci right 2.312396e-02	k: 866	n:40000
MMP9   40000 perm   8 sec   (4932 perm/sec)   p_kst 2.165000e-02   p_cons 7.048250e-01   p_joint 5.865750e-01

Joint ci ratio: 1.472442e-02	ci left: 5.820083e-01	ci right 5.906617e-01	k: 29317	n:50000
Cons ci ratio: 1.136672e-02	ci left: 6.999971e-01	ci right 7.080192e-01	k: 35201	n:50000
KS ci ratio: 1.201053e-01	ci left: 1.960578e-02	ci right 2.213028e-02	k: 1042	n:50000
MMP9   50000 perm   10 sec   (4798 perm/sec)   p_kst 2.084000e-02   p_cons 7.040200e-01   p_joint 5.863400e-01

Joint ci ratio: 1.378404e-02	ci left: 5.701149e-01	ci right 5.780446e-01	k: 34445	n:60000
Cons ci ratio: 1.038143e-02	ci left: 7.001453e-01	ci right 7.074683e-01	k: 42229	n:60000
KS ci ratio: 1.102087e-01	ci left: 1.951079e-02	ci right 2.180257e-02	k: 1238	n:60000
MMP9   60000 perm   13 sec   (4689 perm/sec)   p_kst 2.063333e-02   p_cons 7.038167e-01   p_joint 5.740833e-01

Joint ci ratio: 1.610066e-02	ci left: 4.548177e-01	ci right 4.622143e-01	k: 32096	n:70000
Cons ci ratio: 9.595928e-03	ci left: 7.010901e-01	ci right 7.078644e-01	k: 49314	n:70000
KS ci ratio: 1.022323e-01	ci left: 1.951875e-02	ci right 2.163554e-02	k: 1439	n:70000
MMP9   70000 perm   15 sec   (4592 perm/sec)   p_kst 2.055714e-02   p_cons 7.044857e-01   p_joint 4.585143e-01

Joint ci ratio: 4.520481e-03	ci left: 9.017863e-01	ci right 9.058844e-01	k: 72308	n:80000
Cons ci ratio: 8.967247e-03	ci left: 7.017259e-01	ci right 7.080592e-01	k: 56392	n:80000
KS ci ratio: 9.550278e-02	ci left: 1.963910e-02	ci right 2.162088e-02	k: 1649	n:80000
MMP9   80000 perm   18 sec   (4504 perm/sec)   p_kst 2.061250e-02   p_cons 7.049000e-01   p_joint 9.038500e-01

Outputting figure to mutsig2_images.part000000000106/MMP9.2_2176_80000_0.020612_0.7049_0.90385.png
                gene_name: MMP9
               theta_stop: 0.096 
                    nperm: 80000 
                     p_ks: 0.021 
        ci_ks_bounds_left: 0.020 
       ci_ks_bounds_right: 0.022 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.90 
     ci_joint_bounds_left: 0.90 
    ci_joint_bounds_right: 0.91 

Current progress: 86 percent done.
MOGS
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.282482e-03	ci left: 9.859942e-01	ci right 9.903144e-01	k: 9883	n:10000
Cons ci ratio: 7.079331e-03	ci left: 9.648873e-01	ci right 9.718363e-01	k: 9685	n:10000
KS ci ratio: 2.613224e-02	ci left: 6.831489e-01	ci right 7.013390e-01	k: 6923	n:10000
MOGS   10000 perm   2 sec   (5947 perm/sec)   p_kst 6.923000e-01   p_cons 9.685000e-01   p_joint 9.883000e-01

Outputting figure to mutsig2_images.part000000000106/MOGS.2_2530_10000_0.6923_0.9685_0.9883.png
                gene_name: MOGS
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.69 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.70 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.96 
     ci_cons_bounds_right: 0.97 
                  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.165.3896/
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/181708/iteration1/scatter.0000000106
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 106 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120081: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000107> was used as the working directory.
Started at Wed Oct 10 10:43:49 2012
Results reported at Wed Oct 10 10:44:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000107.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000107.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 107  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     65.99 sec.
    Max Memory :      1291 MB
    Max Swap   :      3996 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.165.3896/
-whichjob
107
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 107: processing genes 9591 - 9680
Calculating significance of each gene.
Using projection method.
9591	MORC2	1
9592	MORC3	8.470877e-02
9593	MORC4	1
9594	MORF4	1
9595	MORF4L1	1.110659e-01
9596	MORF4L2	1
9597	MORN1	1
9598	MORN3	1
9599	MORN4	1
9600	MORN5	1
9601	MOS	1.232146e-01
9602	MOSC1	1
9603	MOSC2	1
9604	MOSPD1	6.103195e-02
9605	MOSPD2	1
9606	MOSPD3	1
9607	MOV10	4.024883e-01
9608	MOV10L1	3.967660e-01
9609	MOXD1	1
9610	MPDU1	1
9611	MPDZ	9.905765e-02
9612	MPEG1	1
9613	MPG	1
9614	MPHOSPH10	1
9615	MPHOSPH6	1
9616	MPHOSPH8	2.013460e-01
9617	MPHOSPH9	1
9618	MPI	1
9619	MPL	1.913462e-01
9620	MPND	1
9621	MPO	2.721193e-01
9622	MPP1	1
9623	MPP2	1
9624	MPP3	1
9625	MPP4	1
9626	MPP5	1
9627	MPP6	1
9628	MPP7	1
9629	MPPE1	1
9630	MPPED1	1
9631	MPPED2	1
9632	MPRIP	1
9633	MPST	1
9634	MPV17	1
9635	MPV17L	1
9636	MPV17L2	7.761708e-02
9637	MPZ	1.194970e-02
9638	MPZL1	1
9639	MPZL2	1
9640	MPZL3	1
9641	MR1	1
9642	MRAP	1
9643	MRAP2	1
9644	MRAS	1
9645	MRC2	1
9646	MRE11A	1
9647	MREG	1
9648	MRFAP1	1
9649	MRFAP1L1	1
9650	MRGPRD	1
9651	MRGPRE	1
9652	MRGPRF	1
9653	MRGPRX1	6.050032e-02
9654	MRGPRX2	4.499784e-02
9655	MRGPRX3	1
9656	MRGPRX4	1
9657	MRI1	1
9658	MRM1	2.344159e-02
9659	MRO	1
9660	MRP63	5.743945e-02
9661	MRPL1	1
9662	MRPL10	1
9663	MRPL11	1
9664	MRPL12	1
9665	MRPL13	1
9666	MRPL14	1
9667	MRPL15	1
9668	MRPL16	1
9669	MRPL17	1
9670	MRPL18	1
9671	MRPL19	1
9672	MRPL2	1
9673	MRPL20	1
9674	MRPL21	1
9675	MRPL22	1.060255e-01
9676	MRPL23	1
9677	MRPL24	1
9678	MRPL27	1
9679	MRPL28	1
9680	MRPL3	1.431258e-01
Done

Running MutSig 2:
Scatter job 107: processing genes 9591 - 9680
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MORC3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.675337e-02	ci left: 6.729719e-01	ci right 6.913219e-01	k: 6822	n:10000
Cons ci ratio: 4.228605e-02	ci left: 4.522906e-01	ci right 4.719315e-01	k: 4621	n:10000
KS ci ratio: 1.884446e-02	ci left: 8.045063e-01	ci right 8.199113e-01	k: 8123	n:10000
MORC3   10000 perm   2 sec   (5715 perm/sec)   p_kst 8.123000e-01   p_cons 4.621000e-01   p_joint 6.822000e-01

Outputting figure to mutsig2_images.part000000000107/MORC3.2_2888_10000_0.8123_0.4621_0.6822.png
                gene_name: MORC3
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.81 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.47 
                  p_joint: 0.68 
     ci_joint_bounds_left: 0.67 
    ci_joint_bounds_right: 0.69 

Current progress: 50 percent done.
MPDZ
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.811095e-02	ci left: 3.892832e-01	ci right 4.085757e-01	k: 3989	n:10000
Cons ci ratio: 6.413009e-02	ci left: 2.631968e-01	ci right 2.807362e-01	k: 2719	n:10000
KS ci ratio: 3.256613e-02	ci left: 5.818905e-01	ci right 6.012561e-01	k: 5916	n:10000
MPDZ   10000 perm   2 sec   (4743 perm/sec)   p_kst 5.916000e-01   p_cons 2.719000e-01   p_joint 3.989000e-01

Outputting figure to mutsig2_images.part000000000107/MPDZ.2_6306_10000_0.5916_0.2719_0.3989.png
                gene_name: MPDZ
               theta_stop: 0.064 
                    nperm: 10000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.27 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.28 
                  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.165.3896/
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/181708/iteration1/scatter.0000000107
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 107 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120084: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000108> was used as the working directory.
Started at Wed Oct 10 10:43:49 2012
Results reported at Wed Oct 10 10:45:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000108.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000108.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 108  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    105.47 sec.
    Max Memory :       614 MB
    Max Swap   :      3408 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.165.3896/
-whichjob
108
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 108: processing genes 9681 - 9771
Calculating significance of each gene.
Using projection method.
9681	MRPL30	1
9682	MRPL32	1
9683	MRPL33	1
9684	MRPL34	1
9685	MRPL35	1.479720e-02
9686	MRPL36	1
9687	MRPL37	1
9688	MRPL38	1
9689	MRPL39	1
9690	MRPL4	1
9691	MRPL40	1
9692	MRPL41	1
9693	MRPL42	1
9694	MRPL43	1
9695	MRPL44	1
9696	MRPL45	1
9697	MRPL46	1
9698	MRPL47	1
9699	MRPL48	1
9700	MRPL49	1
9701	MRPL50	1
9702	MRPL51	1
9703	MRPL52	1
9704	MRPL53	2.935035e-02
9705	MRPL54	1
9706	MRPL55	1
9707	MRPL9	1
9708	MRPS10	1
9709	MRPS11	1
9710	MRPS12	1
9711	MRPS14	1
9712	MRPS15	1
9713	MRPS16	1
9714	MRPS17	1
9715	MRPS18A	1
9716	MRPS18B	1
9717	MRPS18C	1
9718	MRPS2	1
9719	MRPS21	1
9720	MRPS22	1.124660e-01
9721	MRPS23	1
9722	MRPS24	1
9723	MRPS25	1
9724	MRPS26	1
9725	MRPS27	1
9726	MRPS28	1
9727	MRPS30	1
9728	MRPS31	1
9729	MRPS33	1
9730	MRPS34	1
9731	MRPS35	8.813670e-02
9732	MRPS36	4.903639e-03
9733	MRPS5	1
9734	MRPS6	1
9735	MRPS7	1
9736	MRPS9	1
9737	MRRF	1
9738	MRS2	1
9739	MRTO4	1
9740	MRVI1	1
9741	MS4A1	9.030643e-02
9742	MS4A10	1
9743	MS4A12	1
9744	MS4A13	1
9745	MS4A14	1
9746	MS4A15	1
9747	MS4A2	1
9748	MS4A3	1
9749	MS4A4A	1
9750	MS4A5	1
9751	MS4A6A	1
9752	MS4A6E	1
9753	MS4A7	1
9754	MS4A8B	3.257017e-02
9755	MSC	1
9756	MSGN1	1
9757	MSH2	3.342509e-01
9758	MSH3	4.017571e-01
9759	MSH4	1
9760	MSH5	1.468615e-01
9761	MSH6	1
9762	MSI1	1
9763	MSI2	1
9764	MSL1	1
9765	MSL2	2.328724e-01
9766	MSL3	1.562030e-01
9767	MSL3L2	1
9768	MSLN	1
9769	MSLNL	2.865115e-02
9770	MSMB	1
9771	MSMP	1
Done

Running MutSig 2:
Scatter job 108: processing genes 9681 - 9771
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MSLNL
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: 3.708012e-02	ci left: 5.178584e-01	ci right 5.375255e-01	k: 5277	n:10000
KS ci ratio: 6.529986e-02	ci left: 2.561716e-01	ci right 2.735656e-01	k: 2648	n:10000
MSLNL   10000 perm   3 sec   (3890 perm/sec)   p_kst 2.648000e-01   p_cons 5.277000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000108/MSLNL.2_3226_10000_0.2648_0.5277_1.png
                gene_name: MSLNL
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.27 
                   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.165.3896/
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/181708/iteration1/scatter.0000000108
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 108 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120088: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000109> was used as the working directory.
Started at Wed Oct 10 10:43:49 2012
Results reported at Wed Oct 10 10:47:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000109.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000109.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 109  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    226.16 sec.
    Max Memory :      1263 MB
    Max Swap   :      3849 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.165.3896/
-whichjob
109
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 109: processing genes 9772 - 9861
Calculating significance of each gene.
Using projection method.
9772	MSN	1
9773	MSR1	1
9774	MSRA	1
9775	MSRB2	1
9776	MSRB3	1
9777	MST1	1
9778	MST1R	4.211178e-02
9779	MST4	1
9780	MSTN	1
9781	MSTO1	1
9782	MSX1	9.276880e-02
9783	MSX2	1
9784	MT1A	1
9785	MT1B	1
9786	MT1E	1
9787	MT1F	1
9788	MT1G	1
9789	MT1H	1
9790	MT1M	1
9791	MT1X	1
9792	MT2A	1
9793	MT3	1
9794	MT4	1
9795	MTA1	1
9796	MTA2	1
9797	MTA3	1
9798	MTAP	1
9799	MTBP	2.883986e-01
9800	MTCH1	1
9801	MTCH2	1
9802	MTCP1	1
9803	MTCP1NB	1.866032e-02
9804	MTDH	1
9805	MTERF	1
9806	MTERFD1	1
9807	MTERFD2	7.086390e-04
9808	MTERFD3	1
9809	MTF1	1
9810	MTF2	2.526880e-01
9811	MTFMT	1
9812	MTFR1	1
9813	MTG1	1
9814	MTHFD1	1
9815	MTHFD1L	1
9816	MTHFD2	4.111374e-02
9817	MTHFD2L	1
9818	MTHFR	2.361300e-01
9819	MTHFS	1
9820	MTHFSD	1
9821	MTIF2	1
9822	MTIF3	1
9823	MTL5	1
9824	MTM1	1.065108e-01
9825	MTMR1	1
9826	MTMR10	1
9827	MTMR11	5.440487e-02
9828	MTMR12	2.219646e-01
9829	MTMR14	1
9830	MTMR15	1
9831	MTMR2	1
9832	MTMR3	1
9833	MTMR4	1
9834	MTMR6	1
9835	MTMR7	1
9836	MTMR8	1.169345e-01
9837	MTMR9	7.429987e-02
9838	MTNR1A	1
9839	MTNR1B	1
9840	MTO1	1
9841	MTOR	7.564111e-01
9842	MTP18	1
9843	MTPAP	1.867652e-01
9844	MTPN	1
9845	MTR	1
9846	MTRF1	1
9847	MTRF1L	1
9848	MTRR	1
9849	MTSS1	1
9850	MTSS1L	1
9851	MTTP	1
9852	MTUS1	4.072010e-01
9853	MTUS2	1
9854	MTX1	1
9855	MTX2	1
9856	MTX3	1.191673e-01
9857	MUC1	1
9858	MUC13	1
9859	MUC15	1
9860	MUC16	9.712655e-01
9861	MUC17	1
Done

Running MutSig 2:
Scatter job 109: processing genes 9772 - 9861
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: 1.269727e-02	ci left: 8.991872e-01	ci right 9.107756e-01	k: 9051	n:10000
Cons ci ratio: 1.315740e-02	ci left: 8.927222e-01	ci right 9.046444e-01	k: 8988	n:10000
KS ci ratio: 3.566848e-02	ci left: 5.371811e-01	ci right 5.567915e-01	k: 5470	n:10000
MUC16   10000 perm   7 sec   (1437 perm/sec)   p_kst 5.470000e-01   p_cons 8.988000e-01   p_joint 9.051000e-01

Outputting figure to mutsig2_images.part000000000109/MUC16.8_43860_10000_0.547_0.8988_0.9051.png
                gene_name: MUC16
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.90 
      ci_cons_bounds_left: 0.89 
     ci_cons_bounds_right: 0.90 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.90 
    ci_joint_bounds_right: 0.91 

Current progress: 25 percent done.
MTERFD2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.711794e-03	ci left: 9.763158e-01	ci right 9.820003e-01	k: 9793	n:10000
Cons ci ratio: 2.961459e-02	ci left: 6.270843e-01	ci right 6.460361e-01	k: 6366	n:10000
KS ci ratio: 6.079590e-03	ci left: 9.734446e-01	ci right 9.794734e-01	k: 9766	n:10000
MTERFD2   10000 perm   2 sec   (6299 perm/sec)   p_kst 9.766000e-01   p_cons 6.366000e-01   p_joint 9.793000e-01

Outputting figure to mutsig2_images.part000000000109/MTERFD2.3_1162_10000_0.9766_0.6366_0.9793.png
                gene_name: MTERFD2
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.98 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.98 
                   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: 50 percent done.
MST1R
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.787022e-01	ci left: 8.595766e-03	ci right 1.269681e-02	k: 105	n:10000
Cons ci ratio: 8.046551e-02	ci left: 1.840255e-01	ci right 1.995545e-01	k: 1917	n:10000
KS ci ratio: 3.498200e-01	ci left: 1.023265e-02	ci right 1.465817e-02	k: 123	n:10000
MST1R   10000 perm   2 sec   (5254 perm/sec)   p_kst 1.230000e-02   p_cons 1.917000e-01   p_joint 1.050000e-02

Joint ci ratio: 3.188563e-01	ci left: 6.305286e-03	ci right 8.741182e-03	k: 149	n:20000
Cons ci ratio: 5.705493e-02	ci left: 1.854735e-01	ci right 1.964165e-01	k: 3818	n:20000
KS ci ratio: 2.478726e-01	ci left: 1.081866e-02	ci right 1.392552e-02	k: 246	n:20000
MST1R   20000 perm   4 sec   (4773 perm/sec)   p_kst 1.230000e-02   p_cons 1.909000e-01   p_joint 7.450000e-03

Joint ci ratio: 2.331652e-01	ci left: 8.244884e-03	ci right 1.045170e-02	k: 279	n:30000
Cons ci ratio: 4.615020e-02	ci left: 1.893733e-01	ci right 1.983527e-01	k: 5815	n:30000
KS ci ratio: 1.995451e-01	ci left: 1.143190e-02	ci right 1.399710e-02	k: 380	n:30000
MST1R   30000 perm   7 sec   (4541 perm/sec)   p_kst 1.266667e-02   p_cons 1.938333e-01   p_joint 9.300000e-03

Joint ci ratio: 2.456646e-01	ci left: 5.548131e-03	ci right 7.124827e-03	k: 252	n:40000
Cons ci ratio: 4.004314e-02	ci left: 1.893904e-01	ci right 1.971541e-01	k: 7730	n:40000
KS ci ratio: 1.758159e-01	ci left: 1.119504e-02	ci right 1.337662e-02	k: 490	n:40000
MST1R   40000 perm   9 sec   (4399 perm/sec)   p_kst 1.225000e-02   p_cons 1.932500e-01   p_joint 6.300000e-03

Joint ci ratio: 1.809366e-01	ci left: 8.458135e-03	ci right 1.015957e-02	k: 464	n:50000
Cons ci ratio: 3.581745e-02	ci left: 1.897870e-01	ci right 1.967286e-01	k: 9662	n:50000
KS ci ratio: 1.565783e-01	ci left: 1.140995e-02	ci right 1.336727e-02	k: 618	n:50000
MST1R   50000 perm   12 sec   (4291 perm/sec)   p_kst 1.236000e-02   p_cons 1.932400e-01   p_joint 9.280000e-03

Joint ci ratio: 1.924588e-01	ci left: 6.205638e-03	ci right 7.542730e-03	k: 411	n:60000
Cons ci ratio: 3.274154e-02	ci left: 1.896666e-01	ci right 1.959965e-01	k: 11569	n:60000
KS ci ratio: 1.434059e-01	ci left: 1.141730e-02	ci right 1.319700e-02	k: 737	n:60000
MST1R   60000 perm   14 sec   (4198 perm/sec)   p_kst 1.228333e-02   p_cons 1.928167e-01   p_joint 6.850000e-03

Joint ci ratio: 1.710968e-01	ci left: 6.805803e-03	ci right 8.092675e-03	k: 520	n:70000
Cons ci ratio: 3.041099e-02	ci left: 1.889032e-01	ci right 1.947509e-01	k: 13427	n:70000
KS ci ratio: 1.339546e-01	ci left: 1.127557e-02	ci right 1.290810e-02	k: 845	n:70000
MST1R   70000 perm   17 sec   (4114 perm/sec)   p_kst 1.207143e-02   p_cons 1.918143e-01   p_joint 7.428571e-03

Joint ci ratio: 1.982669e-01	ci left: 4.380366e-03	ci right 5.356074e-03	k: 388	n:80000
Cons ci ratio: 2.846787e-02	ci left: 1.888654e-01	ci right 1.943320e-01	k: 15327	n:80000
KS ci ratio: 1.264234e-01	ci left: 1.112375e-02	ci right 1.263696e-02	k: 949	n:80000
MST1R   80000 perm   20 sec   (4037 perm/sec)   p_kst 1.186250e-02   p_cons 1.915875e-01   p_joint 4.850000e-03

Joint ci ratio: 1.874938e-01	ci left: 4.380102e-03	ci right 5.296706e-03	k: 434	n:90000
Cons ci ratio: 2.684074e-02	ci left: 1.890111e-01	ci right 1.941644e-01	k: 17242	n:90000
KS ci ratio: 1.192356e-01	ci left: 1.115864e-02	ci right 1.258419e-02	k: 1067	n:90000
MST1R   90000 perm   23 sec   (3964 perm/sec)   p_kst 1.185556e-02   p_cons 1.915778e-01   p_joint 4.822222e-03

Joint ci ratio: 1.366657e-01	ci left: 7.602053e-03	ci right 8.726755e-03	k: 815	n:100000
Cons ci ratio: 2.548138e-02	ci left: 1.889259e-01	ci right 1.938120e-01	k: 19136	n:100000
KS ci ratio: 1.123843e-01	ci left: 1.134404e-02	ci right 1.270448e-02	k: 1201	n:100000
MST1R   100000 perm   26 sec   (3901 perm/sec)   p_kst 1.201000e-02   p_cons 1.913600e-01   p_joint 8.150000e-03

Joint ci ratio: 1.191407e-01	ci left: 9.164509e-03	ci right 1.033428e-02	k: 1071	n:110000
Cons ci ratio: 2.431104e-02	ci left: 1.888435e-01	ci right 1.935000e-01	k: 21028	n:110000
KS ci ratio: 1.069580e-01	ci left: 1.141799e-02	ci right 1.271702e-02	k: 1326	n:110000
MST1R   110000 perm   29 sec   (3841 perm/sec)   p_kst 1.205455e-02   p_cons 1.911636e-01   p_joint 9.736364e-03

Joint ci ratio: 1.139925e-01	ci left: 9.201760e-03	ci right 1.032212e-02	k: 1170	n:120000
Cons ci ratio: 2.323020e-02	ci left: 1.895508e-01	ci right 1.940141e-01	k: 23013	n:120000
KS ci ratio: 1.023200e-01	ci left: 1.146468e-02	ci right 1.270906e-02	k: 1449	n:120000
MST1R   120000 perm   33 sec   (3638 perm/sec)   p_kst 1.207500e-02   p_cons 1.917750e-01   p_joint 9.750000e-03

Joint ci ratio: 1.183985e-01	ci left: 7.866227e-03	ci right 8.863582e-03	k: 1086	n:130000
Cons ci ratio: 2.230051e-02	ci left: 1.898926e-01	ci right 1.941827e-01	k: 24964	n:130000
KS ci ratio: 9.730237e-02	ci left: 1.173041e-02	ci right 1.293764e-02	k: 1602	n:130000
MST1R   130000 perm   36 sec   (3579 perm/sec)   p_kst 1.232308e-02   p_cons 1.920308e-01   p_joint 8.353846e-03

Joint ci ratio: 1.395175e-01	ci left: 5.215803e-03	ci right 6.004885e-03	k: 784	n:140000
Cons ci ratio: 2.148357e-02	ci left: 1.900534e-01	ci right 1.941879e-01	k: 26896	n:140000
KS ci ratio: 9.357946e-02	ci left: 1.179896e-02	ci right 1.296423e-02	k: 1732	n:140000
MST1R   140000 perm   41 sec   (3413 perm/sec)   p_kst 1.237143e-02   p_cons 1.921143e-01   p_joint 5.600000e-03

Joint ci ratio: 1.187405e-01	ci left: 6.784826e-03	ci right 7.647720e-03	k: 1081	n:150000
Cons ci ratio: 2.074139e-02	ci left: 1.903281e-01	ci right 1.943238e-01	k: 28848	n:150000
KS ci ratio: 9.010676e-02	ci left: 1.189823e-02	ci right 1.302740e-02	k: 1868	n:150000
MST1R   150000 perm   45 sec   (3342 perm/sec)   p_kst 1.245333e-02   p_cons 1.923200e-01   p_joint 7.206667e-03

Joint ci ratio: 1.150269e-01	ci left: 6.791553e-03	ci right 7.626454e-03	k: 1152	n:160000
Cons ci ratio: 2.006229e-02	ci left: 1.907076e-01	ci right 1.945786e-01	k: 30822	n:160000
KS ci ratio: 8.745899e-02	ci left: 1.185737e-02	ci right 1.294790e-02	k: 1983	n:160000
MST1R   160000 perm   48 sec   (3312 perm/sec)   p_kst 1.239375e-02   p_cons 1.926375e-01   p_joint 7.200000e-03

Joint ci ratio: 1.114580e-01	ci left: 6.820736e-03	ci right 7.631499e-03	k: 1227	n:170000
Cons ci ratio: 1.947892e-02	ci left: 1.905168e-01	ci right 1.942702e-01	k: 32706	n:170000
KS ci ratio: 8.470540e-02	ci left: 1.191389e-02	ci right 1.297342e-02	k: 2114	n:170000
MST1R   170000 perm   53 sec   (3208 perm/sec)   p_kst 1.243529e-02   p_cons 1.923882e-01   p_joint 7.217647e-03

Joint ci ratio: 1.079519e-01	ci left: 6.879471e-03	ci right 7.669856e-03	k: 1308	n:180000
Cons ci ratio: 1.894702e-02	ci left: 1.902933e-01	ci right 1.939388e-01	k: 34580	n:180000
KS ci ratio: 8.193831e-02	ci left: 1.204081e-02	ci right 1.307497e-02	k: 2259	n:180000
MST1R   180000 perm   57 sec   (3180 perm/sec)   p_kst 1.255000e-02   p_cons 1.921111e-01   p_joint 7.266667e-03

Joint ci ratio: 1.052925e-01	ci left: 6.860618e-03	ci right 7.628216e-03	k: 1375	n:190000
Cons ci ratio: 1.843017e-02	ci left: 1.905352e-01	ci right 1.940847e-01	k: 36538	n:190000
KS ci ratio: 7.993219e-02	ci left: 1.200009e-02	ci right 1.300434e-02	k: 2374	n:190000
MST1R   190000 perm   60 sec   (3153 perm/sec)   p_kst 1.249474e-02   p_cons 1.923053e-01   p_joint 7.236842e-03

Joint ci ratio: 1.024990e-01	ci left: 6.887718e-03	ci right 7.636671e-03	k: 1451	n:200000
Cons ci ratio: 1.797801e-02	ci left: 1.903306e-01	ci right 1.937883e-01	k: 38411	n:200000
KS ci ratio: 7.775095e-02	ci left: 1.206179e-02	ci right 1.304241e-02	k: 2509	n:200000
MST1R   200000 perm   64 sec   (3129 perm/sec)   p_kst 1.254500e-02   p_cons 1.920550e-01   p_joint 7.255000e-03

Joint ci ratio: 9.985078e-02	ci left: 6.921767e-03	ci right 7.653837e-03	k: 1529	n:210000
Cons ci ratio: 1.754813e-02	ci left: 1.903125e-01	ci right 1.936864e-01	k: 40319	n:210000
KS ci ratio: 7.579711e-02	ci left: 1.209926e-02	ci right 1.305712e-02	k: 2640	n:210000
MST1R   210000 perm   68 sec   (3091 perm/sec)   p_kst 1.257143e-02   p_cons 1.919952e-01   p_joint 7.280952e-03

Outputting figure to mutsig2_images.part000000000109/MST1R.2_4283_210000_0.012571_0.192_0.007281.png
                gene_name: MST1R
               theta_stop: 0.100 
                    nperm: 210000 
                     p_ks: 0.013 
        ci_ks_bounds_left: 0.012 
       ci_ks_bounds_right: 0.013 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.0073 
     ci_joint_bounds_left: 0.0069 
    ci_joint_bounds_right: 0.0077 

Current progress: 75 percent done.
MTMR11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.112025e-02	ci left: 1.815648e-01	ci right 1.970166e-01	k: 1892	n:10000
Cons ci ratio: 8.157234e-02	ci left: 1.798919e-01	ci right 1.952906e-01	k: 1875	n:10000
KS ci ratio: 4.944042e-02	ci left: 3.763431e-01	ci right 3.955234e-01	k: 3859	n:10000
MTMR11   10000 perm   2 sec   (6399 perm/sec)   p_kst 3.859000e-01   p_cons 1.875000e-01   p_joint 1.892000e-01

Outputting figure to mutsig2_images.part000000000109/MTMR11.2_2237_10000_0.3859_0.1875_0.1892.png
                gene_name: MTMR11
               theta_stop: 0.082 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.20 

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.165.3896/
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/181708/iteration1/scatter.0000000109
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 109 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120090: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000110> was used as the working directory.
Started at Wed Oct 10 10:43:49 2012
Results reported at Wed Oct 10 10:46:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000110.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000110.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 110  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    201.95 sec.
    Max Memory :      1521 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.165.3896/
-whichjob
110
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 110: processing genes 9862 - 9952
Calculating significance of each gene.
Using projection method.
9862	MUC2	1
9863	MUC20	1
9864	MUC21	2.605323e-01
9865	MUC4	1
9866	MUC5B	3.988744e-01
9867	MUC6	4.754097e-01
9868	MUC7	8.165322e-02
9869	MUCL1	1
9870	MUDENG	2.241090e-01
9871	MUL1	1
9872	MUM1	5.874223e-02
9873	MUM1L1	1
9874	MURC	1
9875	MUS81	1
9876	MUSK	1
9877	MUSTN1	1
9878	MUT	1
9879	MUTED	1
9880	MUTYH	1
9881	MVD	1
9882	MVK	1
9883	MVP	1
9884	MX1	1
9885	MX2	1
9886	MXD1	1
9887	MXD3	1
9888	MXD4	1
9889	MXI1	1
9890	MXRA5	2.456814e-01
9891	MXRA7	1
9892	MXRA8	1
9893	MYADM	1
9894	MYB	3.193324e-01
9895	MYBBP1A	1
9896	MYBL1	1
9897	MYBL2	1
9898	MYBPC1	1.307742e-01
9899	MYBPC2	1
9900	MYBPC3	1
9901	MYBPH	1.367549e-01
9902	MYBPHL	1
9903	MYC	1
9904	MYCBP	1
9905	MYCBP2	4.970737e-01
9906	MYCBPAP	1
9907	MYCL1	1
9908	MYCN	3.570691e-02
9909	MYCT1	1
9910	MYD88	1
9911	MYEF2	1
9912	MYEOV	1
9913	MYEOV2	1
9914	MYF5	1
9915	MYF6	1
9916	MYH1	5.472877e-01
9917	MYH10	1
9918	MYH11	1
9919	MYH13	8.706349e-02
9920	MYH14	1
9921	MYH15	3.080508e-01
9922	MYH2	3.915423e-02
9923	MYH3	1
9924	MYH4	2.156575e-01
9925	MYH6	1
9926	MYH7	9.323475e-03
9927	MYH7B	2.515553e-02
9928	MYH8	3.162624e-01
9929	MYH9	2.515469e-01
9930	MYL1	1
9931	MYL10	1
9932	MYL12A	1
9933	MYL12B	1
9934	MYL2	1
9935	MYL3	1
9936	MYL4	1
9937	MYL5	1
9938	MYL6	1
9939	MYL6B	1
9940	MYL7	1
9941	MYL9	1
9942	MYLIP	1
9943	MYLK	2.114264e-01
9944	MYLK2	1
9945	MYLK3	1
9946	MYLK4	1
9947	MYLPF	1
9948	MYNN	1
9949	MYO10	6.229758e-01
9950	MYO15A	2.739359e-01
9951	MYO16	1
9952	MYO18A	5.447312e-01
Done

Running MutSig 2:
Scatter job 110: processing genes 9862 - 9952
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
MYH7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.851453e-02	ci left: 3.853009e-01	ci right 4.045604e-01	k: 3949	n:10000
Cons ci ratio: 7.954312e-02	ci left: 1.875697e-01	ci right 2.032082e-01	k: 1953	n:10000
KS ci ratio: 3.564690e-02	ci left: 5.374815e-01	ci right 5.570909e-01	k: 5473	n:10000
MYH7   10000 perm   2 sec   (4241 perm/sec)   p_kst 5.473000e-01   p_cons 1.953000e-01   p_joint 3.949000e-01

Outputting figure to mutsig2_images.part000000000110/MYH7.4_5960_10000_0.5473_0.1953_0.3949.png
                gene_name: MYH7
               theta_stop: 0.080 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.39 
    ci_joint_bounds_right: 0.40 

Current progress: 7 percent done.
MYH1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.852074e-02	ci left: 1.916074e-01	ci right 2.073681e-01	k: 1994	n:10000
Cons ci ratio: 1.389664e-01	ci left: 6.855690e-02	ci right 7.889307e-02	k: 736	n:10000
KS ci ratio: 4.260207e-02	ci left: 4.485975e-01	ci right 4.682268e-01	k: 4584	n:10000
MYH1   10000 perm   2 sec   (4586 perm/sec)   p_kst 4.584000e-01   p_cons 7.360000e-02   p_joint 1.994000e-01

Joint ci ratio: 4.068187e-02	ci left: 3.105533e-01	ci right 3.235000e-01	k: 6340	n:20000
Cons ci ratio: 9.730737e-02	ci left: 7.138662e-02	ci right 7.873749e-02	k: 1500	n:20000
KS ci ratio: 3.017226e-02	ci left: 4.507270e-01	ci right 4.645854e-01	k: 9153	n:20000
MYH1   20000 perm   5 sec   (4089 perm/sec)   p_kst 4.576500e-01   p_cons 7.500000e-02   p_joint 3.170000e-01

Outputting figure to mutsig2_images.part000000000110/MYH1.3_5972_20000_0.45765_0.075_0.317.png
                gene_name: MYH1
               theta_stop: 0.097 
                    nperm: 20000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.075 
      ci_cons_bounds_left: 0.071 
     ci_cons_bounds_right: 0.079 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.32 

Current progress: 13 percent done.
MYH2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.207474e-02	ci left: 3.521745e-01	ci right 3.711061e-01	k: 3616	n:10000
Cons ci ratio: 1.216940e-01	ci left: 8.825186e-02	ci right 9.978590e-02	k: 939	n:10000
KS ci ratio: 3.178368e-02	ci left: 5.936327e-01	ci right 6.129071e-01	k: 6033	n:10000
MYH2   10000 perm   2 sec   (4456 perm/sec)   p_kst 6.033000e-01   p_cons 9.390000e-02   p_joint 3.616000e-01

Joint ci ratio: 3.722844e-02	ci left: 3.499578e-01	ci right 3.632839e-01	k: 7132	n:20000
Cons ci ratio: 8.736650e-02	ci left: 8.744074e-02	ci right 9.547849e-02	k: 1828	n:20000
KS ci ratio: 2.233974e-02	ci left: 5.993886e-01	ci right 6.129806e-01	k: 12124	n:20000
MYH2   20000 perm   5 sec   (3927 perm/sec)   p_kst 6.062000e-01   p_cons 9.140000e-02   p_joint 3.566000e-01

Outputting figure to mutsig2_images.part000000000110/MYH2.3_5978_20000_0.6062_0.0914_0.3566.png
                gene_name: MYH2
               theta_stop: 0.087 
                    nperm: 20000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.091 
      ci_cons_bounds_left: 0.087 
     ci_cons_bounds_right: 0.095 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.36 

Current progress: 20 percent done.
MYH7B
Processing conservation and coverage...
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: 3.521033e-02	ci left: 5.435919e-01	ci right 5.631770e-01	k: 5534	n:10000
KS ci ratio: 6.213439e-02	ci left: 2.757699e-01	ci right 2.935557e-01	k: 2846	n:10000
MYH7B   10000 perm   2 sec   (4037 perm/sec)   p_kst 2.846000e-01   p_cons 5.534000e-01   p_joint 3.265000e-01

Outputting figure to mutsig2_images.part000000000110/MYH7B.3_6124_10000_0.2846_0.5534_0.3265.png
                gene_name: MYH7B
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.55 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 27 percent done.
MUC4
Processing conservation and coverage...
Processing mutations... 
Skipping 2 mutations outside exons of this gene.
Fewer than 2 mutations to analyze: skipping this gene...
Current progress: 33 percent done.
MUC5B
Processing conservation and coverage...
57% 
Processing mutations... 
Skipping 1 mutations outside transcript range of this gene.
Fewer than 2 mutations to analyze: skipping this gene...
Current progress: 40 percent done.
MXRA5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.377056e-02	ci left: 8.839084e-01	ci right 8.962634e-01	k: 8902	n:10000
Cons ci ratio: 8.215927e-03	ci left: 9.538829e-01	ci right 9.618476e-01	k: 9580	n:10000
KS ci ratio: 2.228902e-01	ci left: 2.664945e-02	ci right 3.342800e-02	k: 299	n:10000
MXRA5   10000 perm   3 sec   (3709 perm/sec)   p_kst 2.990000e-02   p_cons 9.580000e-01   p_joint 8.902000e-01

Joint ci ratio: 2.481355e-02	ci left: 5.481801e-01	ci right 5.620039e-01	k: 11102	n:20000
Cons ci ratio: 5.942305e-03	ci left: 9.531686e-01	ci right 9.588979e-01	k: 19122	n:20000
KS ci ratio: 1.578823e-01	ci left: 2.753511e-02	ci right 3.230286e-02	k: 597	n:20000
MXRA5   20000 perm   6 sec   (3505 perm/sec)   p_kst 2.985000e-02   p_cons 9.561000e-01   p_joint 5.551000e-01

Joint ci ratio: 1.866501e-02	ci left: 5.895865e-01	ci right 6.007284e-01	k: 17855	n:30000
Cons ci ratio: 4.771656e-03	ci left: 9.551217e-01	ci right 9.597225e-01	k: 28724	n:30000
KS ci ratio: 1.295830e-01	ci left: 2.767889e-02	ci right 3.154626e-02	k: 887	n:30000
MXRA5   30000 perm   9 sec   (3492 perm/sec)   p_kst 2.956667e-02   p_cons 9.574667e-01   p_joint 5.951667e-01

Joint ci ratio: 1.590639e-02	ci left: 5.980851e-01	ci right 6.076999e-01	k: 24116	n:40000
Cons ci ratio: 4.113839e-03	ci left: 9.558093e-01	ci right 9.597738e-01	k: 38313	n:40000
KS ci ratio: 1.116410e-01	ci left: 2.822835e-02	ci right 3.159035e-02	k: 1195	n:40000
MXRA5   40000 perm   12 sec   (3461 perm/sec)   p_kst 2.987500e-02   p_cons 9.578250e-01   p_joint 6.029000e-01

Joint ci ratio: 1.547916e-02	ci left: 5.575376e-01	ci right 5.662552e-01	k: 28095	n:50000
Cons ci ratio: 3.695932e-03	ci left: 9.556543e-01	ci right 9.592124e-01	k: 47873	n:50000
KS ci ratio: 1.002705e-01	ci left: 2.817084e-02	ci right 3.116409e-02	k: 1482	n:50000
MXRA5   50000 perm   15 sec   (3428 perm/sec)   p_kst 2.964000e-02   p_cons 9.574600e-01   p_joint 5.619000e-01

Joint ci ratio: 1.599067e-02	ci left: 4.963743e-01	ci right 5.043923e-01	k: 30023	n:60000
Cons ci ratio: 3.121311e-03	ci left: 9.618326e-01	ci right 9.648557e-01	k: 57802	n:60000
KS ci ratio: 9.123350e-02	ci left: 2.848650e-02	ci right 3.122589e-02	k: 1790	n:60000
MXRA5   60000 perm   18 sec   (3391 perm/sec)   p_kst 2.983333e-02   p_cons 9.633667e-01   p_joint 5.003833e-01

Outputting figure to mutsig2_images.part000000000110/MXRA5.2_8511_60000_0.029833_0.96337_0.50038.png
                gene_name: MXRA5
               theta_stop: 0.091 
                    nperm: 60000 
                     p_ks: 0.030 
        ci_ks_bounds_left: 0.028 
       ci_ks_bounds_right: 0.031 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.96 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.50 
    ci_joint_bounds_right: 0.50 

Current progress: 47 percent done.
MYBPC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.974422e-02	ci left: 3.734575e-01	ci right 3.926107e-01	k: 3830	n:10000
Cons ci ratio: 3.342919e-02	ci left: 5.691511e-01	ci right 5.886029e-01	k: 5789	n:10000
KS ci ratio: 7.376657e-02	ci left: 2.120120e-01	ci right 2.283513e-01	k: 2201	n:10000
MYBPC1   10000 perm   2 sec   (5625 perm/sec)   p_kst 2.201000e-01   p_cons 5.789000e-01   p_joint 3.830000e-01

Outputting figure to mutsig2_images.part000000000110/MYBPC1.2_3698_10000_0.2201_0.5789_0.383.png
                gene_name: MYBPC1
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 53 percent done.
MYCBP2
Processing conservation and coverage...
69% 
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: 1.028186e-01	ci left: 1.203376e-01	ci right 1.334806e-01	k: 1268	n:10000
KS ci ratio: 4.555035e-02	ci left: 4.156828e-01	ci right 4.351607e-01	k: 4254	n:10000
MYCBP2   10000 perm   3 sec   (3245 perm/sec)   p_kst 4.254000e-01   p_cons 1.268000e-01   p_joint 9.200000e-01

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	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: 3.187486e-02	ci left: 4.236732e-01	ci right 4.374470e-01	k: 8611	n:20000
MYCBP2   20000 perm   7 sec   (2998 perm/sec)   p_kst 4.305500e-01   p_cons 1.257000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000110/MYCBP2.2_14369_20000_0.43055_0.1257_1.png
                gene_name: MYCBP2
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.13 
      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: 60 percent done.
MYH13
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.063072e-02	ci left: 7.748905e-01	ci right 7.911443e-01	k: 7831	n:10000
Cons ci ratio: 2.574656e-02	ci left: 6.894995e-01	ci right 7.075847e-01	k: 6986	n:10000
KS ci ratio: 2.748407e-02	ci left: 6.610882e-01	ci right 6.796124e-01	k: 6704	n:10000
MYH13   10000 perm   2 sec   (4774 perm/sec)   p_kst 6.704000e-01   p_cons 6.986000e-01   p_joint 7.831000e-01

Outputting figure to mutsig2_images.part000000000110/MYH13.2_5973_10000_0.6704_0.6986_0.7831.png
                gene_name: MYH13
               theta_stop: 0.027 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.68 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.69 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.79 

Current progress: 67 percent done.
MYH15
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: 3.347034e-02	ci left: 5.685494e-01	ci right 5.880049e-01	k: 5783	n:10000
KS ci ratio: 1.914655e-02	ci left: 7.995320e-01	ci right 8.150886e-01	k: 8074	n:10000
MYH15   10000 perm   2 sec   (4917 perm/sec)   p_kst 8.074000e-01   p_cons 5.783000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000110/MYH15.2_6009_10000_0.8074_0.5783_1.png
                gene_name: MYH15
               theta_stop: 0.033 
                    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: 73 percent done.
MYH4
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: 6.635571e-02	ci left: 2.500393e-01	ci right 2.673015e-01	k: 2586	n:10000
KS ci ratio: 1.488668e-02	ci left: 8.673368e-01	ci right 8.804445e-01	k: 8740	n:10000
MYH4   10000 perm   2 sec   (4099 perm/sec)   p_kst 8.740000e-01   p_cons 2.586000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000110/MYH4.2_5972_10000_0.874_0.2586_1.png
                gene_name: MYH4
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.87 
       ci_ks_bounds_right: 0.88 
                   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: 80 percent done.
MYH9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.358024e-02	ci left: 5.669450e-01	ci right 5.864103e-01	k: 5767	n:10000
Cons ci ratio: 3.727395e-02	ci left: 5.152564e-01	ci right 5.349290e-01	k: 5251	n:10000
KS ci ratio: 4.758343e-02	ci left: 3.945608e-01	ci right 4.138950e-01	k: 4042	n:10000
MYH9   10000 perm   2 sec   (4938 perm/sec)   p_kst 4.042000e-01   p_cons 5.251000e-01   p_joint 5.767000e-01

Outputting figure to mutsig2_images.part000000000110/MYH9.2_6043_10000_0.4042_0.5251_0.5767.png
                gene_name: MYH9
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.40 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.41 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 87 percent done.
MYLK
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.885068e-03	ci left: 9.822058e-01	ci right 9.871060e-01	k: 9848	n:10000
Cons ci ratio: 2.397226e-02	ci left: 7.189609e-01	ci right 7.365063e-01	k: 7278	n:10000
KS ci ratio: 3.476387e-02	ci left: 5.499041e-01	ci right 5.694611e-01	k: 5597	n:10000
MYLK   10000 perm   2 sec   (5154 perm/sec)   p_kst 5.597000e-01   p_cons 7.278000e-01   p_joint 9.848000e-01

Outputting figure to mutsig2_images.part000000000110/MYLK.2_5869_10000_0.5597_0.7278_0.9848.png
                gene_name: MYLK
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.74 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.99 

Current progress: 93 percent done.
MYO15A
Processing conservation and coverage...
92% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.312848e-02	ci left: 5.735640e-01	ci right 5.929874e-01	k: 5833	n:10000
Cons ci ratio: 6.673845e-02	ci left: 2.478638e-01	ci right 2.650783e-01	k: 2564	n:10000
KS ci ratio: 1.813674e-02	ci left: 8.160871e-01	ci right 8.311239e-01	k: 8237	n:10000
MYO15A   10000 perm   3 sec   (3905 perm/sec)   p_kst 8.237000e-01   p_cons 2.564000e-01   p_joint 5.833000e-01

Outputting figure to mutsig2_images.part000000000110/MYO15A.2_10849_10000_0.8237_0.2564_0.5833.png
                gene_name: MYO15A
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  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.165.3896/
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/181708/iteration1/scatter.0000000110
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 110 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120095: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000111> was used as the working directory.
Started at Wed Oct 10 10:43:59 2012
Results reported at Wed Oct 10 10:46:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000111.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000111.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 111  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    166.04 sec.
    Max Memory :      1430 MB
    Max Swap   :      3803 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.165.3896/
-whichjob
111
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 111: processing genes 9953 - 10042
Calculating significance of each gene.
Using projection method.
9953	MYO18B	2.189124e-01
9954	MYO19	1.746145e-01
9955	MYO1A	3.251199e-01
9956	MYO1B	1
9957	MYO1C	4.001582e-02
9958	MYO1D	3.200363e-01
9959	MYO1E	1
9960	MYO1F	3.412063e-01
9961	MYO1G	1
9962	MYO1H	1
9963	MYO3A	8.382453e-02
9964	MYO3B	1
9965	MYO5A	1
9966	MYO5B	1.570052e-01
9967	MYO5C	1
9968	MYO6	1.143104e-01
9969	MYO7A	4.775588e-01
9970	MYO7B	1
9971	MYO9A	6.100242e-01
9972	MYO9B	1
9973	MYOC	1.321987e-01
9974	MYOCD	1.661711e-01
9975	MYOD1	1
9976	MYOF	1.531165e-01
9977	MYOG	1.167276e-01
9978	MYOM1	4.274015e-01
9979	MYOM2	1
9980	MYOM3	1.181367e-01
9981	MYOT	1.905350e-02
9982	MYOZ1	1
9983	MYOZ2	1.763257e-02
9984	MYOZ3	1
9985	MYPN	1
9986	MYPOP	1
9987	MYRIP	1
9988	MYSM1	1
9989	MYST1	1
9990	MYST2	1
9991	MYST3	3.785525e-01
9992	MYST4	1.759229e-01
9993	MYT1	1
9994	MYT1L	4.243813e-01
9995	MZF1	1.163324e-01
9996	N4BP1	1.925504e-01
9997	N4BP2	1
9998	N4BP2L1	1
9999	N4BP2L2	2.333452e-01
10000/18094 10000	N4BP3	1
10001	N6AMT1	1
10002	N6AMT2	1
10003	NAA10	1
10004	NAA11	1
10005	NAA15	1.967057e-02
10006	NAA16	3.669611e-01
10007	NAA20	1
10008	NAA25	3.330403e-04
10009	NAA30	1
10010	NAA35	7.607242e-02
10011	NAA38	1
10012	NAA40	1
10013	NAA50	1
10014	NAAA	1
10015	NAALAD2	1
10016	NAALADL1	1
10017	NAALADL2	1
10018	NAB1	1
10019	NAB2	1
10020	NACA	1
10021	NACA2	1
10022	NACC1	1
10023	NACC2	1
10024	NADK	9.042303e-02
10025	NADSYN1	1
10026	NAE1	1
10027	NAF1	1
10028	NAGA	8.114986e-02
10029	NAGK	1
10030	NAGLU	1
10031	NAGPA	1.537266e-01
10032	NAGS	1
10033	NAIF1	1
10034	NALCN	3.379966e-01
10035	NAMPT	1
10036	NANOG	2.409997e-02
10037	NANOS2	1
10038	NANOS3	6.027267e-02
10039	NANP	1
10040	NANS	1
10041	NAP1L1	1
10042	NAP1L2	1
Done

Running MutSig 2:
Scatter job 111: processing genes 9953 - 10042
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NAA25
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.136050e-02	ci left: 2.234596e-01	ci right 2.400969e-01	k: 2317	n:10000
Cons ci ratio: 1.691241e-02	ci left: 8.358217e-01	ci right 8.501778e-01	k: 8431	n:10000
KS ci ratio: 1.109326e-01	ci left: 1.048095e-01	ci right 1.172181e-01	k: 1109	n:10000
NAA25   10000 perm   2 sec   (4925 perm/sec)   p_kst 1.109000e-01   p_cons 8.431000e-01   p_joint 2.317000e-01

Joint ci ratio: 5.368043e-02	ci left: 2.048181e-01	ci right 2.161662e-01	k: 4209	n:20000
Cons ci ratio: 1.194241e-02	ci left: 8.383391e-01	ci right 8.484609e-01	k: 16869	n:20000
KS ci ratio: 7.725382e-02	ci left: 1.096268e-01	ci right 1.184858e-01	k: 2280	n:20000
NAA25   20000 perm   6 sec   (3237 perm/sec)   p_kst 1.140000e-01   p_cons 8.434500e-01   p_joint 2.104500e-01

Outputting figure to mutsig2_images.part000000000111/NAA25.4_3015_20000_0.114_0.84345_0.21045.png
                gene_name: NAA25
               theta_stop: 0.077 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.85 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.22 

Current progress: 8 percent done.
MYO18B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.116368e-02	ci left: 4.656703e-01	ci right 4.853440e-01	k: 4755	n:10000
Cons ci ratio: 6.340926e-02	ci left: 2.676508e-01	ci right 2.852796e-01	k: 2764	n:10000
KS ci ratio: 3.746117e-02	ci left: 5.127548e-01	ci right 5.324320e-01	k: 5226	n:10000
MYO18B   10000 perm   2 sec   (4288 perm/sec)   p_kst 5.226000e-01   p_cons 2.764000e-01   p_joint 4.755000e-01

Outputting figure to mutsig2_images.part000000000111/MYO18B.2_7872_10000_0.5226_0.2764_0.4755.png
                gene_name: MYO18B
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.29 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 17 percent done.
MYO1C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.157470e-02	ci left: 2.794346e-01	ci right 2.972888e-01	k: 2883	n:10000
Cons ci ratio: 1.244153e-01	ci left: 8.465526e-02	ci right 9.598471e-02	k: 902	n:10000
KS ci ratio: 4.385883e-02	ci left: 4.342293e-01	ci right 4.538033e-01	k: 4440	n:10000
MYO1C   10000 perm   2 sec   (5524 perm/sec)   p_kst 4.440000e-01   p_cons 9.020000e-02   p_joint 2.883000e-01

Joint ci ratio: 5.760555e-02	ci left: 1.825563e-01	ci right 1.934346e-01	k: 3759	n:20000
Cons ci ratio: 9.062170e-02	ci left: 8.166013e-02	ci right 8.946085e-02	k: 1710	n:20000
KS ci ratio: 3.084964e-02	ci left: 4.397432e-01	ci right 4.535723e-01	k: 8933	n:20000
MYO1C   20000 perm   4 sec   (4975 perm/sec)   p_kst 4.466500e-01   p_cons 8.550000e-02   p_joint 1.879500e-01

Outputting figure to mutsig2_images.part000000000111/MYO1C.2_3342_20000_0.44665_0.0855_0.18795.png
                gene_name: MYO1C
               theta_stop: 0.091 
                    nperm: 20000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.086 
      ci_cons_bounds_left: 0.082 
     ci_cons_bounds_right: 0.089 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.19 

Current progress: 25 percent done.
MYO3A
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: 3.489805e-02	ci left: 5.480002e-01	ci right 5.675661e-01	k: 5578	n:10000
KS ci ratio: 3.423102e-02	ci left: 5.575209e-01	ci right 5.770399e-01	k: 5673	n:10000
MYO3A   10000 perm   2 sec   (5052 perm/sec)   p_kst 5.673000e-01   p_cons 5.578000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000111/MYO3A.2_4983_10000_0.5673_0.5578_1.png
                gene_name: MYO3A
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   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: 33 percent done.
MYO5B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.573306e-02	ci left: 8.543705e-01	ci right 8.680184e-01	k: 8613	n:10000
Cons ci ratio: 2.682742e-02	ci left: 6.717631e-01	ci right 6.901314e-01	k: 6810	n:10000
KS ci ratio: 2.689535e-02	ci left: 6.706551e-01	ci right 6.890400e-01	k: 6799	n:10000
MYO5B   10000 perm   2 sec   (4821 perm/sec)   p_kst 6.799000e-01   p_cons 6.810000e-01   p_joint 8.613000e-01

Outputting figure to mutsig2_images.part000000000111/MYO5B.2_5707_10000_0.6799_0.681_0.8613.png
                gene_name: MYO5B
               theta_stop: 0.027 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.87 

Current progress: 42 percent done.
MYO6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.600319e-01	ci left: 5.205444e-02	ci right 6.120599e-02	k: 565	n:10000
Cons ci ratio: 2.276270e-01	ci left: 2.551545e-02	ci right 3.216281e-02	k: 287	n:10000
KS ci ratio: 2.452330e-02	ci left: 7.097745e-01	ci right 7.274979e-01	k: 7187	n:10000
MYO6   10000 perm   2 sec   (5370 perm/sec)   p_kst 7.187000e-01   p_cons 2.870000e-02   p_joint 5.650000e-02

Joint ci ratio: 3.704661e-02	ci left: 3.521982e-01	ci right 3.655428e-01	k: 7177	n:20000
Cons ci ratio: 1.616844e-01	ci left: 2.623765e-02	ci right 3.090076e-02	k: 570	n:20000
KS ci ratio: 1.715240e-02	ci left: 7.168414e-01	ci right 7.292937e-01	k: 14462	n:20000
MYO6   20000 perm   4 sec   (4778 perm/sec)   p_kst 7.231000e-01   p_cons 2.850000e-02   p_joint 3.588500e-01

Joint ci ratio: 4.141768e-02	ci left: 2.251483e-01	ci right 2.347040e-01	k: 6897	n:30000
Cons ci ratio: 1.332622e-01	ci left: 2.616234e-02	ci right 2.992980e-02	k: 840	n:30000
KS ci ratio: 1.395253e-02	ci left: 7.195068e-01	ci right 7.296497e-01	k: 21738	n:30000
MYO6   30000 perm   7 sec   (4485 perm/sec)   p_kst 7.246000e-01   p_cons 2.800000e-02   p_joint 2.299000e-01

Joint ci ratio: 3.762992e-02	ci left: 2.093685e-01	ci right 2.174231e-01	k: 8535	n:40000
Cons ci ratio: 1.159061e-01	ci left: 2.618647e-02	ci right 2.943257e-02	k: 1111	n:40000
KS ci ratio: 1.207420e-02	ci left: 7.204950e-01	ci right 7.292723e-01	k: 28996	n:40000
MYO6   40000 perm   9 sec   (4338 perm/sec)   p_kst 7.249000e-01   p_cons 2.777500e-02   p_joint 2.133750e-01

Joint ci ratio: 4.193875e-02	ci left: 1.456117e-01	ci right 1.518692e-01	k: 7436	n:50000
Cons ci ratio: 1.028732e-01	ci left: 2.676641e-02	ci right 2.968870e-02	k: 1410	n:50000
KS ci ratio: 1.082821e-02	ci left: 7.198982e-01	ci right 7.277558e-01	k: 36192	n:50000
MYO6   50000 perm   12 sec   (4252 perm/sec)   p_kst 7.238400e-01   p_cons 2.820000e-02   p_joint 1.487200e-01

Joint ci ratio: 4.591614e-02	ci left: 1.058241e-01	ci right 1.108138e-01	k: 6498	n:60000
Cons ci ratio: 9.282141e-02	ci left: 2.752516e-02	ci right 3.022067e-02	k: 1731	n:60000
KS ci ratio: 9.864339e-03	ci left: 7.210734e-01	ci right 7.282382e-01	k: 43480	n:60000
MYO6   60000 perm   14 sec   (4172 perm/sec)   p_kst 7.246667e-01   p_cons 2.885000e-02   p_joint 1.083000e-01

Outputting figure to mutsig2_images.part000000000111/MYO6.2_3994_60000_0.72467_0.02885_0.1083.png
                gene_name: MYO6
               theta_stop: 0.093 
                    nperm: 60000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.029 
      ci_cons_bounds_left: 0.028 
     ci_cons_bounds_right: 0.030 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.11 

Current progress: 50 percent done.
MYO9B
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: 3.960380e-02	ci left: 4.849534e-01	ci right 5.046496e-01	k: 4948	n:10000
KS ci ratio: 1.965582e-02	ci left: 7.911103e-01	ci right 8.069151e-01	k: 7991	n:10000
MYO9B   10000 perm   2 sec   (4695 perm/sec)   p_kst 7.991000e-01   p_cons 4.948000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000111/MYO9B.2_6641_10000_0.7991_0.4948_1.png
                gene_name: MYO9B
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.80 
        ci_ks_bounds_left: 0.79 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 58 percent done.
MYOF
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: 2.434755e-02	ci left: 7.127015e-01	ci right 7.303692e-01	k: 7216	n:10000
KS ci ratio: 6.198219e-02	ci left: 2.767603e-01	ci right 2.945647e-01	k: 2856	n:10000
MYOF   10000 perm   2 sec   (4626 perm/sec)   p_kst 2.856000e-01   p_cons 7.216000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000111/MYOF.2_6402_10000_0.2856_0.7216_1.png
                gene_name: MYOF
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.29 
                   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: 67 percent done.
MYOM3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.584033e-02	ci left: 4.125930e-01	ci right 4.320522e-01	k: 4223	n:10000
Cons ci ratio: 2.945480e-02	ci left: 6.295976e-01	ci right 6.485213e-01	k: 6391	n:10000
KS ci ratio: 7.757470e-02	ci left: 1.954493e-01	ci right 2.113238e-01	k: 2033	n:10000
MYOM3   10000 perm   2 sec   (4372 perm/sec)   p_kst 2.033000e-01   p_cons 6.391000e-01   p_joint 4.223000e-01

Outputting figure to mutsig2_images.part000000000111/MYOM3.2_4458_10000_0.2033_0.6391_0.4223.png
                gene_name: MYOM3
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.42 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.43 

Current progress: 75 percent done.
MYOT
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.251794e-02	ci left: 2.732942e-01	ci right 2.910328e-01	k: 2821	n:10000
Cons ci ratio: 7.798399e-02	ci left: 1.937745e-01	ci right 2.095997e-01	k: 2016	n:10000
KS ci ratio: 3.716947e-02	ci left: 5.166574e-01	ci right 5.363271e-01	k: 5265	n:10000
MYOT   10000 perm   2 sec   (6350 perm/sec)   p_kst 5.265000e-01   p_cons 2.016000e-01   p_joint 2.821000e-01

Outputting figure to mutsig2_images.part000000000111/MYOT.2_1533_10000_0.5265_0.2016_0.2821.png
                gene_name: MYOT
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.28 
     ci_joint_bounds_left: 0.27 
    ci_joint_bounds_right: 0.29 

Current progress: 83 percent done.
MYST4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.104853e-01	ci left: 1.055899e-01	ci right 1.180372e-01	k: 1117	n:10000
Cons ci ratio: 1.234410e-01	ci left: 8.591861e-02	ci right 9.732058e-02	k: 915	n:10000
KS ci ratio: 6.825929e-02	ci left: 2.394614e-01	ci right 2.564857e-01	k: 2479	n:10000
MYST4   10000 perm   2 sec   (4613 perm/sec)   p_kst 2.479000e-01   p_cons 9.150000e-02   p_joint 1.117000e-01

Joint ci ratio: 8.454669e-02	ci left: 9.293210e-02	ci right 1.011855e-01	k: 1940	n:20000
Cons ci ratio: 8.805710e-02	ci left: 8.616660e-02	ci right 9.415302e-02	k: 1802	n:20000
KS ci ratio: 4.830587e-02	ci left: 2.416798e-01	ci right 2.536936e-01	k: 4953	n:20000
MYST4   20000 perm   5 sec   (4183 perm/sec)   p_kst 2.476500e-01   p_cons 9.010000e-02   p_joint 9.700000e-02

Outputting figure to mutsig2_images.part000000000111/MYST4.2_6286_20000_0.24765_0.0901_0.097.png
                gene_name: MYST4
               theta_stop: 0.088 
                    nperm: 20000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.090 
      ci_cons_bounds_left: 0.086 
     ci_cons_bounds_right: 0.094 
                  p_joint: 0.097 
     ci_joint_bounds_left: 0.093 
    ci_joint_bounds_right: 0.10 

Current progress: 92 percent done.
NAA15
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: 1.130334e-02	ci left: 9.179100e-01	ci right 9.284419e-01	k: 9233	n:10000
KS ci ratio: 1.836726e-02	ci left: 8.123272e-01	ci right 8.274859e-01	k: 8200	n:10000
NAA15   10000 perm   2 sec   (6000 perm/sec)   p_kst 8.200000e-01   p_cons 9.233000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000111/NAA15.2_2681_10000_0.82_0.9233_1.png
                gene_name: NAA15
               theta_stop: 0.018 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.83 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000111
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 111 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120100: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000112> was used as the working directory.
Started at Wed Oct 10 10:43:59 2012
Results reported at Wed Oct 10 10:47:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000112.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000112.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 112  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    227.61 sec.
    Max Memory :      1600 MB
    Max Swap   :      3897 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.165.3896/
-whichjob
112
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 112: processing genes 10043 - 10133
Calculating significance of each gene.
Using projection method.
10043	NAP1L3	1
10044	NAP1L4	1
10045	NAP1L5	1
10046	NAPA	1
10047	NAPB	1
10048	NAPEPLD	1
10049	NAPG	1
10050	NAPRT1	1
10051	NAPSA	1
10052	NARF	1.350750e-02
10053	NARFL	1
10054	NARG2	1
10055	NARS	1
10056	NARS2	1
10057	NASP	1
10058	NAT1	3.367918e-02
10059	NAT10	1
10060	NAT15	1
10061	NAT2	1
10062	NAT6	1
10063	NAT8	1
10064	NAT8B	1
10065	NAT8L	1
10066	NAT9	1
10067	NAV1	1
10068	NAV2	5.939799e-01
10069	NAV3	5.427370e-01
10070	NBAS	1
10071	NBEA	1.860601e-01
10072	NBEAL1	1
10073	NBEAL2	1
10074	NBL1	1
10075	NBN	4.604384e-02
10076	NBPF1	1
10077	NBPF10	1.668231e-02
10078	NBPF14	5.013287e-02
10079	NBPF15	1
10080	NBPF16	1
10081	NBPF3	1
10082	NBPF7	1
10083	NBPF9	6.992759e-02
10084	NBR1	5.288985e-02
10085	NCALD	1
10086	NCAM1	1
10087	NCAM2	3.657186e-01
10088	NCAN	1
10089	NCAPD2	1.614241e-01
10090	NCAPD3	5.714296e-01
10091	NCAPG	1
10092	NCAPG2	1
10093	NCAPH	1
10094	NCAPH2	1
10095	NCBP1	1
10096	NCBP2	1
10097	NCCRP1	1
10098	NCDN	1
10099	NCEH1	1
10100	NCF1	1
10101	NCF2	7.513897e-03
10102	NCF4	1
10103	NCK1	1
10104	NCK2	1
10105	NCKAP1	1
10106	NCKAP1L	1
10107	NCKAP5	5.897852e-01
10108	NCKAP5L	1
10109	NCKIPSD	1
10110	NCL	1
10111	NCLN	1
10112	NCOA1	3.407761e-01
10113	NCOA2	1
10114	NCOA3	2.944015e-01
10115	NCOA4	1
10116	NCOA5	1.363827e-01
10117	NCOA6	1
10118	NCOA7	1
10119	NCOR1	1.915635e-01
10120	NCOR2	3.722491e-02
10121	NCR1	1
10122	NCR2	1.314190e-01
10123	NCR3	1
10124	NCS1	1
10125	NCSTN	1
10126	NDC80	3.121268e-02
10127	NDE1	1
10128	NDEL1	1
10129	NDFIP1	1
10130	NDFIP2	1
10131	NDN	1
10132	NDNL2	1
10133	NDOR1	1
Done

Running MutSig 2:
Scatter job 112: processing genes 10043 - 10133
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NBPF10
Processing conservation and coverage...
90% 
Processing mutations... 
Skipping 1 mutations outside transcript range of this gene.
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: 5.968344e-03	ci left: 9.743620e-01	ci right 9.802874e-01	k: 9760	n:9985
KS ci ratio: 3.383810e-03	ci left: 9.908300e-01	ci right 9.942737e-01	k: 9927	n:10000
NBPF10   10000 perm   4 sec   (2671 perm/sec)   p_kst 9.927000e-01   p_cons 9.774662e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000112/NBPF10.2_10996_10000_0.9927_0.97747_1.png
                gene_name: NBPF10
               theta_stop: 0.0060 
                    nperm: 10000 
                     p_ks: 0.99 
        ci_ks_bounds_left: 0.99 
       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: 8 percent done.
NBPF9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.478600e-01	ci left: 2.137124e-02	ci right 2.751008e-02	k: 243	n:10000
Cons ci ratio: 1.338395e-01	ci left: 7.368948e-02	ci right 8.435729e-02	k: 789	n:10000
KS ci ratio: 1.396839e-01	ci left: 6.787957e-02	ci right 7.817082e-02	k: 729	n:10000
NBPF9   10000 perm   2 sec   (5203 perm/sec)   p_kst 7.290000e-02   p_cons 7.890000e-02   p_joint 2.430000e-02

Joint ci ratio: 1.362337e-01	ci left: 3.703607e-02	ci right 4.249877e-02	k: 794	n:20000
Cons ci ratio: 9.664763e-02	ci left: 7.231533e-02	ci right 7.970850e-02	k: 1519	n:20000
KS ci ratio: 1.002250e-01	ci left: 6.747821e-02	ci right 7.464710e-02	k: 1420	n:20000
NBPF9   20000 perm   4 sec   (4626 perm/sec)   p_kst 7.100000e-02   p_cons 7.595000e-02   p_joint 3.970000e-02

Joint ci ratio: 7.585851e-02	ci left: 7.862445e-02	ci right 8.485683e-02	k: 2451	n:30000
Cons ci ratio: 7.806395e-02	ci left: 7.449868e-02	ci right 8.058343e-02	k: 2325	n:30000
KS ci ratio: 8.139290e-02	ci left: 6.883823e-02	ci right 7.471169e-02	k: 2152	n:30000
NBPF9   30000 perm   7 sec   (4420 perm/sec)   p_kst 7.173333e-02   p_cons 7.750000e-02   p_joint 8.170000e-02

Outputting figure to mutsig2_images.part000000000112/NBPF9.3_2907_30000_0.071733_0.0775_0.0817.png
                gene_name: NBPF9
               theta_stop: 0.081 
                    nperm: 30000 
                     p_ks: 0.072 
        ci_ks_bounds_left: 0.069 
       ci_ks_bounds_right: 0.075 
                   p_cons: 0.077 
      ci_cons_bounds_left: 0.074 
     ci_cons_bounds_right: 0.081 
                  p_joint: 0.082 
     ci_joint_bounds_left: 0.079 
    ci_joint_bounds_right: 0.085 

Current progress: 17 percent done.
NBR1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.037572e-01	ci left: 1.183824e-01	ci right 1.314370e-01	k: 1248	n:10000
Cons ci ratio: 1.300347e-01	ci left: 7.785885e-02	ci right 8.878533e-02	k: 832	n:10000
KS ci ratio: 4.549450e-02	ci left: 4.162808e-01	ci right 4.357623e-01	k: 4260	n:10000
NBR1   10000 perm   2 sec   (5648 perm/sec)   p_kst 4.260000e-01   p_cons 8.320000e-02   p_joint 1.248000e-01

Joint ci ratio: 4.713597e-02	ci left: 2.508553e-01	ci right 2.630154e-01	k: 5138	n:20000
Cons ci ratio: 9.114699e-02	ci left: 8.077881e-02	ci right 8.854244e-02	k: 1692	n:20000
KS ci ratio: 3.261371e-02	ci left: 4.124984e-01	ci right 4.262251e-01	k: 8387	n:20000
NBR1   20000 perm   4 sec   (4892 perm/sec)   p_kst 4.193500e-01   p_cons 8.460000e-02   p_joint 2.569000e-01

Outputting figure to mutsig2_images.part000000000112/NBR1.3_2981_20000_0.41935_0.0846_0.2569.png
                gene_name: NBR1
               theta_stop: 0.091 
                    nperm: 20000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.085 
      ci_cons_bounds_left: 0.081 
     ci_cons_bounds_right: 0.089 
                  p_joint: 0.26 
     ci_joint_bounds_left: 0.25 
    ci_joint_bounds_right: 0.26 

Current progress: 25 percent done.
NCAPD2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.412142e-02	ci left: 1.708424e-01	ci right 1.859454e-01	k: 1783	n:10000
Cons ci ratio: 1.070219e-02	ci left: 9.255458e-01	ci right 9.356016e-01	k: 9307	n:10000
KS ci ratio: 1.789177e-01	ci left: 4.168977e-02	ci right 4.997740e-02	k: 457	n:10000
NCAPD2   10000 perm   2 sec   (4650 perm/sec)   p_kst 4.570000e-02   p_cons 9.307000e-01   p_joint 1.783000e-01

Joint ci ratio: 6.178335e-02	ci left: 1.623483e-01	ci right 1.727485e-01	k: 3350	n:20000
Cons ci ratio: 7.447743e-03	ci left: 9.291394e-01	ci right 9.361342e-01	k: 18654	n:20000
KS ci ratio: 1.273200e-01	ci left: 4.236218e-02	ci right 4.817095e-02	k: 904	n:20000
NCAPD2   20000 perm   5 sec   (4172 perm/sec)   p_kst 4.520000e-02   p_cons 9.327000e-01   p_joint 1.675000e-01

Joint ci ratio: 5.849579e-02	ci left: 1.263783e-01	ci right 1.340268e-01	k: 3905	n:30000
Cons ci ratio: 6.151215e-03	ci left: 9.283111e-01	ci right 9.340717e-01	k: 27937	n:30000
KS ci ratio: 1.047476e-01	ci left: 4.225917e-02	ci right 4.696287e-02	k: 1337	n:30000
NCAPD2   30000 perm   7 sec   (4002 perm/sec)   p_kst 4.456667e-02   p_cons 9.312333e-01   p_joint 1.301667e-01

Joint ci ratio: 5.224509e-02	ci left: 1.201424e-01	ci right 1.266124e-01	k: 4934	n:40000
Cons ci ratio: 5.350054e-03	ci left: 9.281419e-01	ci right 9.331454e-01	k: 37227	n:40000
KS ci ratio: 9.179683e-02	ci left: 4.159509e-02	ci right 4.562151e-02	k: 1743	n:40000
NCAPD2   40000 perm   10 sec   (3891 perm/sec)   p_kst 4.357500e-02   p_cons 9.306750e-01   p_joint 1.233500e-01

Outputting figure to mutsig2_images.part000000000112/NCAPD2.3_4330_40000_0.043575_0.93068_0.12335.png
                gene_name: NCAPD2
               theta_stop: 0.092 
                    nperm: 40000 
                     p_ks: 0.044 
        ci_ks_bounds_left: 0.042 
       ci_ks_bounds_right: 0.046 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 33 percent done.
NCOR2
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: 6.490955e-03	ci left: 9.700550e-01	ci right 9.764653e-01	k: 9734	n:10000
KS ci ratio: 8.751644e-03	ci left: 9.482515e-01	ci right 9.566824e-01	k: 9526	n:10000
NCOR2   10000 perm   3 sec   (3223 perm/sec)   p_kst 9.526000e-01   p_cons 9.734000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000112/NCOR2.3_7757_10000_0.9526_0.9734_1.png
                gene_name: NCOR2
               theta_stop: 0.0088 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.96 
                   p_cons: 0.97 
      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: 42 percent done.
NARF
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: 3.515339e-02	ci left: 5.443933e-01	ci right 5.639751e-01	k: 5542	n:10000
KS ci ratio: 4.865692e-02	ci left: 3.839072e-01	ci right 4.031548e-01	k: 3935	n:10000
NARF   10000 perm   2 sec   (6067 perm/sec)   p_kst 3.935000e-01   p_cons 5.542000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000112/NARF.2_1557_10000_0.3935_0.5542_1.png
                gene_name: NARF
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.55 
      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.
NBEA
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: 6.247168e-02	ci left: 2.735913e-01	ci right 2.913356e-01	k: 2824	n:10000
KS ci ratio: 4.965508e-03	ci left: 9.816675e-01	ci right 9.866446e-01	k: 9843	n:10000
NBEA   10000 perm   3 sec   (3181 perm/sec)   p_kst 9.843000e-01   p_cons 2.824000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000112/NBEA.2_9073_10000_0.9843_0.2824_1.png
                gene_name: NBEA
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.98 
        ci_ks_bounds_left: 0.98 
       ci_ks_bounds_right: 0.99 
                   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: 58 percent done.
NBN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.087600e-02	ci left: 4.691661e-01	ci right 4.888461e-01	k: 4790	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: 1.675368e-01	ci left: 4.753733e-02	ci right 5.632602e-02	k: 518	n:10000
NBN   10000 perm   2 sec   (5811 perm/sec)   p_kst 5.180000e-02   p_cons 3.910000e-01   p_joint 4.790000e-01

Joint ci ratio: 2.828492e-02	ci left: 4.828988e-01	ci right 4.968041e-01	k: 9797	n:20000
Cons ci ratio: 3.297459e-02	ci left: 4.071617e-01	ci right 4.208633e-01	k: 8280	n:20000
KS ci ratio: 1.185293e-01	ci left: 4.876885e-02	ci right 5.496225e-02	k: 1036	n:20000
NBN   20000 perm   4 sec   (5095 perm/sec)   p_kst 5.180000e-02   p_cons 4.140000e-01   p_joint 4.898500e-01

Joint ci ratio: 3.521554e-02	ci left: 2.871238e-01	ci right 2.974498e-01	k: 8768	n:30000
Cons ci ratio: 2.799788e-02	ci left: 3.896282e-01	ci right 4.007254e-01	k: 11855	n:30000
KS ci ratio: 9.739180e-02	ci left: 4.873281e-02	ci right 5.375454e-02	k: 1536	n:30000
NBN   30000 perm   6 sec   (4812 perm/sec)   p_kst 5.120000e-02   p_cons 3.951667e-01   p_joint 2.922667e-01

Outputting figure to mutsig2_images.part000000000112/NBN.2_2329_30000_0.0512_0.39517_0.29227.png
                gene_name: NBN
               theta_stop: 0.097 
                    nperm: 30000 
                     p_ks: 0.051 
        ci_ks_bounds_left: 0.049 
       ci_ks_bounds_right: 0.054 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.29 
    ci_joint_bounds_right: 0.30 

Current progress: 67 percent done.
NBPF1
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: 5.719572e-02	ci left: 3.103647e-01	ci right 3.287406e-01	k: 3195	n:10000
KS ci ratio: 3.639408e-02	ci left: 5.271675e-01	ci right 5.468110e-01	k: 5370	n:10000
NBPF1   10000 perm   2 sec   (4696 perm/sec)   p_kst 5.370000e-01   p_cons 3.195000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000112/NBPF1.2_3517_10000_0.537_0.3195_1.png
                gene_name: NBPF1
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
NCF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.248696e-02	ci left: 7.438177e-01	ci right 7.608351e-01	k: 7524	n:10000
Cons ci ratio: 3.441962e-02	ci left: 5.548147e-01	ci right 5.743477e-01	k: 5646	n:10000
KS ci ratio: 3.796719e-02	ci left: 5.060517e-01	ci right 5.257390e-01	k: 5159	n:10000
NCF2   10000 perm   2 sec   (6145 perm/sec)   p_kst 5.159000e-01   p_cons 5.646000e-01   p_joint 7.524000e-01

Outputting figure to mutsig2_images.part000000000112/NCF2.2_1641_10000_0.5159_0.5646_0.7524.png
                gene_name: NCF2
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.55 
     ci_cons_bounds_right: 0.57 
                  p_joint: 0.75 
     ci_joint_bounds_left: 0.74 
    ci_joint_bounds_right: 0.76 

Current progress: 83 percent done.
NCOR1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.722914e-02	ci left: 5.158568e-01	ci right 5.355282e-01	k: 5257	n:10000
Cons ci ratio: 2.535597e-02	ci left: 6.959529e-01	ci right 7.139275e-01	k: 7050	n:10000
KS ci ratio: 7.340334e-02	ci left: 2.136891e-01	ci right 2.300732e-01	k: 2218	n:10000
NCOR1   10000 perm   3 sec   (3731 perm/sec)   p_kst 2.218000e-01   p_cons 7.050000e-01   p_joint 5.257000e-01

Outputting figure to mutsig2_images.part000000000112/NCOR1.2_7503_10000_0.2218_0.705_0.5257.png
                gene_name: NCOR1
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.53 
     ci_joint_bounds_left: 0.52 
    ci_joint_bounds_right: 0.54 

Current progress: 92 percent done.
NDC80
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.401013e-02	ci left: 4.325336e-01	ci right 4.521000e-01	k: 4423	n:10000
Cons ci ratio: 5.581766e-02	ci left: 3.209831e-01	ci right 3.395159e-01	k: 3302	n:10000
KS ci ratio: 1.433170e-01	ci left: 6.459169e-02	ci right 7.466078e-02	k: 695	n:10000
NDC80   10000 perm   2 sec   (5861 perm/sec)   p_kst 6.950000e-02   p_cons 3.302000e-01   p_joint 4.423000e-01

Joint ci ratio: 4.145049e-02	ci left: 3.025494e-01	ci right 3.154061e-01	k: 6179	n:20000
Cons ci ratio: 3.968415e-02	ci left: 3.213446e-01	ci right 3.344055e-01	k: 6557	n:20000
KS ci ratio: 1.031050e-01	ci left: 6.391463e-02	ci right 7.091178e-02	k: 1347	n:20000
NDC80   20000 perm   4 sec   (5178 perm/sec)   p_kst 6.735000e-02   p_cons 3.278500e-01   p_joint 3.089500e-01

Joint ci ratio: 2.319316e-02	ci left: 4.820619e-01	ci right 4.934072e-01	k: 14632	n:30000
Cons ci ratio: 3.248055e-02	ci left: 3.214927e-01	ci right 3.321409e-01	k: 9804	n:30000
KS ci ratio: 8.449954e-02	ci left: 6.409812e-02	ci right 6.978610e-02	k: 2007	n:30000
NDC80   30000 perm   6 sec   (4912 perm/sec)   p_kst 6.690000e-02   p_cons 3.268000e-01   p_joint 4.877333e-01

Outputting figure to mutsig2_images.part000000000112/NDC80.2_1993_30000_0.0669_0.3268_0.48773.png
                gene_name: NDC80
               theta_stop: 0.084 
                    nperm: 30000 
                     p_ks: 0.067 
        ci_ks_bounds_left: 0.064 
       ci_ks_bounds_right: 0.070 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.49 

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.165.3896/
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/181708/iteration1/scatter.0000000112
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 112 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1420>
Subject: Job 1120102: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, 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/181708/iteration1/scatter.0000000113> was used as the working directory.
Started at Wed Oct 10 10:43:59 2012
Results reported at Wed Oct 10 10:46:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000113.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000113.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 113  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    169.68 sec.
    Max Memory :      1336 MB
    Max Swap   :      3880 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.165.3896/
-whichjob
113
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 113: processing genes 10134 - 10223
Calculating significance of each gene.
Using projection method.
10134	NDP	1
10135	NDRG1	1
10136	NDRG2	1
10137	NDRG3	1
10138	NDRG4	1.341033e-01
10139	NDST1	1
10140	NDST2	1.514486e-01
10141	NDST3	3.795378e-01
10142	NDST4	1
10143	NDUFA1	1
10144	NDUFA10	1
10145	NDUFA11	1
10146	NDUFA12	1
10147	NDUFA13	1
10148	NDUFA2	1
10149	NDUFA3	1
10150	NDUFA4	1
10151	NDUFA4L2	1
10152	NDUFA5	3.960641e-02
10153	NDUFA6	1
10154	NDUFA7	1
10155	NDUFA8	1
10156	NDUFA9	1
10157	NDUFAB1	1
10158	NDUFAF1	1
10159	NDUFAF2	1
10160	NDUFAF3	1
10161	NDUFAF4	1
10162	NDUFB1	1
10163	NDUFB10	1
10164	NDUFB11	1
10165	NDUFB2	1
10166	NDUFB3	1
10167	NDUFB4	1
10168	NDUFB5	1
10169	NDUFB6	3.801153e-02
10170	NDUFB7	1
10171	NDUFB8	1
10172	NDUFB9	1
10173	NDUFC1	1
10174	NDUFC2	1
10175	NDUFS1	6.892658e-02
10176	NDUFS2	1
10177	NDUFS3	1
10178	NDUFS4	1
10179	NDUFS5	1
10180	NDUFS6	1
10181	NDUFS7	1
10182	NDUFS8	1
10183	NDUFV1	1
10184	NDUFV2	1
10185	NDUFV3	1
10186	NEB	8.604164e-01
10187	NEBL	3.578401e-01
10188	NECAB1	1
10189	NECAB2	1.322663e-01
10190	NECAB3	1
10191	NECAP1	5.578375e-02
10192	NECAP2	1
10193	NEDD1	1
10194	NEDD4	5.076995e-01
10195	NEDD4L	1
10196	NEDD8	1
10197	NEDD9	1
10198	NEFH	1
10199	NEFL	1
10200	NEFM	1
10201	NEGR1	1
10202	NEIL1	1
10203	NEIL2	1
10204	NEIL3	1
10205	NEK1	1
10206	NEK10	1.609365e-01
10207	NEK11	1.649616e-02
10208	NEK2	1
10209	NEK3	5.040966e-02
10210	NEK4	1
10211	NEK5	2.981336e-02
10212	NEK6	1
10213	NEK7	1
10214	NEK8	2.903423e-01
10215	NEK9	1
10216	NELF	1
10217	NELL1	1
10218	NELL2	2.602755e-02
10219	NENF	1
10220	NEO1	2.985557e-01
10221	NES	7.693096e-03
10222	NET1	1
10223	NETO1	1
Done

Running MutSig 2:
Scatter job 113: processing genes 10134 - 10223
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NES
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.218348e-02	ci left: 5.876103e-01	ci right 6.069330e-01	k: 5973	n:10000
Cons ci ratio: 6.809499e-02	ci left: 2.403508e-01	ci right 2.573957e-01	k: 2488	n:10000
KS ci ratio: 5.541190e-03	ci left: 9.775957e-01	ci right 9.831195e-01	k: 9805	n:10000
NES   10000 perm   3 sec   (3971 perm/sec)   p_kst 9.805000e-01   p_cons 2.488000e-01   p_joint 5.973000e-01

Outputting figure to mutsig2_images.part000000000113/NES.4_4882_10000_0.9805_0.2488_0.5973.png
                gene_name: NES
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.98 
        ci_ks_bounds_left: 0.98 
       ci_ks_bounds_right: 0.98 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.60 
     ci_joint_bounds_left: 0.59 
    ci_joint_bounds_right: 0.61 

Current progress: 20 percent done.
NEB
Processing conservation and coverage...
37% 75% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.077061e-02	ci left: 6.090969e-01	ci right 6.282339e-01	k: 6187	n:10000
Cons ci ratio: 6.776877e-02	ci left: 2.421299e-01	ci right 2.592155e-01	k: 2506	n:10000
KS ci ratio: 1.611926e-02	ci left: 8.483534e-01	ci right 8.622389e-01	k: 8554	n:10000
NEB   10000 perm   6 sec   (1592 perm/sec)   p_kst 8.554000e-01   p_cons 2.506000e-01   p_joint 6.187000e-01

Outputting figure to mutsig2_images.part000000000113/NEB.2_26407_10000_0.8554_0.2506_0.6187.png
                gene_name: NEB
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.62 
     ci_joint_bounds_left: 0.61 
    ci_joint_bounds_right: 0.63 

Current progress: 40 percent done.
NEK11
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: 2.914447e-03	ci left: 9.929600e-01	ci right 9.959408e-01	k: 9946	n:10000
KS ci ratio: 6.679098e-02	ci left: 2.475672e-01	ci right 2.647751e-01	k: 2561	n:10000
NEK11   10000 perm   2 sec   (5482 perm/sec)   p_kst 2.561000e-01   p_cons 9.946000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000113/NEK11.2_2020_10000_0.2561_0.9946_1.png
                gene_name: NEK11
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 1.00 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 60 percent done.
NEK5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.127940e-02	ci left: 9.182193e-01	ci right 9.287325e-01	k: 9236	n:10000
Cons ci ratio: 4.497695e-03	ci left: 9.846908e-01	ci right 9.892189e-01	k: 9871	n:10000
KS ci ratio: 7.623591e-02	ci left: 2.010665e-01	ci right 2.171033e-01	k: 2090	n:10000
NEK5   10000 perm   2 sec   (5938 perm/sec)   p_kst 2.090000e-01   p_cons 9.871000e-01   p_joint 9.236000e-01

Outputting figure to mutsig2_images.part000000000113/NEK5.2_2207_10000_0.209_0.9871_0.9236.png
                gene_name: NEK5
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.92 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

Current progress: 80 percent done.
NELL2
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: 3.297202e-02	ci left: 5.758711e-01	ci right 5.952790e-01	k: 5856	n:10000
KS ci ratio: 1.348025e-02	ci left: 8.881088e-01	ci right 9.002605e-01	k: 8943	n:10000
NELL2   10000 perm   2 sec   (5213 perm/sec)   p_kst 8.943000e-01   p_cons 5.856000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000113/NELL2.2_2783_10000_0.8943_0.5856_1.png
                gene_name: NELL2
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000113
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 113 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120105: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000114> was used as the working directory.
Started at Wed Oct 10 10:44:04 2012
Results reported at Wed Oct 10 10:47:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000114.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000114.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 114  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    211.37 sec.
    Max Memory :      1540 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.165.3896/
-whichjob
114
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 114: processing genes 10224 - 10314
Calculating significance of each gene.
Using projection method.
10224	NETO2	1
10225	NEU1	1
10226	NEU2	1.130886e-02
10227	NEU3	1
10228	NEU4	1
10229	NEURL	1
10230	NEURL2	1
10231	NEURL4	1
10232	NEUROD1	1.885082e-01
10233	NEUROD2	1
10234	NEUROD4	1
10235	NEUROD6	1
10236	NEUROG1	1
10237	NEUROG2	1
10238	NEUROG3	1
10239	NEXN	1
10240	NF1	3.205052e-01
10241	NF2	1.407035e-01
10242	NFAM1	2.172939e-02
10243	NFASC	1
10244	NFAT5	3.124270e-01
10245	NFATC1	1
10246	NFATC2	1
10247	NFATC2IP	1
10248	NFATC3	1
10249	NFATC4	1
10250	NFE2	1
10251	NFE2L1	1.553786e-01
10252	NFE2L2	1.680121e-05
10253	NFE2L3	1
10254	NFIA	1
10255	NFIB	1
10256	NFIC	1
10257	NFIL3	1
10258	NFIX	8.370872e-02
10259	NFKB1	1
10260	NFKB2	1
10261	NFKBIA	1
10262	NFKBIB	1
10263	NFKBID	2.193107e-02
10264	NFKBIE	9.684906e-02
10265	NFKBIL1	1
10266	NFKBIL2	1
10267	NFKBIZ	1
10268	NFRKB	1
10269	NFS1	1
10270	NFU1	1
10271	NFX1	1
10272	NFXL1	1
10273	NFYA	1
10274	NFYB	1
10275	NFYC	1
10276	NGB	1
10277	NGDN	1
10278	NGEF	1
10279	NGF	1
10280	NGFR	1
10281	NGFRAP1	1
10282	NGLY1	1
10283	NGRN	1
10284	NHEDC1	1
10285	NHEDC2	1
10286	NHEJ1	1
10287	NHLH1	1
10288	NHLH2	1
10289	NHLRC1	1.041430e-01
10290	NHLRC2	1
10291	NHLRC3	1
10292	NHLRC4	1
10293	NHP2	1
10294	NHP2L1	1
10295	NHS	1
10296	NHSL2	1
10297	NICN1	1
10298	NID1	3.618565e-01
10299	NID2	9.624299e-02
10300	NIF3L1	1.104891e-01
10301	NIN	1
10302	NINJ1	1
10303	NINJ2	1
10304	NINL	3.172652e-01
10305	NIP7	1
10306	NIPA1	1
10307	NIPA2	1
10308	NIPAL1	1
10309	NIPAL2	1
10310	NIPAL3	1
10311	NIPAL4	1
10312	NIPBL	1.092388e-01
10313	NIPSNAP1	1
10314	NIPSNAP3A	1
Done

Running MutSig 2:
Scatter job 114: processing genes 10224 - 10314
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: 1.842512e-01	ci left: 3.929883e-02	ci right 4.736993e-02	k: 432	n:10000
Cons ci ratio: 4.509198e-01	ci left: 5.814929e-03	ci right 9.281233e-03	k: 74	n:10000
KS ci ratio: 6.609721e-02	ci left: 2.515227e-01	ci right 2.688172e-01	k: 2601	n:10000
NFE2L2   10000 perm   2 sec   (4515 perm/sec)   p_kst 2.601000e-01   p_cons 7.400000e-03   p_joint 4.320000e-02

Joint ci ratio: 1.570719e-01	ci left: 2.782361e-02	ci right 3.261426e-02	k: 603	n:20000
Cons ci ratio: 3.254805e-01	ci left: 6.029406e-03	ci right 8.417230e-03	k: 143	n:20000
KS ci ratio: 4.709897e-02	ci left: 2.511530e-01	ci right 2.633177e-01	k: 5144	n:20000
NFE2L2   20000 perm   7 sec   (2944 perm/sec)   p_kst 2.572000e-01   p_cons 7.150000e-03   p_joint 3.015000e-02

Joint ci ratio: 1.181960e-01	ci left: 3.327262e-02	ci right 3.748464e-02	k: 1060	n:30000
Cons ci ratio: 2.586157e-01	ci left: 6.617327e-03	ci right 8.613141e-03	k: 227	n:30000
KS ci ratio: 3.850158e-02	ci left: 2.518304e-01	ci right 2.617501e-01	k: 7703	n:30000
NFE2L2   30000 perm   9 sec   (3233 perm/sec)   p_kst 2.567667e-01   p_cons 7.566667e-03   p_joint 3.533333e-02

Joint ci ratio: 1.178836e-01	ci left: 2.531211e-02	ci right 2.850707e-02	k: 1075	n:40000
Cons ci ratio: 2.250905e-01	ci left: 6.677907e-03	ci right 8.394749e-03	k: 300	n:40000
KS ci ratio: 3.338931e-02	ci left: 2.519771e-01	ci right 2.605583e-01	k: 10250	n:40000
NFE2L2   40000 perm   12 sec   (3368 perm/sec)   p_kst 2.562500e-01   p_cons 7.500000e-03   p_joint 2.687500e-02

Joint ci ratio: 9.720566e-02	ci left: 2.996674e-02	ci right 3.304796e-02	k: 1574	n:50000
Cons ci ratio: 2.024831e-01	ci left: 6.686484e-03	ci right 8.211540e-03	k: 371	n:50000
KS ci ratio: 2.997244e-02	ci left: 2.510645e-01	ci right 2.587240e-01	k: 12744	n:50000
NFE2L2   50000 perm   14 sec   (3499 perm/sec)   p_kst 2.548800e-01   p_cons 7.420000e-03   p_joint 3.148000e-02

Joint ci ratio: 9.922986e-02	ci left: 2.409068e-02	ci right 2.662218e-02	k: 1520	n:60000
Cons ci ratio: 1.772757e-01	ci left: 7.366459e-03	ci right 8.815062e-03	k: 484	n:60000
KS ci ratio: 2.742837e-02	ci left: 2.504708e-01	ci right 2.574530e-01	k: 15237	n:60000
NFE2L2   60000 perm   17 sec   (3575 perm/sec)   p_kst 2.539500e-01   p_cons 8.066667e-03   p_joint 2.533333e-02

Joint ci ratio: 1.021961e-01	ci left: 1.953267e-02	ci right 2.165019e-02	k: 1440	n:70000
Cons ci ratio: 1.654324e-01	ci left: 7.298584e-03	ci right 8.628403e-03	k: 556	n:70000
KS ci ratio: 2.535424e-02	ci left: 2.513190e-01	ci right 2.577871e-01	k: 17818	n:70000
NFE2L2   70000 perm   19 sec   (3619 perm/sec)   p_kst 2.545429e-01   p_cons 7.942857e-03   p_joint 2.057143e-02

Joint ci ratio: 1.029505e-01	ci left: 1.688284e-02	ci right 1.872737e-02	k: 1423	n:80000
Cons ci ratio: 1.577186e-01	ci left: 7.057896e-03	ci right 8.278215e-03	k: 612	n:80000
KS ci ratio: 2.370546e-02	ci left: 2.517084e-01	ci right 2.577593e-01	k: 20378	n:80000
NFE2L2   80000 perm   22 sec   (3640 perm/sec)   p_kst 2.547250e-01   p_cons 7.650000e-03   p_joint 1.778750e-02

Joint ci ratio: 1.015431e-01	ci left: 1.546112e-02	ci right 1.712583e-02	k: 1465	n:90000
Cons ci ratio: 1.473719e-01	ci left: 7.224905e-03	ci right 8.384934e-03	k: 701	n:90000
KS ci ratio: 2.239651e-02	ci left: 2.510921e-01	ci right 2.567904e-01	k: 22854	n:90000
NFE2L2   90000 perm   25 sec   (3580 perm/sec)   p_kst 2.539333e-01   p_cons 7.788889e-03   p_joint 1.627778e-02

Joint ci ratio: 1.042189e-01	ci left: 1.322246e-02	ci right 1.468593e-02	k: 1394	n:100000
Cons ci ratio: 1.398094e-01	ci left: 7.254412e-03	ci right 8.354425e-03	k: 779	n:100000
KS ci ratio: 2.123287e-02	ci left: 2.514935e-01	ci right 2.569007e-01	k: 25419	n:100000
NFE2L2   100000 perm   30 sec   (3329 perm/sec)   p_kst 2.541900e-01   p_cons 7.790000e-03   p_joint 1.394000e-02

Joint ci ratio: 1.008968e-01	ci left: 1.285292e-02	ci right 1.422745e-02	k: 1488	n:110000
Cons ci ratio: 1.333814e-01	ci left: 7.271010e-03	ci right 8.318828e-03	k: 856	n:110000
KS ci ratio: 2.026662e-02	ci left: 2.512121e-01	ci right 2.563645e-01	k: 27916	n:110000
NFE2L2   110000 perm   34 sec   (3282 perm/sec)   p_kst 2.537818e-01   p_cons 7.781818e-03   p_joint 1.352727e-02

Joint ci ratio: 1.078372e-01	ci left: 1.030398e-02	ci right 1.148650e-02	k: 1306	n:120000
Cons ci ratio: 1.270140e-01	ci left: 7.374574e-03	ci right 8.382760e-03	k: 944	n:120000
KS ci ratio: 1.942985e-02	ci left: 2.508163e-01	ci right 2.557457e-01	k: 30393	n:120000
NFE2L2   120000 perm   37 sec   (3260 perm/sec)   p_kst 2.532750e-01   p_cons 7.866667e-03   p_joint 1.088333e-02

Joint ci ratio: 9.096202e-02	ci left: 1.344353e-02	ci right 1.473212e-02	k: 1830	n:130000
Cons ci ratio: 1.224386e-01	ci left: 7.343860e-03	ci right 8.309058e-03	k: 1016	n:130000
KS ci ratio: 1.833635e-02	ci left: 2.577245e-01	ci right 2.625016e-01	k: 33814	n:130000
NFE2L2   130000 perm   40 sec   (3253 perm/sec)   p_kst 2.601077e-01   p_cons 7.815385e-03   p_joint 1.407692e-02

Joint ci ratio: 7.849967e-02	ci left: 1.681257e-02	ci right 1.819323e-02	k: 2449	n:140000
Cons ci ratio: 1.230227e-01	ci left: 6.756860e-03	ci right 7.649448e-03	k: 1007	n:140000
KS ci ratio: 1.768351e-02	ci left: 2.575043e-01	ci right 2.621056e-01	k: 36372	n:140000
NFE2L2   140000 perm   43 sec   (3244 perm/sec)   p_kst 2.598000e-01   p_cons 7.192857e-03   p_joint 1.749286e-02

Joint ci ratio: 7.848117e-02	ci left: 1.571752e-02	ci right 1.700794e-02	k: 2453	n:150000
Cons ci ratio: 1.180284e-01	ci left: 6.868943e-03	ci right 7.736932e-03	k: 1094	n:150000
KS ci ratio: 1.708895e-02	ci left: 2.574691e-01	ci right 2.619135e-01	k: 38953	n:150000
NFE2L2   150000 perm   46 sec   (3226 perm/sec)   p_kst 2.596867e-01   p_cons 7.293333e-03   p_joint 1.635333e-02

Joint ci ratio: 7.816689e-02	ci left: 1.486973e-02	ci right 1.608542e-02	k: 2475	n:160000
Cons ci ratio: 1.150269e-01	ci left: 6.791553e-03	ci right 7.626454e-03	k: 1152	n:160000
KS ci ratio: 1.656002e-02	ci left: 2.572224e-01	ci right 2.615238e-01	k: 41499	n:160000
NFE2L2   160000 perm   50 sec   (3216 perm/sec)   p_kst 2.593687e-01   p_cons 7.200000e-03   p_joint 1.546875e-02

Joint ci ratio: 7.244890e-02	ci left: 1.631569e-02	ci right 1.754792e-02	k: 2877	n:170000
Cons ci ratio: 1.117333e-01	ci left: 6.786421e-03	ci right 7.595228e-03	k: 1221	n:170000
KS ci ratio: 1.607955e-02	ci left: 2.569539e-01	ci right 2.611249e-01	k: 44036	n:170000
NFE2L2   170000 perm   53 sec   (3196 perm/sec)   p_kst 2.590353e-01   p_cons 7.182353e-03   p_joint 1.692353e-02

Joint ci ratio: 7.140693e-02	ci left: 1.587832e-02	ci right 1.705955e-02	k: 2963	n:180000
Cons ci ratio: 1.079519e-01	ci left: 6.879471e-03	ci right 7.669856e-03	k: 1308	n:180000
KS ci ratio: 1.562548e-02	ci left: 2.570383e-01	ci right 2.610917e-01	k: 46631	n:180000
NFE2L2   180000 perm   57 sec   (3183 perm/sec)   p_kst 2.590611e-01   p_cons 7.266667e-03   p_joint 1.646111e-02

Joint ci ratio: 6.423994e-02	ci left: 1.860321e-02	ci right 1.984310e-02	k: 3651	n:190000
Cons ci ratio: 1.049092e-01	ci left: 6.911875e-03	ci right 7.682220e-03	k: 1385	n:190000
KS ci ratio: 1.520115e-02	ci left: 2.572832e-01	ci right 2.612294e-01	k: 49258	n:190000
NFE2L2   190000 perm   60 sec   (3164 perm/sec)   p_kst 2.592526e-01   p_cons 7.289474e-03   p_joint 1.921579e-02

Joint ci ratio: 6.264835e-02	ci left: 1.859814e-02	ci right 1.980585e-02	k: 3839	n:200000
Cons ci ratio: 1.015176e-01	ci left: 7.024170e-03	ci right 7.780213e-03	k: 1479	n:200000
KS ci ratio: 1.480981e-02	ci left: 2.575000e-01	ci right 2.613469e-01	k: 51884	n:200000
NFE2L2   200000 perm   64 sec   (3144 perm/sec)   p_kst 2.594200e-01   p_cons 7.395000e-03   p_joint 1.919500e-02

Joint ci ratio: 6.331026e-02	ci left: 1.736064e-02	ci right 1.850034e-02	k: 3764	n:210000
Cons ci ratio: 9.932893e-02	ci left: 6.996073e-03	ci right 7.731909e-03	k: 1545	n:210000
KS ci ratio: 1.445580e-02	ci left: 2.574693e-01	ci right 2.612230e-01	k: 54462	n:210000
NFE2L2   210000 perm   67 sec   (3123 perm/sec)   p_kst 2.593429e-01   p_cons 7.357143e-03   p_joint 1.792381e-02

Outputting figure to mutsig2_images.part000000000114/NFE2L2.4_1838_210000_0.25934_0.0073571_0.017924.png
                gene_name: NFE2L2
               theta_stop: 0.099 
                    nperm: 210000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.0074 
      ci_cons_bounds_left: 0.0070 
     ci_cons_bounds_right: 0.0077 
                  p_joint: 0.018 
     ci_joint_bounds_left: 0.017 
    ci_joint_bounds_right: 0.019 

Current progress: 14 percent done.
NIN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.843462e-02	ci left: 6.457901e-01	ci right 6.645195e-01	k: 6552	n:10000
Cons ci ratio: 5.673863e-02	ci left: 3.138374e-01	ci right 3.322658e-01	k: 3230	n:10000
KS ci ratio: 3.272810e-02	ci left: 5.794826e-01	ci right 5.988655e-01	k: 5892	n:10000
NIN   10000 perm   2 sec   (4362 perm/sec)   p_kst 5.892000e-01   p_cons 3.230000e-01   p_joint 6.552000e-01

Outputting figure to mutsig2_images.part000000000114/NIN.3_6666_10000_0.5892_0.323_0.6552.png
                gene_name: NIN
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.66 
     ci_joint_bounds_left: 0.65 
    ci_joint_bounds_right: 0.66 

Current progress: 29 percent done.
NIPBL
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: 4.750450e-02	ci left: 3.953575e-01	ci right 4.146978e-01	k: 4050	n:10000
KS ci ratio: 2.202230e-02	ci left: 7.516055e-01	ci right 7.684428e-01	k: 7601	n:10000
NIPBL   10000 perm   3 sec   (3296 perm/sec)   p_kst 7.601000e-01   p_cons 4.050000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000114/NIPBL.3_8644_10000_0.7601_0.405_1.png
                gene_name: NIPBL
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.76 
        ci_ks_bounds_left: 0.75 
       ci_ks_bounds_right: 0.77 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.41 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 43 percent done.
NEU2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.746117e-02	ci left: 5.127548e-01	ci right 5.324320e-01	k: 5226	n:10000
Cons ci ratio: 5.864716e-02	ci left: 2.996526e-01	ci right 3.178589e-01	k: 3087	n:10000
KS ci ratio: 1.118988e-01	ci left: 1.031515e-01	ci right 1.154771e-01	k: 1092	n:10000
NEU2   10000 perm   2 sec   (6374 perm/sec)   p_kst 1.092000e-01   p_cons 3.087000e-01   p_joint 5.226000e-01

Joint ci ratio: 6.051847e-02	ci left: 1.681264e-01	ci right 1.786687e-01	k: 3467	n:20000
Cons ci ratio: 4.153801e-02	ci left: 3.016547e-01	ci right 3.145011e-01	k: 6161	n:20000
KS ci ratio: 7.947324e-02	ci left: 1.041236e-01	ci right 1.127906e-01	k: 2168	n:20000
NEU2   20000 perm   4 sec   (5705 perm/sec)   p_kst 1.084000e-01   p_cons 3.080500e-01   p_joint 1.733500e-01

Outputting figure to mutsig2_images.part000000000114/NEU2.2_1150_20000_0.1084_0.30805_0.17335.png
                gene_name: NEU2
               theta_stop: 0.079 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.31 
                  p_joint: 0.17 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 57 percent done.
NF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.868672e-02	ci left: 6.417660e-01	ci right 6.605459e-01	k: 6512	n:10000
Cons ci ratio: 1.474450e-02	ci left: 8.694829e-01	ci right 8.824972e-01	k: 8761	n:10000
KS ci ratio: 5.450658e-02	ci left: 3.315077e-01	ci right 3.501851e-01	k: 3408	n:10000
NF1   10000 perm   2 sec   (4195 perm/sec)   p_kst 3.408000e-01   p_cons 8.761000e-01   p_joint 6.512000e-01

Outputting figure to mutsig2_images.part000000000114/NF1.2_8813_10000_0.3408_0.8761_0.6512.png
                gene_name: NF1
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.34 
        ci_ks_bounds_left: 0.33 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.88 
                  p_joint: 0.65 
     ci_joint_bounds_left: 0.64 
    ci_joint_bounds_right: 0.66 

Current progress: 71 percent done.
NHLRC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.654243e-02	ci left: 4.052191e-01	ci right 4.246305e-01	k: 4149	n:10000
Cons ci ratio: 5.221033e-02	ci left: 3.509817e-01	ci right 3.698997e-01	k: 3604	n:10000
KS ci ratio: 2.674103e-02	ci left: 6.731734e-01	ci right 6.915203e-01	k: 6824	n:10000
NHLRC1   10000 perm   1 sec   (6669 perm/sec)   p_kst 6.824000e-01   p_cons 3.604000e-01   p_joint 4.149000e-01

Outputting figure to mutsig2_images.part000000000114/NHLRC1.2_1192_10000_0.6824_0.3604_0.4149.png
                gene_name: NHLRC1
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.41 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.42 

Current progress: 86 percent done.
NID2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.087845e-02	ci left: 3.629130e-01	ci right 3.819614e-01	k: 3724	n:10000
Cons ci ratio: 7.215091e-02	ci left: 2.196098e-01	ci right 2.361490e-01	k: 2278	n:10000
KS ci ratio: 9.009714e-03	ci left: 9.454415e-01	ci right 9.540941e-01	k: 9499	n:10000
NID2   10000 perm   2 sec   (5299 perm/sec)   p_kst 9.499000e-01   p_cons 2.278000e-01   p_joint 3.724000e-01

Outputting figure to mutsig2_images.part000000000114/NID2.2_4216_10000_0.9499_0.2278_0.3724.png
                gene_name: NID2
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.95 
                   p_cons: 0.23 
      ci_cons_bounds_left: 0.22 
     ci_cons_bounds_right: 0.24 
                  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.165.3896/
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/181708/iteration1/scatter.0000000114
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 114 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120109: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000115> was used as the working directory.
Started at Wed Oct 10 10:44:04 2012
Results reported at Wed Oct 10 10:46:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000115.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000115.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 115  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    125.52 sec.
    Max Memory :      1440 MB
    Max Swap   :      3937 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.165.3896/
-whichjob
115
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 115: processing genes 10315 - 10404
Calculating significance of each gene.
Using projection method.
10315	NIPSNAP3B	1
10316	NISCH	2.996423e-02
10317	NIT1	1
10318	NIT2	1
10319	NKAIN1	1
10320	NKAIN2	1
10321	NKAIN3	1
10322	NKAIN4	1
10323	NKAP	1
10324	NKAPL	1
10325	NKD1	1
10326	NKD2	1
10327	NKG7	1
10328	NKIRAS1	1
10329	NKIRAS2	1
10330	NKPD1	1
10331	NKRF	1.324967e-01
10332	NKTR	8.942375e-03
10333	NKX2-1	1
10334	NKX2-2	1
10335	NKX2-3	1
10336	NKX2-5	1
10337	NKX3-1	1
10338	NKX3-2	1
10339	NKX6-1	1
10340	NKX6-2	1
10341	NKX6-3	1
10342	NLE1	1
10343	NLGN1	1.216308e-01
10344	NLGN2	1
10345	NLGN3	1
10346	NLGN4X	1
10347	NLGN4Y	1
10348	NLK	1
10349	NLN	1
10350	NLRC3	2.613931e-01
10351	NLRC4	2.966761e-01
10352	NLRC5	3.791527e-01
10353	NLRP1	1
10354	NLRP10	4.145430e-02
10355	NLRP11	1
10356	NLRP12	1
10357	NLRP13	1
10358	NLRP14	2.372262e-02
10359	NLRP2	1
10360	NLRP3	1
10361	NLRP4	7.874322e-02
10362	NLRP5	1
10363	NLRP6	1
10364	NLRP7	8.021274e-03
10365	NLRP8	3.051030e-02
10366	NLRP9	8.479958e-02
10367	NLRX1	1
10368	NMB	1
10369	NMBR	1
10370	NMD3	2.058271e-02
10371	NME1	1
10372	NME1-NME2	1
10373	NME2	1
10374	NME3	1
10375	NME4	1.554545e-02
10376	NME5	1
10377	NME6	1
10378	NME7	1
10379	NMI	1
10380	NMNAT1	1
10381	NMNAT2	1
10382	NMNAT3	1
10383	NMRAL1	1
10384	NMS	1
10385	NMT1	1
10386	NMT2	1
10387	NMU	1
10388	NMUR1	1
10389	NMUR2	1
10390	NNAT	1
10391	NNMT	1
10392	NNT	1.123185e-01
10393	NOB1	6.263191e-02
10394	NOBOX	1
10395	NOC2L	2.908615e-01
10396	NOC3L	1
10397	NOC4L	1
10398	NOD1	1
10399	NOD2	1
10400	NODAL	1
10401	NOG	1
10402	NOL10	1
10403	NOL11	1
10404	NOL12	1
Done

Running MutSig 2:
Scatter job 115: processing genes 10315 - 10404
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NKTR
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: 3.868797e-02	ci left: 4.966503e-01	ci right 5.163459e-01	k: 5065	n:10000
KS ci ratio: 1.138285e-02	ci left: 9.168793e-01	ci right 9.274733e-01	k: 9223	n:10000
NKTR   10000 perm   2 sec   (4924 perm/sec)   p_kst 9.223000e-01   p_cons 5.065000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000115/NKTR.4_4453_10000_0.9223_0.5065_1.png
                gene_name: NKTR
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   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: 11 percent done.
NISCH
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.553891e-02	ci left: 6.929276e-01	ci right 7.109546e-01	k: 7020	n:10000
Cons ci ratio: 4.652327e-02	ci left: 4.054184e-01	ci right 4.248311e-01	k: 4151	n:10000
KS ci ratio: 5.153763e-03	ci left: 9.803783e-01	ci right 9.855349e-01	k: 9831	n:10000
NISCH   10000 perm   2 sec   (4007 perm/sec)   p_kst 9.831000e-01   p_cons 4.151000e-01   p_joint 7.020000e-01

Outputting figure to mutsig2_images.part000000000115/NISCH.3_4599_10000_0.9831_0.4151_0.702.png
                gene_name: NISCH
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.98 
        ci_ks_bounds_left: 0.98 
       ci_ks_bounds_right: 0.99 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.70 
     ci_joint_bounds_left: 0.69 
    ci_joint_bounds_right: 0.71 

Current progress: 22 percent done.
NLRP7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.982611e-02	ci left: 6.237671e-01	ci right 6.427552e-01	k: 6333	n:10000
Cons ci ratio: 5.864716e-02	ci left: 2.996526e-01	ci right 3.178589e-01	k: 3087	n:10000
KS ci ratio: 2.934637e-02	ci left: 6.313068e-01	ci right 6.502111e-01	k: 6408	n:10000
NLRP7   10000 perm   2 sec   (5469 perm/sec)   p_kst 6.408000e-01   p_cons 3.087000e-01   p_joint 6.333000e-01

Outputting figure to mutsig2_images.part000000000115/NLRP7.3_3154_10000_0.6408_0.3087_0.6333.png
                gene_name: NLRP7
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.63 
     ci_joint_bounds_left: 0.62 
    ci_joint_bounds_right: 0.64 

Current progress: 33 percent done.
NLRP10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.442374e-02	ci left: 8.742881e-01	ci right 8.870892e-01	k: 8808	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: 5.246035e-02	ci left: 3.487950e-01	ci right 3.676877e-01	k: 3582	n:10000
NLRP10   10000 perm   2 sec   (5183 perm/sec)   p_kst 3.582000e-01   p_cons 8.766000e-01   p_joint 8.808000e-01

Outputting figure to mutsig2_images.part000000000115/NLRP10.2_1976_10000_0.3582_0.8766_0.8808.png
                gene_name: NLRP10
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.88 
      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: 0.89 

Current progress: 44 percent done.
NLRP14
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.202335e-02	ci left: 4.553853e-01	ci right 4.750350e-01	k: 4652	n:10000
Cons ci ratio: 3.342233e-02	ci left: 5.692514e-01	ci right 5.887025e-01	k: 5790	n:10000
KS ci ratio: 1.140181e-01	ci left: 9.964203e-02	ci right 1.117887e-01	k: 1056	n:10000
NLRP14   10000 perm   2 sec   (5574 perm/sec)   p_kst 1.056000e-01   p_cons 5.790000e-01   p_joint 4.652000e-01

Joint ci ratio: 3.206080e-02	ci left: 4.208292e-01	ci right 4.345918e-01	k: 8554	n:20000
Cons ci ratio: 2.368063e-02	ci left: 5.711695e-01	ci right 5.849078e-01	k: 11561	n:20000
KS ci ratio: 8.177543e-02	ci left: 9.882035e-02	ci right 1.072955e-01	k: 2060	n:20000
NLRP14   20000 perm   4 sec   (5008 perm/sec)   p_kst 1.030000e-01   p_cons 5.780500e-01   p_joint 4.277000e-01

Outputting figure to mutsig2_images.part000000000115/NLRP14.2_3326_20000_0.103_0.57805_0.4277.png
                gene_name: NLRP14
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.099 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.58 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.43 

Current progress: 56 percent done.
NLRP4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.113069e-02	ci left: 4.660698e-01	ci right 4.857443e-01	k: 4759	n:10000
Cons ci ratio: 4.046070e-02	ci left: 4.742610e-01	ci right 4.939483e-01	k: 4841	n:10000
KS ci ratio: 7.577795e-02	ci left: 2.030380e-01	ci right 2.191306e-01	k: 2110	n:10000
NLRP4   10000 perm   2 sec   (4991 perm/sec)   p_kst 2.110000e-01   p_cons 4.841000e-01   p_joint 4.759000e-01

Outputting figure to mutsig2_images.part000000000115/NLRP4.2_3021_10000_0.211_0.4841_0.4759.png
                gene_name: NLRP4
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.20 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 67 percent done.
NLRP8
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: 4.850438e-02	ci left: 3.854004e-01	ci right 4.046607e-01	k: 3950	n:10000
NLRP8   10000 perm   2 sec   (5139 perm/sec)   p_kst 3.950000e-01   p_cons 9.873000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000115/NLRP8.2_3187_10000_0.395_0.9873_1.png
                gene_name: NLRP8
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.40 
        ci_ks_bounds_left: 0.39 
       ci_ks_bounds_right: 0.40 
                   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: 78 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: 3.143295e-02	ci left: 5.989536e-01	ci right 6.181831e-01	k: 6086	n:10000
KS ci ratio: 2.172642e-02	ci left: 7.565633e-01	ci right 7.732821e-01	k: 7650	n:10000
NLRP9   10000 perm   2 sec   (5898 perm/sec)   p_kst 7.650000e-01   p_cons 6.086000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000115/NLRP9.2_3012_10000_0.765_0.6086_1.png
                gene_name: NLRP9
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.77 
        ci_ks_bounds_left: 0.76 
       ci_ks_bounds_right: 0.77 
                   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: 89 percent done.
NMD3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.081773e-02	ci left: 9.241000e-01	ci right 9.342483e-01	k: 9293	n:10000
Cons ci ratio: 4.308563e-02	ci left: 4.430089e-01	ci right 4.626186e-01	k: 4528	n:10000
KS ci ratio: 2.800172e-02	ci left: 6.527333e-01	ci right 6.713722e-01	k: 6621	n:10000
NMD3   10000 perm   2 sec   (6285 perm/sec)   p_kst 6.621000e-01   p_cons 4.528000e-01   p_joint 9.293000e-01

Outputting figure to mutsig2_images.part000000000115/NMD3.2_1572_10000_0.6621_0.4528_0.9293.png
                gene_name: NMD3
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

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.165.3896/
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/181708/iteration1/scatter.0000000115
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 115 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120112: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000116> was used as the working directory.
Started at Wed Oct 10 10:44:04 2012
Results reported at Wed Oct 10 10:45:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000116.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000116.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 116  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    127.63 sec.
    Max Memory :      1086 MB
    Max Swap   :      3871 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.165.3896/
-whichjob
116
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 116: processing genes 10405 - 10495
Calculating significance of each gene.
Using projection method.
10405	NOL3	1
10406	NOL4	3.138181e-01
10407	NOL6	1
10408	NOL7	1
10409	NOL8	1
10410	NOL9	2.702004e-01
10411	NOLC1	1
10412	NOM1	1
10413	NOMO1	1
10414	NOMO2	1
10415	NOMO3	1
10416	NONO	1
10417	NOP10	1
10418	NOP14	2.653327e-01
10419	NOP16	1
10420	NOP2	1
10421	NOP56	1
10422	NOP58	1
10423	NOS1	5.566705e-01
10424	NOS1AP	1
10425	NOS2	2.121810e-02
10426	NOS3	1
10427	NOSIP	7.550064e-02
10428	NOSTRIN	1.747137e-01
10429	NOTCH1	7.599836e-02
10430	NOTCH2	6.357428e-02
10431	NOTCH2NL	1
10432	NOTCH3	3.203583e-01
10433	NOTCH4	3.794224e-01
10434	NOTUM	2.839415e-02
10435	NOV	1
10436	NOVA1	1
10437	NOVA2	1
10438	NOX1	1
10439	NOX3	1
10440	NOX4	1
10441	NOX5	1
10442	NOXA1	1
10443	NOXO1	1
10444	NPAS1	1
10445	NPAS2	1
10446	NPAS3	1.995809e-01
10447	NPAS4	1
10448	NPAT	1
10449	NPB	1
10450	NPBWR1	1
10451	NPBWR2	1.752749e-02
10452	NPC1	1
10453	NPC1L1	3.083954e-01
10454	NPC2	1
10455	NPDC1	5.616689e-02
10456	NPEPL1	1
10457	NPEPPS	1
10458	NPFF	5.450398e-02
10459	NPFFR1	1
10460	NPFFR2	6.750162e-02
10461	NPHP1	1
10462	NPHP3	3.407314e-01
10463	NPHP4	1
10464	NPHS1	1
10465	NPHS2	1
10466	NPIP	1
10467	NPL	1
10468	NPLOC4	1
10469	NPM1	1
10470	NPM2	1
10471	NPM3	1
10472	NPNT	1
10473	NPPA	1
10474	NPPB	1
10475	NPPC	1
10476	NPR1	1
10477	NPR2	1
10478	NPR3	1
10479	NPRL2	1
10480	NPRL3	1
10481	NPS	1
10482	NPSR1	1
10483	NPTN	1
10484	NPTX1	1
10485	NPTX2	1
10486	NPTXR	1
10487	NPVF	1
10488	NPW	1
10489	NPY	1
10490	NPY1R	1
10491	NPY2R	1
10492	NPY5R	1.375896e-01
10493	NQO1	1
10494	NQO2	1
10495	NR0B1	1
Done

Running MutSig 2:
Scatter job 116: processing genes 10405 - 10495
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NOTCH2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.655262e-02	ci left: 1.627829e-01	ci right 1.776098e-01	k: 1701	n:10000
Cons ci ratio: 3.713756e-03	ci left: 9.891692e-01	ci right 9.929363e-01	k: 9912	n:10000
KS ci ratio: 2.198857e-01	ci left: 2.740624e-02	ci right 3.427066e-02	k: 307	n:10000
NOTCH2   10000 perm   2 sec   (4119 perm/sec)   p_kst 3.070000e-02   p_cons 9.912000e-01   p_joint 1.701000e-01

Joint ci ratio: 1.004153e-01	ci left: 6.723404e-02	ci right 7.439135e-02	k: 1415	n:20000
Cons ci ratio: 2.626352e-03	ci left: 9.897531e-01	ci right 9.924012e-01	k: 19823	n:20000
KS ci ratio: 1.595400e-01	ci left: 2.695830e-02	ci right 3.167987e-02	k: 585	n:20000
NOTCH2   20000 perm   8 sec   (2614 perm/sec)   p_kst 2.925000e-02   p_cons 9.911500e-01   p_joint 7.075000e-02

Joint ci ratio: 7.441371e-02	ci left: 8.150739e-02	ci right 8.783998e-02	k: 2539	n:30000
Cons ci ratio: 2.156620e-03	ci left: 9.899010e-01	ci right 9.920689e-01	k: 29731	n:30000
KS ci ratio: 1.250818e-01	ci left: 2.971393e-02	ci right 3.371077e-02	k: 950	n:30000
NOTCH2   30000 perm   11 sec   (2841 perm/sec)   p_kst 3.166667e-02   p_cons 9.910333e-01   p_joint 8.463333e-02

Joint ci ratio: 6.905644e-02	ci left: 7.196979e-02	ci right 7.714218e-02	k: 2981	n:40000
Cons ci ratio: 2.031014e-03	ci left: 9.883476e-01	ci right 9.903804e-01	k: 39576	n:40000
KS ci ratio: 1.085013e-01	ci left: 2.988292e-02	ci right 3.333552e-02	k: 1263	n:40000
NOTCH2   40000 perm   14 sec   (2918 perm/sec)   p_kst 3.157500e-02   p_cons 9.894000e-01   p_joint 7.452500e-02

Joint ci ratio: 5.616317e-02	ci left: 8.628112e-02	ci right 9.128674e-02	k: 4438	n:50000
Cons ci ratio: 1.836814e-03	ci left: 9.882134e-01	ci right 9.900491e-01	k: 49458	n:50000
KS ci ratio: 9.788146e-02	ci left: 2.955668e-02	ci right 3.261808e-02	k: 1553	n:50000
NOTCH2   50000 perm   17 sec   (2979 perm/sec)   p_kst 3.106000e-02   p_cons 9.891600e-01   p_joint 8.876000e-02

Outputting figure to mutsig2_images.part000000000116/NOTCH2.3_7552_50000_0.03106_0.98916_0.08876.png
                gene_name: NOTCH2
               theta_stop: 0.098 
                    nperm: 50000 
                     p_ks: 0.031 
        ci_ks_bounds_left: 0.030 
       ci_ks_bounds_right: 0.033 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.089 
     ci_joint_bounds_left: 0.086 
    ci_joint_bounds_right: 0.091 

Current progress: 33 percent done.
NOS2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.035205e-01	ci left: 1.188712e-01	ci right 1.319479e-01	k: 1253	n:10000
Cons ci ratio: 1.059997e-01	ci left: 1.138876e-01	ci right 1.267345e-01	k: 1202	n:10000
KS ci ratio: 7.530342e-02	ci left: 2.051084e-01	ci right 2.212590e-01	k: 2131	n:10000
NOS2   10000 perm   2 sec   (5512 perm/sec)   p_kst 2.131000e-01   p_cons 1.202000e-01   p_joint 1.253000e-01

Joint ci ratio: 8.246861e-02	ci left: 9.729878e-02	ci right 1.057175e-01	k: 2029	n:20000
Cons ci ratio: 7.708228e-02	ci left: 1.100691e-01	ci right 1.189433e-01	k: 2289	n:20000
KS ci ratio: 5.312152e-02	ci left: 2.082834e-01	ci right 2.196999e-01	k: 4279	n:20000
NOS2   20000 perm   4 sec   (4943 perm/sec)   p_kst 2.139500e-01   p_cons 1.144500e-01   p_joint 1.014500e-01

Outputting figure to mutsig2_images.part000000000116/NOS2.2_3566_20000_0.21395_0.11445_0.10145.png
                gene_name: NOS2
               theta_stop: 0.082 
                    nperm: 20000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.10 
     ci_joint_bounds_left: 0.097 
    ci_joint_bounds_right: 0.11 

Current progress: 67 percent done.
NOTCH1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.342919e-02	ci left: 5.691511e-01	ci right 5.886029e-01	k: 5789	n:10000
Cons ci ratio: 5.603282e-02	ci left: 3.192957e-01	ci right 3.378043e-01	k: 3285	n:10000
KS ci ratio: 1.770450e-02	ci left: 8.231021e-01	ci right 8.379049e-01	k: 8306	n:10000
NOTCH1   10000 perm   3 sec   (3727 perm/sec)   p_kst 8.306000e-01   p_cons 3.285000e-01   p_joint 5.789000e-01

Outputting figure to mutsig2_images.part000000000116/NOTCH1.2_7804_10000_0.8306_0.3285_0.5789.png
                gene_name: NOTCH1
               theta_stop: 0.056 
                    nperm: 10000 
                     p_ks: 0.83 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.84 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.34 
                  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.165.3896/
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/181708/iteration1/scatter.0000000116
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 116 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1534>
Subject: Job 1120116: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1534>, 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/181708/iteration1/scatter.0000000117> was used as the working directory.
Started at Wed Oct 10 10:44:04 2012
Results reported at Wed Oct 10 10:46:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000117.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000117.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 117  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    165.08 sec.
    Max Memory :      1444 MB
    Max Swap   :      3852 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.165.3896/
-whichjob
117
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 117: processing genes 10496 - 10585
Calculating significance of each gene.
Using projection method.
10496	NR0B2	1
10497	NR1D1	1
10498	NR1D2	1
10499	NR1H2	1
10500	NR1H3	1
10501	NR1H4	1
10502	NR1I2	1
10503	NR1I3	1
10504	NR2C1	1
10505	NR2C2	1.790379e-01
10506	NR2C2AP	1
10507	NR2E1	1
10508	NR2E3	1
10509	NR2F1	1.188248e-01
10510	NR2F2	9.533211e-02
10511	NR2F6	1
10512	NR3C1	1
10513	NR3C2	9.148989e-02
10514	NR4A1	1
10515	NR4A2	2.737035e-01
10516	NR4A3	1
10517	NR5A1	1
10518	NR5A2	1
10519	NR6A1	1
10520	NRAP	5.421765e-01
10521	NRARP	1
10522	NRAS	3.457274e-02
10523	NRBF2	1
10524	NRBP1	7.005585e-03
10525	NRBP2	1
10526	NRCAM	1
10527	NRD1	1
10528	NRF1	1
10529	NRG1	1
10530	NRG2	1
10531	NRG3	2.463143e-02
10532	NRG4	1
10533	NRGN	1
10534	NRIP1	2.178246e-01
10535	NRIP2	1
10536	NRIP3	1
10537	NRK	1
10538	NRL	1
10539	NRM	1
10540	NRN1	1
10541	NRN1L	1
10542	NRP1	1
10543	NRP2	1
10544	NRSN1	1
10545	NRSN2	4.286280e-02
10546	NRTN	1
10547	NRXN1	8.319170e-03
10548	NRXN2	1
10549	NRXN3	1.489626e-01
10550	NSA2	1
10551	NSD1	9.975315e-02
10552	NSDHL	1
10553	NSF	1
10554	NSFL1C	1.231559e-01
10555	NSL1	1
10556	NSMAF	2.490034e-01
10557	NSMCE1	1
10558	NSMCE2	9.775914e-02
10559	NSMCE4A	1
10560	NSUN2	1
10561	NSUN3	1
10562	NSUN4	1
10563	NSUN5	1
10564	NSUN6	1
10565	NSUN7	2.269167e-01
10566	NT5C	1
10567	NT5C1A	1
10568	NT5C1B	1.866841e-01
10569	NT5C2	1.411137e-01
10570	NT5C3	1
10571	NT5C3L	1
10572	NT5DC1	1
10573	NT5DC2	1
10574	NT5DC3	1
10575	NT5E	2.120561e-01
10576	NT5M	1
10577	NTAN1	1
10578	NTF3	1
10579	NTF4	1
10580	NTHL1	1
10581	NTM	1
10582	NTN1	1
10583	NTN3	1
10584	NTN4	1
10585	NTN5	1
Done

Running MutSig 2:
Scatter job 117: processing genes 10496 - 10585
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: 3.919216e-04	ci left: 9.996312e-01	ci right 1	k: 10000	n:10000
Cons ci ratio: 1.995523e-02	ci left: 7.861410e-01	ci right 8.020873e-01	k: 7942	n:10000
KS ci ratio: 1.417551e-02	ci left: 8.779709e-01	ci right 8.906043e-01	k: 8844	n:10000
NRIP1   10000 perm   2 sec   (4548 perm/sec)   p_kst 8.844000e-01   p_cons 7.942000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000117/NRIP1.3_3481_10000_0.8844_0.7942_1.png
                gene_name: NRIP1
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.88 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   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: 14 percent done.
NRXN1
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: 8.935079e-02	ci left: 1.541405e-01	ci right 1.686573e-01	k: 1613	n:10000
KS ci ratio: 5.600744e-02	ci left: 3.194942e-01	ci right 3.380056e-01	k: 3287	n:10000
NRXN1   10000 perm   2 sec   (4670 perm/sec)   p_kst 3.287000e-01   p_cons 1.613000e-01   p_joint 3.411000e-01

Outputting figure to mutsig2_images.part000000000117/NRXN1.3_4999_10000_0.3287_0.1613_0.3411.png
                gene_name: NRXN1
               theta_stop: 0.089 
                    nperm: 10000 
                     p_ks: 0.33 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.34 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.34 
     ci_joint_bounds_left: 0.33 
    ci_joint_bounds_right: 0.35 

Current progress: 29 percent done.
NSD1
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: 1.195230e-02	ci left: 9.093624e-01	ci right 9.203945e-01	k: 9150	n:10000
KS ci ratio: 1.391793e-02	ci left: 8.817580e-01	ci right 8.942150e-01	k: 8881	n:10000
NSD1   10000 perm   3 sec   (3110 perm/sec)   p_kst 8.881000e-01   p_cons 9.150000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000117/NSD1.3_8179_10000_0.8881_0.915_1.png
                gene_name: NSD1
               theta_stop: 0.014 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   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: 43 percent done.
NR3C2
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: 4.052554e-02	ci left: 4.734617e-01	ci right 4.931480e-01	k: 4833	n:10000
KS ci ratio: 1.790536e-02	ci left: 8.198482e-01	ci right 8.347606e-01	k: 8274	n:10000
NR3C2   10000 perm   2 sec   (5804 perm/sec)   p_kst 8.274000e-01   p_cons 4.833000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000117/NR3C2.2_2987_10000_0.8274_0.4833_1.png
                gene_name: NR3C2
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 0.83 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.83 
                   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: 57 percent done.
NRBP1
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: 4.224355e-02	ci left: 4.527897e-01	ci right 4.724321e-01	k: 4626	n:10000
KS ci ratio: 6.528325e-03	ci left: 9.697378e-01	ci right 9.761827e-01	k: 9731	n:10000
NRBP1   10000 perm   2 sec   (6278 perm/sec)   p_kst 9.731000e-01   p_cons 4.626000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000117/NRBP1.2_1676_10000_0.9731_0.4626_1.png
                gene_name: NRBP1
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.98 
                   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: 71 percent done.
NRG3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.612611e-02	ci left: 6.832497e-01	ci right 7.014381e-01	k: 6924	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: 4.868751e-02	ci left: 3.836086e-01	ci right 4.028536e-01	k: 3932	n:10000
NRG3   10000 perm   2 sec   (5856 perm/sec)   p_kst 3.932000e-01   p_cons 5.820000e-01   p_joint 6.924000e-01

Outputting figure to mutsig2_images.part000000000117/NRG3.2_2371_10000_0.3932_0.582_0.6924.png
                gene_name: NRG3
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.69 
     ci_joint_bounds_left: 0.68 
    ci_joint_bounds_right: 0.70 

Current progress: 86 percent done.
NSMCE2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.648733e-01	ci left: 4.907401e-02	ci right 5.798834e-02	k: 534	n:10000
Cons ci ratio: 4.874877e-02	ci left: 3.830114e-01	ci right 4.022512e-01	k: 3926	n:10000
KS ci ratio: 1.565438e-01	ci left: 5.436451e-02	ci right 6.369444e-02	k: 589	n:10000
NSMCE2   10000 perm   1 sec   (6853 perm/sec)   p_kst 5.890000e-02   p_cons 3.926000e-01   p_joint 5.340000e-02

Joint ci ratio: 9.748302e-02	ci left: 7.114225e-02	ci right 7.848193e-02	k: 1495	n:20000
Cons ci ratio: 3.432982e-02	ci left: 3.878169e-01	ci right 4.014137e-01	k: 7892	n:20000
KS ci ratio: 1.093720e-01	ci left: 5.704007e-02	ci right 6.368846e-02	k: 1206	n:20000
NSMCE2   20000 perm   3 sec   (5889 perm/sec)   p_kst 6.030000e-02   p_cons 3.946000e-01   p_joint 7.475000e-02

Joint ci ratio: 6.770759e-02	ci left: 9.708702e-02	ci right 1.039239e-01	k: 3014	n:30000
Cons ci ratio: 2.815664e-02	ci left: 3.869351e-01	ci right 3.980191e-01	k: 11774	n:30000
KS ci ratio: 9.079278e-02	ci left: 5.583789e-02	ci right 6.118135e-02	k: 1754	n:30000
NSMCE2   30000 perm   5 sec   (5647 perm/sec)   p_kst 5.846667e-02   p_cons 3.924667e-01   p_joint 1.004667e-01

Outputting figure to mutsig2_images.part000000000117/NSMCE2.2_768_30000_0.058467_0.39247_0.10047.png
                gene_name: NSMCE2
               theta_stop: 0.091 
                    nperm: 30000 
                     p_ks: 0.058 
        ci_ks_bounds_left: 0.056 
       ci_ks_bounds_right: 0.061 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.10 
     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.165.3896/
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/181708/iteration1/scatter.0000000117
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 117 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1699>
Subject: Job 1120118: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, 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/181708/iteration1/scatter.0000000118> was used as the working directory.
Started at Wed Oct 10 10:44:04 2012
Results reported at Wed Oct 10 10:46:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000118.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000118.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 118  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    178.11 sec.
    Max Memory :      1565 MB
    Max Swap   :      3911 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.165.3896/
-whichjob
118
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 118: processing genes 10586 - 10675
Calculating significance of each gene.
Using projection method.
10586	NTNG1	1.434021e-01
10587	NTNG2	1
10588	NTRK1	2.382358e-01
10589	NTRK2	1
10590	NTRK3	1
10591	NTS	1
10592	NTSR1	1
10593	NTSR2	1
10594	NUAK1	2.000691e-01
10595	NUAK2	7.622071e-02
10596	NUB1	1
10597	NUBP1	1
10598	NUBP2	1
10599	NUBPL	1
10600	NUCB1	1
10601	NUCB2	1
10602	NUCKS1	1
10603	NUDC	1
10604	NUDCD1	1
10605	NUDCD2	1
10606	NUDCD3	1
10607	NUDT1	1
10608	NUDT10	1
10609	NUDT11	1
10610	NUDT12	2.140735e-01
10611	NUDT13	1
10612	NUDT14	1.240239e-02
10613	NUDT15	1
10614	NUDT16	1
10615	NUDT16L1	1
10616	NUDT17	4.225406e-02
10617	NUDT18	1
10618	NUDT19	1
10619	NUDT2	1
10620	NUDT21	1
10621	NUDT22	1
10622	NUDT3	1
10623	NUDT4	1
10624	NUDT5	1
10625	NUDT6	1
10626	NUDT7	1
10627	NUDT8	1
10628	NUDT9	1
10629	NUF2	1
10630	NUFIP1	1
10631	NUFIP2	1.478293e-01
10632	NUMA1	2.592173e-01
10633	NUMB	1
10634	NUMBL	1
10635	NUP107	4.283605e-02
10636	NUP133	1
10637	NUP153	6.563235e-02
10638	NUP155	3.200957e-01
10639	NUP160	4.575116e-01
10640	NUP188	3.916907e-02
10641	NUP205	1
10642	NUP210	1
10643	NUP210L	4.750980e-01
10644	NUP214	1.010451e-01
10645	NUP35	1
10646	NUP37	1
10647	NUP43	1.385051e-01
10648	NUP50	1
10649	NUP54	1
10650	NUP62	1
10651	NUP62CL	1
10652	NUP85	1
10653	NUP88	1
10654	NUP93	1
10655	NUP98	2.548259e-01
10656	NUPL1	1
10657	NUPL2	9.603692e-02
10658	NUPR1	1
10659	NUS1	1
10660	NUSAP1	1.581999e-01
10661	NUTF2	1
10662	NVL	2.164299e-01
10663	NWD1	1
10664	NXF1	2.734838e-01
10665	NXF3	1
10666	NXF5	1
10667	NXN	1
10668	NXNL1	1
10669	NXNL2	1
10670	NXPH1	1
10671	NXPH2	5.196915e-02
10672	NXPH3	1
10673	NXPH4	1
10674	NXT1	1
10675	NXT2	1
Done

Running MutSig 2:
Scatter job 118: processing genes 10586 - 10675
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
NUP188
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.735992e-02	ci left: 1.963361e-01	ci right 2.122365e-01	k: 2042	n:10000
Cons ci ratio: 1.178575e-01	ci left: 9.370045e-02	ci right 1.055340e-01	k: 995	n:10000
KS ci ratio: 4.442278e-02	ci left: 4.279459e-01	ci right 4.474904e-01	k: 4377	n:10000
NUP188   10000 perm   2 sec   (4481 perm/sec)   p_kst 4.377000e-01   p_cons 9.950000e-02   p_joint 2.042000e-01

Joint ci ratio: 4.356663e-02	ci left: 2.818297e-01	ci right 2.944319e-01	k: 5762	n:20000
Cons ci ratio: 8.009590e-02	ci left: 1.026501e-01	ci right 1.112645e-01	k: 2138	n:20000
KS ci ratio: 3.126171e-02	ci left: 4.332045e-01	ci right 4.470129e-01	k: 8802	n:20000
NUP188   20000 perm   9 sec   (2351 perm/sec)   p_kst 4.401000e-01   p_cons 1.069000e-01   p_joint 2.881000e-01

Outputting figure to mutsig2_images.part000000000118/NUP188.3_5426_20000_0.4401_0.1069_0.2881.png
                gene_name: NUP188
               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: 0.29 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.29 

Current progress: 17 percent done.
NUMA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.173503e-01	ci left: 2.806894e-02	ci right 3.500749e-02	k: 314	n:10000
Cons ci ratio: 3.428867e-01	ci left: 1.068957e-02	ci right 1.520079e-02	k: 128	n:10000
KS ci ratio: 7.146083e-02	ci left: 2.229660e-01	ci right 2.395908e-01	k: 2312	n:10000
NUMA1   10000 perm   2 sec   (4516 perm/sec)   p_kst 2.312000e-01   p_cons 1.280000e-02   p_joint 3.140000e-02

Joint ci ratio: 1.773270e-01	ci left: 2.173197e-02	ci right 2.600799e-02	k: 476	n:20000
Cons ci ratio: 2.396559e-01	ci left: 1.161730e-02	ci right 1.482653e-02	k: 263	n:20000
KS ci ratio: 5.008043e-02	ci left: 2.285925e-01	ci right 2.403848e-01	k: 4689	n:20000
NUMA1   20000 perm   5 sec   (4135 perm/sec)   p_kst 2.344500e-01   p_cons 1.315000e-02   p_joint 2.380000e-02

Joint ci ratio: 1.564386e-01	ci left: 1.889435e-02	ci right 2.213278e-02	k: 614	n:30000
Cons ci ratio: 1.961824e-01	ci left: 1.184400e-02	ci right 1.445155e-02	k: 393	n:30000
KS ci ratio: 4.087166e-02	ci left: 2.298472e-01	ci right 2.394709e-01	k: 7039	n:30000
NUMA1   30000 perm   9 sec   (3167 perm/sec)   p_kst 2.346333e-01   p_cons 1.310000e-02   p_joint 2.046667e-02

Joint ci ratio: 1.393465e-01	ci left: 1.804668e-02	ci right 2.077372e-02	k: 775	n:40000
Cons ci ratio: 1.701186e-01	ci left: 1.198474e-02	ci right 1.423677e-02	k: 523	n:40000
KS ci ratio: 3.536314e-02	ci left: 2.308269e-01	ci right 2.391616e-01	k: 9399	n:40000
NUMA1   40000 perm   12 sec   (3202 perm/sec)   p_kst 2.349750e-01   p_cons 1.307500e-02   p_joint 1.937500e-02

Joint ci ratio: 1.246356e-01	ci left: 1.818962e-02	ci right 2.062663e-02	k: 969	n:50000
Cons ci ratio: 1.522769e-01	ci left: 1.208322e-02	ci right 1.409390e-02	k: 653	n:50000
KS ci ratio: 3.164034e-02	ci left: 2.311498e-01	ci right 2.386010e-01	k: 11743	n:50000
NUMA1   50000 perm   17 sec   (2882 perm/sec)   p_kst 2.348600e-01   p_cons 1.306000e-02   p_joint 1.938000e-02

Joint ci ratio: 1.149398e-01	ci left: 1.792257e-02	ci right 2.012430e-02	k: 1140	n:60000
Cons ci ratio: 1.414774e-01	ci left: 1.173889e-02	ci right 1.354204e-02	k: 757	n:60000
KS ci ratio: 2.885654e-02	ci left: 2.318109e-01	ci right 2.386147e-01	k: 14112	n:60000
NUMA1   60000 perm   21 sec   (2846 perm/sec)   p_kst 2.352000e-01   p_cons 1.261667e-02   p_joint 1.900000e-02

Joint ci ratio: 1.066659e-01	ci left: 1.791799e-02	ci right 1.995074e-02	k: 1324	n:70000
Cons ci ratio: 1.321480e-01	ci left: 1.159333e-02	ci right 1.324745e-02	k: 868	n:70000
KS ci ratio: 2.673314e-02	ci left: 2.318345e-01	ci right 2.381304e-01	k: 16448	n:70000
NUMA1   70000 perm   25 sec   (2763 perm/sec)   p_kst 2.349714e-01   p_cons 1.240000e-02   p_joint 1.891429e-02

Joint ci ratio: 1.051130e-01	ci left: 1.618857e-02	ci right 1.799670e-02	k: 1366	n:80000
Cons ci ratio: 1.236853e-01	ci left: 1.163251e-02	ci right 1.317815e-02	k: 991	n:80000
KS ci ratio: 2.502297e-02	ci left: 2.318039e-01	ci right 2.376903e-01	k: 18779	n:80000
NUMA1   80000 perm   30 sec   (2652 perm/sec)   p_kst 2.347375e-01   p_cons 1.238750e-02   p_joint 1.707500e-02

Joint ci ratio: 9.870645e-02	ci left: 1.637145e-02	ci right 1.808209e-02	k: 1549	n:90000
Cons ci ratio: 1.158261e-01	ci left: 1.183830e-02	ci right 1.330448e-02	k: 1130	n:90000
KS ci ratio: 2.355583e-02	ci left: 2.325206e-01	ci right 2.380742e-01	k: 21176	n:90000
NUMA1   90000 perm   34 sec   (2661 perm/sec)   p_kst 2.352889e-01   p_cons 1.255556e-02   p_joint 1.721111e-02

Joint ci ratio: 9.195043e-02	ci left: 1.702859e-02	ci right 1.867955e-02	k: 1784	n:100000
Cons ci ratio: 1.093839e-01	ci left: 1.198595e-02	ci right 1.338253e-02	k: 1267	n:100000
KS ci ratio: 2.239059e-02	ci left: 2.319664e-01	ci right 2.372290e-01	k: 23459	n:100000
NUMA1   100000 perm   38 sec   (2666 perm/sec)   p_kst 2.345900e-01   p_cons 1.267000e-02   p_joint 1.784000e-02

Joint ci ratio: 8.741106e-02	ci left: 1.716913e-02	ci right 1.874734e-02	k: 1974	n:110000
Cons ci ratio: 1.039843e-01	ci left: 1.209089e-02	ci right 1.342590e-02	k: 1402	n:110000
KS ci ratio: 2.133347e-02	ci left: 2.323429e-01	ci right 2.373620e-01	k: 25833	n:110000
NUMA1   110000 perm   41 sec   (2694 perm/sec)   p_kst 2.348455e-01   p_cons 1.274545e-02   p_joint 1.794545e-02

Joint ci ratio: 8.387916e-02	ci left: 1.712468e-02	ci right 1.863208e-02	k: 2144	n:120000
Cons ci ratio: 9.964141e-02	ci left: 1.209846e-02	ci right 1.337525e-02	k: 1527	n:120000
KS ci ratio: 2.043356e-02	ci left: 2.323044e-01	ci right 2.371085e-01	k: 28164	n:120000
NUMA1   120000 perm   44 sec   (2701 perm/sec)   p_kst 2.347000e-01   p_cons 1.272500e-02   p_joint 1.786667e-02

Outputting figure to mutsig2_images.part000000000118/NUMA1.2_6448_120000_0.2347_0.012725_0.017867.png
                gene_name: NUMA1
               theta_stop: 0.100 
                    nperm: 120000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.013 
      ci_cons_bounds_left: 0.012 
     ci_cons_bounds_right: 0.013 
                  p_joint: 0.018 
     ci_joint_bounds_left: 0.017 
    ci_joint_bounds_right: 0.019 

Current progress: 33 percent done.
NUP107
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: 4.438670e-02	ci left: 4.283448e-01	ci right 4.478913e-01	k: 4381	n:10000
KS ci ratio: 5.895076e-02	ci left: 2.974712e-01	ci right 3.156416e-01	k: 3065	n:10000
NUP107   10000 perm   2 sec   (5697 perm/sec)   p_kst 3.065000e-01   p_cons 4.381000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000118/NUP107.2_2890_10000_0.3065_0.4381_1.png
                gene_name: NUP107
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.44 
      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: 50 percent done.
NUP153
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.767252e-02	ci left: 3.067933e-01	ci right 3.251140e-01	k: 3159	n:10000
Cons ci ratio: 5.714316e-02	ci left: 3.107615e-01	ci right 3.291435e-01	k: 3199	n:10000
KS ci ratio: 9.427484e-02	ci left: 1.404072e-01	ci right 1.543988e-01	k: 1473	n:10000
NUP153   10000 perm   2 sec   (4614 perm/sec)   p_kst 1.473000e-01   p_cons 3.199000e-01   p_joint 3.159000e-01

Outputting figure to mutsig2_images.part000000000118/NUP153.2_4516_10000_0.1473_0.3199_0.3159.png
                gene_name: NUP153
               theta_stop: 0.094 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.33 

Current progress: 67 percent done.
NUP155
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: 83 percent done.
NUP214
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.240852e-02	ci left: 7.451322e-01	ci right 7.621198e-01	k: 7537	n:10000
Cons ci ratio: 4.133093e-03	ci left: 9.868662e-01	ci right 9.910417e-01	k: 9891	n:10000
KS ci ratio: 3.657006e-02	ci left: 5.247648e-01	ci right 5.444151e-01	k: 5346	n:10000
NUP214   10000 perm   2 sec   (4636 perm/sec)   p_kst 5.346000e-01   p_cons 9.891000e-01   p_joint 7.537000e-01

Outputting figure to mutsig2_images.part000000000118/NUP214.2_6417_10000_0.5346_0.9891_0.7537.png
                gene_name: NUP214
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  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.165.3896/
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/181708/iteration1/scatter.0000000118
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 118 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120122: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000119> was used as the working directory.
Started at Wed Oct 10 10:44:04 2012
Results reported at Wed Oct 10 10:46:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000119.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000119.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 119  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    157.03 sec.
    Max Memory :      1333 MB
    Max Swap   :      3858 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.165.3896/
-whichjob
119
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 119: processing genes 10676 - 10766
Calculating significance of each gene.
Using projection method.
10676	NYNRIN	1
10677	OAF	1
10678	OAS1	1
10679	OAS2	1
10680	OAS3	1
10681	OASL	1
10682	OAT	1
10683	OAZ1	1
10684	OAZ2	1
10685	OAZ3	1
10686	OBFC1	1
10687	OBFC2A	1
10688	OBFC2B	1
10689	OBP2A	1
10690	OBP2B	1
10691	OBSCN	6.536826e-01
10692	OBSL1	3.569099e-01
10693	OC90	1
10694	OCA2	1
10695	OCEL1	1
10696	OCIAD1	1
10697	OCIAD2	4.446770e-02
10698	OCLM	1
10699	OCLN	1
10700	OCM	1
10701	OCM2	1
10702	OCRL	1
10703	ODAM	1
10704	ODC1	1
10705	ODF1	1
10706	ODF2	1
10707	ODF2L	1
10708	ODF3	1
10709	ODF3B	1
10710	ODF3L1	1
10711	ODF3L2	1
10712	ODF4	1
10713	ODZ1	2.522308e-01
10714	ODZ2	3.271594e-01
10715	ODZ3	1
10716	ODZ4	3.919279e-01
10717	OFD1	1
10718	OGDH	4.428694e-01
10719	OGDHL	1
10720	OGFOD1	1
10721	OGFOD2	1
10722	OGFR	1
10723	OGFRL1	1
10724	OGG1	2.409374e-01
10725	OGN	6.751761e-02
10726	OGT	2.755336e-01
10727	OIP5	1
10728	OIT3	1
10729	OLA1	1
10730	OLAH	1
10731	OLFM1	1
10732	OLFM2	1
10733	OLFM3	1
10734	OLFM4	6.836625e-02
10735	OLFML1	1
10736	OLFML2A	1
10737	OLFML2B	8.352689e-02
10738	OLFML3	1
10739	OLIG2	1
10740	OLIG3	1
10741	OLR1	1
10742	OMA1	1
10743	OMD	1
10744	OMG	1
10745	OMP	1
10746	ONECUT1	1
10747	ONECUT2	1
10748	OOEP	1
10749	OPA1	4.202467e-01
10750	OPA3	1
10751	OPALIN	1
10752	OPCML	2.312071e-04
10753	OPHN1	1
10754	OPLAH	1
10755	OPN1LW	1
10756	OPN1MW	1
10757	OPN1MW2	1
10758	OPN1SW	1
10759	OPN3	1
10760	OPN4	1
10761	OPN5	1
10762	OPRD1	9.371181e-02
10763	OPRK1	1
10764	OPRL1	1
10765	OPRM1	1
10766	OPTC	1
Done

Running MutSig 2:
Scatter job 119: processing genes 10676 - 10766
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
OPCML
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: 1.384084e-02	ci left: 8.828843e-01	ci right 8.952880e-01	k: 8892	n:10000
OPCML   10000 perm   2 sec   (5139 perm/sec)   p_kst 8.892000e-01   p_cons 9.408000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000119/OPCML.3_1131_10000_0.8892_0.9408_1.png
                gene_name: OPCML
               theta_stop: 0.014 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       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: 20 percent done.
OBSCN
Processing conservation and coverage...
39% 78% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.666854e-02	ci left: 2.482593e-01	ci right 2.654825e-01	k: 2568	n:10000
Cons ci ratio: 5.096562e-02	ci left: 3.621174e-01	ci right 3.811575e-01	k: 3716	n:10000
KS ci ratio: 1.879096e-01	ci left: 3.777051e-02	ci right 4.569926e-02	k: 416	n:10000
OBSCN   10000 perm   5 sec   (2209 perm/sec)   p_kst 4.160000e-02   p_cons 3.716000e-01   p_joint 2.568000e-01

Joint ci ratio: 5.684346e-02	ci left: 1.866108e-01	ci right 1.975789e-01	k: 3841	n:20000
Cons ci ratio: 3.641513e-02	ci left: 3.601157e-01	ci right 3.735231e-01	k: 7336	n:20000
KS ci ratio: 1.357897e-01	ci left: 3.727788e-02	ci right 4.275688e-02	k: 799	n:20000
OBSCN   20000 perm   10 sec   (2086 perm/sec)   p_kst 3.995000e-02   p_cons 3.668000e-01   p_joint 1.920500e-01

Joint ci ratio: 3.994186e-02	ci left: 2.381551e-01	ci right 2.478947e-01	k: 7290	n:30000
Cons ci ratio: 2.968910e-02	ci left: 3.620407e-01	ci right 3.729849e-01	k: 11025	n:30000
KS ci ratio: 1.117486e-01	ci left: 3.719416e-02	ci right 4.162894e-02	k: 1181	n:30000
OBSCN   30000 perm   15 sec   (2033 perm/sec)   p_kst 3.936667e-02   p_cons 3.675000e-01   p_joint 2.430000e-01

Joint ci ratio: 3.305541e-02	ci left: 2.558060e-01	ci right 2.644289e-01	k: 10404	n:40000
Cons ci ratio: 2.582572e-02	ci left: 3.607282e-01	ci right 3.701913e-01	k: 14618	n:40000
KS ci ratio: 9.512444e-02	ci left: 3.878452e-02	ci right 4.268252e-02	k: 1628	n:40000
OBSCN   40000 perm   20 sec   (1998 perm/sec)   p_kst 4.070000e-02   p_cons 3.654500e-01   p_joint 2.601000e-01

Outputting figure to mutsig2_images.part000000000119/OBSCN.2_25533_40000_0.0407_0.36545_0.2601.png
                gene_name: OBSCN
               theta_stop: 0.095 
                    nperm: 40000 
                     p_ks: 0.041 
        ci_ks_bounds_left: 0.039 
       ci_ks_bounds_right: 0.043 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.26 
     ci_joint_bounds_left: 0.26 
    ci_joint_bounds_right: 0.26 

Current progress: 40 percent done.
ODZ1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.223412e-02	ci left: 9.055571e-01	ci right 9.168020e-01	k: 9113	n:10000
Cons ci ratio: 3.207657e-02	ci left: 5.892161e-01	ci right 6.085262e-01	k: 5989	n:10000
KS ci ratio: 2.879412e-02	ci left: 6.400560e-01	ci right 6.588569e-01	k: 6495	n:10000
ODZ1   10000 perm   2 sec   (4297 perm/sec)   p_kst 6.495000e-01   p_cons 5.989000e-01   p_joint 9.113000e-01

Outputting figure to mutsig2_images.part000000000119/ODZ1.2_8327_10000_0.6495_0.5989_0.9113.png
                gene_name: ODZ1
               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: 0.91 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 60 percent done.
ODZ2
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: 1.947207e-02	ci left: 7.941537e-01	ci right 8.098700e-01	k: 8021	n:10000
KS ci ratio: 1.338745e-02	ci left: 8.894412e-01	ci right 9.015273e-01	k: 8956	n:10000
ODZ2   10000 perm   2 sec   (4311 perm/sec)   p_kst 8.956000e-01   p_cons 8.021000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000119/ODZ2.2_8414_10000_0.8956_0.8021_1.png
                gene_name: ODZ2
               theta_stop: 0.019 
                    nperm: 10000 
                     p_ks: 0.90 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   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: 80 percent done.
OPA1
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: 8.516918e-02	ci left: 1.673034e-01	ci right 1.822866e-01	k: 1747	n:10000
KS ci ratio: 3.583430e-02	ci left: 5.348776e-01	ci right 5.544964e-01	k: 5447	n:10000
OPA1   10000 perm   2 sec   (5644 perm/sec)   p_kst 5.447000e-01   p_cons 1.747000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000119/OPA1.2_3168_10000_0.5447_0.1747_1.png
                gene_name: OPA1
               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: 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.165.3896/
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/181708/iteration1/scatter.0000000119
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 119 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120125: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000120> was used as the working directory.
Started at Wed Oct 10 10:44:04 2012
Results reported at Wed Oct 10 10:45:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000120.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000120.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 120  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    105.39 sec.
    Max Memory :       635 MB
    Max Swap   :      3362 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.165.3896/
-whichjob
120
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 120: processing genes 10767 - 10856
Calculating significance of each gene.
Using projection method.
10767	OPTN	1
10768	OR10A2	1.022763e-01
10769	OR10A3	1
10770	OR10A4	1
10771	OR10A5	7.919158e-03
10772	OR10A6	2.730212e-02
10773	OR10A7	1
10774	OR10AD1	1.221820e-01
10775	OR10AG1	1
10776	OR10C1	6.240120e-02
10777	OR10G2	1
10778	OR10G3	1
10779	OR10G4	1
10780	OR10G7	1
10781	OR10G8	7.596836e-02
10782	OR10G9	1
10783	OR10H1	1.449155e-01
10784	OR10H2	1
10785	OR10H3	1
10786	OR10H4	1.021664e-01
10787	OR10H5	1
10788	OR10J1	1
10789	OR10J3	1
10790	OR10J5	1
10791	OR10K1	1
10792	OR10K2	1.560262e-01
10793	OR10P1	1
10794	OR10Q1	1
10795	OR10R2	1
10796	OR10S1	1
10797	OR10T2	6.573926e-02
10798	OR10V1	1
10799	OR10W1	1
10800	OR10X1	1.948116e-02
10801	OR10Z1	1
10802	OR11A1	1
10803	OR11G2	1
10804	OR11H1	1
10805	OR11H12	2.670586e-02
10806	OR11H4	1
10807	OR11H6	1
10808	OR11L1	1
10809	OR12D2	1
10810	OR12D3	1
10811	OR13A1	5.389074e-02
10812	OR13C2	1
10813	OR13C3	1
10814	OR13C4	1
10815	OR13C5	1
10816	OR13C8	1
10817	OR13C9	1
10818	OR13D1	1
10819	OR13F1	1
10820	OR13G1	3.390056e-02
10821	OR13H1	1
10822	OR13J1	1
10823	OR14A16	1
10824	OR14C36	1
10825	OR14I1	1
10826	OR14J1	1
10827	OR1A1	1
10828	OR1A2	1
10829	OR1B1	1
10830	OR1C1	1
10831	OR1D2	1
10832	OR1E1	1
10833	OR1E2	1
10834	OR1F1	1
10835	OR1G1	1
10836	OR1I1	1
10837	OR1J1	1
10838	OR1J2	1
10839	OR1J4	1
10840	OR1K1	1
10841	OR1L1	1
10842	OR1L3	1
10843	OR1L4	1
10844	OR1L6	1
10845	OR1L8	1
10846	OR1M1	1
10847	OR1N1	1
10848	OR1N2	1
10849	OR1Q1	1
10850	OR1S1	2.246212e-02
10851	OR1S2	1.424914e-01
10852	OR2A1	1
10853	OR2A12	1
10854	OR2A14	1
10855	OR2A2	1
10856	OR2A25	1
Done

Running MutSig 2:
Scatter job 120: processing genes 10767 - 10856
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
OR10A5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.828636e-02	ci left: 8.136481e-01	ci right 8.287643e-01	k: 8213	n:10000
Cons ci ratio: 2.208869e-02	ci left: 7.504927e-01	ci right 7.673562e-01	k: 7590	n:10000
KS ci ratio: 3.003189e-02	ci left: 6.205509e-01	ci right 6.395732e-01	k: 6301	n:10000
OR10A5   10000 perm   2 sec   (4869 perm/sec)   p_kst 6.301000e-01   p_cons 7.590000e-01   p_joint 8.213000e-01

Outputting figure to mutsig2_images.part000000000120/OR10A5.2_958_10000_0.6301_0.759_0.8213.png
                gene_name: OR10A5
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.83 

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.165.3896/
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/181708/iteration1/scatter.0000000120
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 120 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1645>
Subject: Job 1120128: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1645>, 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/181708/iteration1/scatter.0000000121> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:45:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000121.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000121.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 121  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    104.15 sec.
    Max Memory :       800 MB
    Max Swap   :      3630 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.165.3896/
-whichjob
121
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 121: processing genes 10857 - 10947
Calculating significance of each gene.
Using projection method.
10857	OR2A4	1
10858	OR2A42	1
10859	OR2A5	1
10860	OR2A7	1
10861	OR2AE1	1
10862	OR2AG1	1
10863	OR2AG2	5.653137e-02
10864	OR2AK2	1
10865	OR2AT4	1
10866	OR2B11	1
10867	OR2B2	1
10868	OR2B3	1
10869	OR2B6	3.201655e-02
10870	OR2C1	1.459305e-01
10871	OR2C3	1
10872	OR2D2	1
10873	OR2D3	1
10874	OR2F1	1
10875	OR2F2	1.144472e-01
10876	OR2G2	1.052229e-01
10877	OR2G3	1
10878	OR2G6	1
10879	OR2H1	1
10880	OR2H2	5.684734e-02
10881	OR2J2	1
10882	OR2J3	1
10883	OR2K2	1
10884	OR2L13	1
10885	OR2L2	4.339655e-02
10886	OR2L3	1
10887	OR2L8	1
10888	OR2M2	1
10889	OR2M3	1
10890	OR2M4	1
10891	OR2M5	1
10892	OR2M7	1
10893	OR2S2	1
10894	OR2T1	2.487313e-02
10895	OR2T10	1
10896	OR2T11	1
10897	OR2T12	1
10898	OR2T2	4.156793e-02
10899	OR2T27	1
10900	OR2T29	1
10901	OR2T3	1
10902	OR2T33	1
10903	OR2T34	1
10904	OR2T4	1
10905	OR2T5	1
10906	OR2T6	7.005960e-03
10907	OR2T8	1
10908	OR2V2	2.785001e-02
10909	OR2W1	1
10910	OR2W3	1
10911	OR2W5	1
10912	OR2Y1	1
10913	OR2Z1	7.305079e-02
10914	OR3A1	1
10915	OR3A2	1
10916	OR3A3	1
10917	OR4A15	1
10918	OR4A16	1
10919	OR4A47	7.253861e-03
10920	OR4A5	1
10921	OR4B1	1
10922	OR4C11	1
10923	OR4C12	1
10924	OR4C13	1
10925	OR4C15	1
10926	OR4C16	1
10927	OR4C3	1
10928	OR4C46	1
10929	OR4C6	5.096019e-02
10930	OR4D1	1
10931	OR4D10	3.678691e-02
10932	OR4D11	1
10933	OR4D2	1
10934	OR4D5	1.524207e-02
10935	OR4D6	5.104610e-02
10936	OR4D9	1
10937	OR4E2	1
10938	OR4F15	1
10939	OR4F17	1
10940	OR4F4	1
10941	OR4F5	1
10942	OR4F6	1
10943	OR4K1	1
10944	OR4K13	1
10945	OR4K14	1
10946	OR4K15	1
10947	OR4K17	1
Done

Running MutSig 2:
Scatter job 121: processing genes 10857 - 10947
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
OR2T6
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.409049e-02	ci left: 4.316360e-01	ci right 4.511982e-01	k: 4414	n:10000
Cons ci ratio: 5.952407e-02	ci left: 2.934065e-01	ci right 3.115087e-01	k: 3024	n:10000
KS ci ratio: 2.880677e-02	ci left: 6.398548e-01	ci right 6.586581e-01	k: 6493	n:10000
OR2T6   10000 perm   2 sec   (6357 perm/sec)   p_kst 6.493000e-01   p_cons 3.024000e-01   p_joint 4.414000e-01

Outputting figure to mutsig2_images.part000000000121/OR2T6.2_931_10000_0.6493_0.3024_0.4414.png
                gene_name: OR2T6
               theta_stop: 0.060 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.30 
      ci_cons_bounds_left: 0.29 
     ci_cons_bounds_right: 0.31 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.45 

Current progress: 50 percent done.
OR4A47
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: 2.737222e-02	ci left: 6.629006e-01	ci right 6.813991e-01	k: 6722	n:10000
KS ci ratio: 5.653175e-02	ci left: 3.154251e-01	ci right 3.338771e-01	k: 3246	n:10000
OR4A47   10000 perm   1 sec   (6794 perm/sec)   p_kst 3.246000e-01   p_cons 6.722000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000121/OR4A47.2_932_10000_0.3246_0.6722_1.png
                gene_name: OR4A47
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.32 
       ci_ks_bounds_right: 0.33 
                   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.165.3896/
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/181708/iteration1/scatter.0000000121
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 121 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1726>
Subject: Job 1120131: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1726>, 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/181708/iteration1/scatter.0000000122> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:45:20 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000122.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000122.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 122  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     51.07 sec.
    Max Memory :       531 MB
    Max Swap   :      3335 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.165.3896/
-whichjob
122
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 122: processing genes 10948 - 11037
Calculating significance of each gene.
Using projection method.
10948	OR4K2	1
10949	OR4K5	9.814502e-02
10950	OR4L1	4.127800e-02
10951	OR4M1	1
10952	OR4M2	1
10953	OR4N2	1
10954	OR4N4	1
10955	OR4N5	1
10956	OR4P4	1
10957	OR4Q3	1
10958	OR4S1	1
10959	OR4S2	1
10960	OR4X1	1
10961	OR4X2	1
10962	OR51A2	1
10963	OR51A4	1
10964	OR51A7	1.428464e-01
10965	OR51B2	1
10966	OR51B4	1
10967	OR51B5	1
10968	OR51B6	1
10969	OR51D1	8.788751e-02
10970	OR51E1	1
10971	OR51E2	1
10972	OR51F1	1
10973	OR51F2	1
10974	OR51G1	1
10975	OR51G2	9.150333e-02
10976	OR51I1	1
10977	OR51I2	1
10978	OR51L1	1
10979	OR51M1	1
10980	OR51Q1	4.777251e-02
10981	OR51S1	9.068129e-02
10982	OR51T1	1
10983	OR51V1	1
10984	OR52A1	1
10985	OR52A4	1
10986	OR52A5	1
10987	OR52B2	1
10988	OR52B4	1
10989	OR52B6	1
10990	OR52D1	1
10991	OR52E2	1
10992	OR52E4	1
10993	OR52E6	1
10994	OR52E8	1
10995	OR52H1	1
10996	OR52I1	1
10997	OR52I2	1
10998	OR52J3	1
10999	OR52K1	3.548846e-02
11000/18094 11000	OR52K2	1
11001	OR52L1	1
11002	OR52M1	1
11003	OR52N1	1
11004	OR52N2	1
11005	OR52N4	1
11006	OR52N5	1
11007	OR52R1	1
11008	OR52W1	1
11009	OR56A1	1
11010	OR56A3	1
11011	OR56A4	1.059431e-01
11012	OR56A5	1
11013	OR56B1	1
11014	OR56B4	4.464862e-02
11015	OR5A1	1
11016	OR5A2	1
11017	OR5AC2	7.346146e-02
11018	OR5AK2	1.067494e-01
11019	OR5AN1	1
11020	OR5AP2	1
11021	OR5AR1	1
11022	OR5AS1	1
11023	OR5AU1	1
11024	OR5B12	1
11025	OR5B17	1
11026	OR5B2	1
11027	OR5B21	6.220956e-02
11028	OR5B3	1
11029	OR5C1	1
11030	OR5D13	1
11031	OR5D14	6.006171e-02
11032	OR5D16	1
11033	OR5D18	3.274251e-02
11034	OR5F1	1
11035	OR5H1	1
11036	OR5H14	1
11037	OR5H15	1
Done

Running MutSig 2:
Scatter job 122: processing genes 10948 - 11037
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.165.3896/
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/181708/iteration1/scatter.0000000122
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 122 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120135: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000123> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:46:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000123.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000123.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 123  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    109.65 sec.
    Max Memory :       899 MB
    Max Swap   :      3668 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.165.3896/
-whichjob
123
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 123: processing genes 11038 - 11128
Calculating significance of each gene.
Using projection method.
11038	OR5H2	1
11039	OR5H6	1
11040	OR5I1	1
11041	OR5J2	1
11042	OR5K1	1
11043	OR5K2	1.366511e-03
11044	OR5K3	1.413150e-01
11045	OR5K4	1
11046	OR5L1	1
11047	OR5L2	1.616998e-01
11048	OR5M1	1
11049	OR5M10	9.115569e-03
11050	OR5M11	1
11051	OR5M3	2.327614e-02
11052	OR5M8	1
11053	OR5M9	1
11054	OR5P2	1
11055	OR5P3	1
11056	OR5R1	1
11057	OR5T1	1
11058	OR5T2	1
11059	OR5T3	1
11060	OR5V1	1
11061	OR5W2	1.073293e-01
11062	OR6A2	1
11063	OR6B1	1.274163e-01
11064	OR6B2	1
11065	OR6B3	1
11066	OR6C1	1
11067	OR6C2	1
11068	OR6C3	1
11069	OR6C4	1
11070	OR6C6	1
11071	OR6C65	1
11072	OR6C68	1
11073	OR6C70	4.933796e-02
11074	OR6C74	1
11075	OR6C75	1
11076	OR6C76	1
11077	OR6F1	1
11078	OR6K2	3.424123e-02
11079	OR6K3	1
11080	OR6K6	1.370128e-01
11081	OR6M1	5.016633e-02
11082	OR6N1	4.392953e-03
11083	OR6N2	1.420685e-01
11084	OR6Q1	1.458284e-01
11085	OR6S1	7.715358e-03
11086	OR6T1	3.449060e-02
11087	OR6V1	1
11088	OR6X1	1
11089	OR6Y1	1.019358e-01
11090	OR7A10	1
11091	OR7A17	1
11092	OR7A5	1.091787e-02
11093	OR7C1	1
11094	OR7C2	1
11095	OR7D2	1
11096	OR7D4	1
11097	OR7E24	1
11098	OR7G1	1
11099	OR7G2	1
11100	OR7G3	1
11101	OR8A1	1
11102	OR8B12	9.319479e-02
11103	OR8B2	1
11104	OR8B3	1
11105	OR8B4	1.019576e-01
11106	OR8B8	1
11107	OR8D1	1.345103e-01
11108	OR8D2	1
11109	OR8D4	1
11110	OR8G1	1
11111	OR8G2	1
11112	OR8G5	1
11113	OR8H1	5.587732e-02
11114	OR8H2	7.865789e-02
11115	OR8H3	1
11116	OR8I2	1
11117	OR8J1	1
11118	OR8J3	1
11119	OR8K1	4.817720e-02
11120	OR8K3	2.042995e-02
11121	OR8K5	1
11122	OR8S1	1
11123	OR8U8	1
11124	OR9A2	1
11125	OR9A4	1
11126	OR9G1	1
11127	OR9G4	6.474336e-02
11128	OR9G9	1
Done

Running MutSig 2:
Scatter job 123: processing genes 11038 - 11128
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
OR5K2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.510876e-02	ci left: 8.639656e-01	ci right 8.772177e-01	k: 8707	n:10000
Cons ci ratio: 3.803565e-02	ci left: 5.051514e-01	ci right 5.248398e-01	k: 5150	n:10000
KS ci ratio: 9.178519e-03	ci left: 9.435701e-01	ci right 9.523667e-01	k: 9481	n:10000
OR5K2   10000 perm   2 sec   (5068 perm/sec)   p_kst 9.481000e-01   p_cons 5.150000e-01   p_joint 8.707000e-01

Outputting figure to mutsig2_images.part000000000123/OR5K2.2_954_10000_0.9481_0.515_0.8707.png
                gene_name: OR5K2
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.94 
       ci_ks_bounds_right: 0.95 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.52 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.88 

Current progress: 20 percent done.
OR5M10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.146199e-02	ci left: 9.158488e-01	ci right 9.265043e-01	k: 9213	n:10000
Cons ci ratio: 2.664240e-02	ci left: 6.747853e-01	ci right 6.931075e-01	k: 6840	n:10000
KS ci ratio: 3.895970e-02	ci left: 4.931507e-01	ci right 5.128476e-01	k: 5030	n:10000
OR5M10   10000 perm   1 sec   (6743 perm/sec)   p_kst 5.030000e-01   p_cons 6.840000e-01   p_joint 9.213000e-01

Outputting figure to mutsig2_images.part000000000123/OR5M10.2_952_10000_0.503_0.684_0.9213.png
                gene_name: OR5M10
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.92 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

Current progress: 40 percent done.
OR6N1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.418225e-02	ci left: 5.582226e-01	ci right 5.777378e-01	k: 5680	n:10000
Cons ci ratio: 3.408486e-02	ci left: 5.596260e-01	ci right 5.791336e-01	k: 5694	n:10000
KS ci ratio: 6.080366e-02	ci left: 2.845862e-01	ci right 3.025342e-01	k: 2935	n:10000
OR6N1   10000 perm   1 sec   (6992 perm/sec)   p_kst 2.935000e-01   p_cons 5.694000e-01   p_joint 5.680000e-01

Outputting figure to mutsig2_images.part000000000123/OR6N1.2_942_10000_0.2935_0.5694_0.568.png
                gene_name: OR6N1
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.57 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.58 
                  p_joint: 0.57 
     ci_joint_bounds_left: 0.56 
    ci_joint_bounds_right: 0.58 

Current progress: 60 percent done.
OR6S1
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: 3.411267e-02	ci left: 5.592250e-01	ci right 5.787348e-01	k: 5690	n:10000
KS ci ratio: 4.697642e-02	ci left: 4.007361e-01	ci right 4.201161e-01	k: 4104	n:10000
OR6S1   10000 perm   2 sec   (4419 perm/sec)   p_kst 4.104000e-01   p_cons 5.690000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000123/OR6S1.2_1000_10000_0.4104_0.569_1.png
                gene_name: OR6S1
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.57 
      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: 80 percent done.
OR7A5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.450460e-02	ci left: 2.086584e-01	ci right 2.249069e-01	k: 2167	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: 9.131491e-02	ci left: 1.484485e-01	ci right 1.627527e-01	k: 1555	n:10000
OR7A5   10000 perm   3 sec   (3637 perm/sec)   p_kst 1.555000e-01   p_cons 2.113000e-01   p_joint 2.167000e-01

Outputting figure to mutsig2_images.part000000000123/OR7A5.2_964_10000_0.1555_0.2113_0.2167.png
                gene_name: OR7A5
               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: 0.22 
     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.165.3896/
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/181708/iteration1/scatter.0000000123
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 123 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120138: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000124> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:45:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000124.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000124.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 124  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     68.31 sec.
    Max Memory :      1362 MB
    Max Swap   :      4062 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.165.3896/
-whichjob
124
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 124: processing genes 11129 - 11218
Calculating significance of each gene.
Using projection method.
11129	OR9I1	8.012728e-02
11130	OR9K2	1
11131	OR9Q1	1.179950e-01
11132	OR9Q2	1.186495e-01
11133	ORAI1	1
11134	ORAI2	5.559871e-02
11135	ORAI3	1
11136	ORAOV1	1
11137	ORC1L	1.381815e-01
11138	ORC2L	1
11139	ORC3L	5.808427e-03
11140	ORC4L	1
11141	ORC5L	1
11142	ORC6L	1
11143	ORM1	1
11144	ORM2	1
11145	ORMDL1	1
11146	ORMDL2	1
11147	ORMDL3	1
11148	OS9	1
11149	OSBP	1
11150	OSBP2	1
11151	OSBPL10	1
11152	OSBPL11	1
11153	OSBPL1A	1
11154	OSBPL2	1
11155	OSBPL3	3.528363e-02
11156	OSBPL5	1
11157	OSBPL6	1
11158	OSBPL7	1
11159	OSBPL8	1
11160	OSBPL9	1
11161	OSCAR	1
11162	OSCP1	1.067893e-01
11163	OSGEP	1
11164	OSGEPL1	1
11165	OSGIN1	1
11166	OSGIN2	1
11167	OSM	1
11168	OSMR	1
11169	OSR1	1
11170	OSR2	1
11171	OSTBETA	1
11172	OSTC	1
11173	OSTF1	1
11174	OSTM1	1
11175	OSTN	1
11176	OSTalpha	3.227778e-02
11177	OTC	1
11178	OTOA	1
11179	OTOF	5.909123e-01
11180	OTOL1	1
11181	OTOP1	1
11182	OTOP2	1.540005e-01
11183	OTOP3	1.357233e-01
11184	OTOR	1
11185	OTOS	1
11186	OTP	1
11187	OTUB1	1
11188	OTUB2	1
11189	OTUD3	1
11190	OTUD4	1
11191	OTUD5	1
11192	OTUD6A	6.561799e-02
11193	OTUD6B	1
11194	OTUD7A	2.048410e-04
11195	OTUD7B	3.412895e-01
11196	OTX1	1
11197	OTX2	1
11198	OVCA2	1
11199	OVCH1	1
11200	OVCH2	1
11201	OVGP1	1
11202	OVOL1	1
11203	OVOL2	1
11204	OXA1L	1
11205	OXCT1	1
11206	OXCT2	1
11207	OXER1	1
11208	OXGR1	1
11209	OXNAD1	1
11210	OXR1	9.316231e-02
11211	OXSM	1
11212	OXSR1	1
11213	OXT	1
11214	OXTR	1
11215	P2RX1	1
11216	P2RX2	1
11217	P2RX3	4.275480e-02
11218	P2RX4	1
Done

Running MutSig 2:
Scatter job 124: processing genes 11129 - 11218
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
OTUD7A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.160559e-02	ci left: 7.585873e-01	ci right 7.752569e-01	k: 7670	n:10000
Cons ci ratio: 3.082932e-02	ci left: 6.081928e-01	ci right 6.273385e-01	k: 6178	n:10000
KS ci ratio: 3.707269e-02	ci left: 5.179584e-01	ci right 5.376254e-01	k: 5278	n:10000
OTUD7A   10000 perm   2 sec   (5563 perm/sec)   p_kst 5.278000e-01   p_cons 6.178000e-01   p_joint 7.670000e-01

Outputting figure to mutsig2_images.part000000000124/OTUD7A.4_2825_10000_0.5278_0.6178_0.767.png
                gene_name: OTUD7A
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.62 
      ci_cons_bounds_left: 0.61 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.77 
     ci_joint_bounds_left: 0.76 
    ci_joint_bounds_right: 0.78 

Current progress: 33 percent done.
ORC3L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.799546e-02	ci left: 6.528339e-01	ci right 6.714715e-01	k: 6622	n:10000
Cons ci ratio: 1.079305e-02	ci left: 9.244098e-01	ci right 9.345383e-01	k: 9296	n:10000
KS ci ratio: 4.501416e-02	ci left: 4.214646e-01	ci right 4.409755e-01	k: 4312	n:10000
ORC3L   10000 perm   2 sec   (6511 perm/sec)   p_kst 4.312000e-01   p_cons 9.296000e-01   p_joint 6.622000e-01

Outputting figure to mutsig2_images.part000000000124/ORC3L.3_2219_10000_0.4312_0.9296_0.6622.png
                gene_name: ORC3L
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.66 
     ci_joint_bounds_left: 0.65 
    ci_joint_bounds_right: 0.67 

Current progress: 67 percent done.
OSBPL3
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: 2.014424e-02	ci left: 7.829981e-01	ci right 7.990320e-01	k: 7911	n:10000
KS ci ratio: 6.951078e-03	ci left: 9.660453e-01	ci right 9.728776e-01	k: 9696	n:10000
OSBPL3   10000 perm   2 sec   (5941 perm/sec)   p_kst 9.696000e-01   p_cons 7.911000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000124/OSBPL3.2_2752_10000_0.9696_0.7911_1.png
                gene_name: OSBPL3
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.97 
       ci_ks_bounds_right: 0.97 
                   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.165.3896/
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/181708/iteration1/scatter.0000000124
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 124 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120142: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000125> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:45:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000125.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000125.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 125  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     72.50 sec.
    Max Memory :      1220 MB
    Max Swap   :      3828 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.165.3896/
-whichjob
125
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 125: processing genes 11219 - 11309
Calculating significance of each gene.
Using projection method.
11219	P2RX5	1
11220	P2RX6	1
11221	P2RX7	1
11222	P2RY1	1
11223	P2RY10	1
11224	P2RY11	1
11225	P2RY12	1
11226	P2RY13	1.446464e-01
11227	P2RY14	1
11228	P2RY2	1
11229	P2RY4	1
11230	P2RY6	1
11231	P2RY8	1
11232	P4HA1	1
11233	P4HA2	1
11234	P4HA3	1
11235	P4HB	1
11236	P4HTM	1
11237	PA2G4	1.974579e-01
11238	PAAF1	1.200791e-01
11239	PABPC1	1
11240	PABPC1L	1
11241	PABPC3	1
11242	PABPC4	1.471386e-01
11243	PABPC5	1
11244	PABPN1	1
11245	PABPN1L	1
11246	PACRG	3.322445e-02
11247	PACRGL	1
11248	PACS1	3.921664e-01
11249	PACS2	1.936512e-01
11250	PACSIN1	1
11251	PACSIN2	1
11252	PACSIN3	1
11253	PADI1	2.101594e-01
11254	PADI2	1.332821e-01
11255	PADI3	1
11256	PADI4	1.429089e-01
11257	PADI6	1
11258	PAEP	1
11259	PAF1	1.074446e-02
11260	PAFAH1B1	1
11261	PAFAH1B2	1
11262	PAFAH1B3	1
11263	PAFAH2	1.974754e-01
11264	PAG1	1
11265	PAGE1	4.622355e-02
11266	PAGE2	1
11267	PAGE2B	1
11268	PAGE4	1
11269	PAGE5	1
11270	PAH	1
11271	PAICS	1
11272	PAIP1	1.001473e-02
11273	PAIP2	1
11274	PAIP2B	1
11275	PAK1	1
11276	PAK1IP1	1
11277	PAK2	1
11278	PAK3	2.345533e-03
11279	PAK4	1
11280	PAK6	1
11281	PAK7	1
11282	PALB2	2.246261e-02
11283	PALLD	1
11284	PALM	4.371279e-02
11285	PALM2	1
11286	PALM2-AKAP2	1
11287	PALMD	1
11288	PAM	1
11289	PAMR1	1
11290	PAN2	1
11291	PAN3	1
11292	PANK1	1
11293	PANK2	1.185709e-01
11294	PANK3	1
11295	PANK4	1
11296	PANX1	1
11297	PANX2	1
11298	PANX3	1.033841e-01
11299	PAOX	5.992151e-02
11300	PAPD4	1
11301	PAPD5	1
11302	PAPD7	1
11303	PAPL	1
11304	PAPLN	1
11305	PAPOLA	3.010980e-01
11306	PAPOLB	1
11307	PAPOLG	1
11308	PAPPA	4.606239e-01
11309	PAPPA2	4.366695e-01
Done

Running MutSig 2:
Scatter job 125: processing genes 11219 - 11309
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PAK3
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: 5.095471e-02	ci left: 3.622168e-01	ci right 3.812580e-01	k: 3717	n:10000
KS ci ratio: 2.166601e-02	ci left: 7.575753e-01	ci right 7.742695e-01	k: 7660	n:10000
PAK3   10000 perm   2 sec   (5660 perm/sec)   p_kst 7.660000e-01   p_cons 3.717000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000125/PAK3.3_1807_10000_0.766_0.3717_1.png
                gene_name: PAK3
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.77 
        ci_ks_bounds_left: 0.76 
       ci_ks_bounds_right: 0.77 
                   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: 25 percent done.
PALB2
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: 2.778118e-03	ci left: 9.935271e-01	ci right 9.963728e-01	k: 9951	n:10000
KS ci ratio: 2.584439e-02	ci left: 6.878865e-01	ci right 7.059987e-01	k: 6970	n:10000
PALB2   10000 perm   2 sec   (5405 perm/sec)   p_kst 6.970000e-01   p_cons 9.951000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000125/PALB2.3_3613_10000_0.697_0.9951_1.png
                gene_name: PALB2
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.71 
                   p_cons: 1.00 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 1.00 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 50 percent done.
PAF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.904803e-02	ci left: 8.011560e-01	ci right 8.166636e-01	k: 8090	n:10000
Cons ci ratio: 2.016252e-02	ci left: 7.826940e-01	ci right 7.987363e-01	k: 7908	n:10000
KS ci ratio: 4.217566e-02	ci left: 4.535883e-01	ci right 4.732330e-01	k: 4634	n:10000
PAF1   10000 perm   2 sec   (6400 perm/sec)   p_kst 4.634000e-01   p_cons 7.908000e-01   p_joint 8.090000e-01

Outputting figure to mutsig2_images.part000000000125/PAF1.2_1652_10000_0.4634_0.7908_0.809.png
                gene_name: PAF1
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.81 
     ci_joint_bounds_left: 0.80 
    ci_joint_bounds_right: 0.82 

Current progress: 75 percent done.
PAIP1
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: 7.368076e-02	ci left: 2.124066e-01	ci right 2.287565e-01	k: 2205	n:10000
KS ci ratio: 1.730686e-02	ci left: 8.295109e-01	ci right 8.440923e-01	k: 8369	n:10000
PAIP1   10000 perm   1 sec   (6691 perm/sec)   p_kst 8.369000e-01   p_cons 2.205000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000125/PAIP1.2_1484_10000_0.8369_0.2205_1.png
                gene_name: PAIP1
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.84 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  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.165.3896/
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/181708/iteration1/scatter.0000000125
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 125 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1642>
Subject: Job 1120144: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, 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/181708/iteration1/scatter.0000000126> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:45:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000126.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000126.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 126  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    109.13 sec.
    Max Memory :      1086 MB
    Max Swap   :      3929 MB

    Max Processes  :         7
    Max Threads    :        95

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/
-whichjob
126
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 126: processing genes 11310 - 11399
Calculating significance of each gene.
Using projection method.
11310	PAPSS1	1
11311	PAPSS2	1
11312	PAQR3	1
11313	PAQR4	1
11314	PAQR5	1
11315	PAQR6	1
11316	PAQR7	1
11317	PAQR8	1
11318	PAQR9	1
11319	PARD3	1
11320	PARD3B	1
11321	PARD6A	5.003576e-02
11322	PARD6B	1
11323	PARD6G	1
11324	PARK2	1
11325	PARK7	1
11326	PARL	1.901126e-02
11327	PARM1	1
11328	PARN	1
11329	PARP1	1
11330	PARP10	1
11331	PARP11	1
11332	PARP12	1
11333	PARP14	4.045595e-01
11334	PARP15	1
11335	PARP16	1
11336	PARP2	1
11337	PARP3	1
11338	PARP4	4.990242e-01
11339	PARP6	2.418002e-01
11340	PARP8	1
11341	PARP9	7.881892e-02
11342	PARS2	1
11343	PARVA	1
11344	PARVB	1
11345	PARVG	1
11346	PASD1	1
11347	PASK	4.378044e-01
11348	PATE1	1
11349	PATE2	1
11350	PATL1	1
11351	PATZ1	1
11352	PAWR	1
11353	PAX1	1
11354	PAX2	1
11355	PAX3	1
11356	PAX4	5.329869e-02
11357	PAX5	1
11358	PAX6	1
11359	PAX7	1
11360	PAX8	1
11361	PAX9	1
11362	PAXIP1	3.634616e-01
11363	PBK	1
11364	PBLD	1
11365	PBOV1	1
11366	PBRM1	1
11367	PBX1	1
11368	PBX2	1
11369	PBX3	1
11370	PBX4	1
11371	PBXIP1	2.056726e-01
11372	PC	1
11373	PCBD1	1
11374	PCBD2	1
11375	PCBP1	1
11376	PCBP2	1
11377	PCBP3	1
11378	PCBP4	1
11379	PCCA	1
11380	PCCB	1
11381	PCDH1	1
11382	PCDH10	4.024502e-01
11383	PCDH11X	2.132604e-01
11384	PCDH11Y	1
11385	PCDH12	1
11386	PCDH15	6.570898e-01
11387	PCDH17	5.667067e-02
11388	PCDH18	1.284073e-01
11389	PCDH19	1
11390	PCDH20	1
11391	PCDH7	4.622101e-01
11392	PCDH8	1
11393	PCDH9	6.938002e-02
11394	PCDHA1	1
11395	PCDHA10	2.503403e-01
11396	PCDHA11	1
11397	PCDHA12	1
11398	PCDHA13	1
11399	PCDHA2	1
Done

Running MutSig 2:
Scatter job 126: processing genes 11310 - 11399
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PARP9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.890621e-02	ci left: 8.034910e-01	ci right 8.189273e-01	k: 8113	n:10000
Cons ci ratio: 2.740949e-02	ci left: 6.622964e-01	ci right 6.808035e-01	k: 6716	n:10000
KS ci ratio: 7.019825e-02	ci left: 2.292855e-01	ci right 2.460676e-01	k: 2376	n:10000
PARP9   10000 perm   2 sec   (5915 perm/sec)   p_kst 2.376000e-01   p_cons 6.716000e-01   p_joint 8.113000e-01

Outputting figure to mutsig2_images.part000000000126/PARP9.2_2658_10000_0.2376_0.6716_0.8113.png
                gene_name: PARP9
               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: 0.81 
     ci_joint_bounds_left: 0.80 
    ci_joint_bounds_right: 0.82 

Current progress: 33 percent done.
PCDH17
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.373378e-03	ci left: 9.854505e-01	ci right 9.898586e-01	k: 9878	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: 3.956422e-02	ci left: 4.854532e-01	ci right 5.051496e-01	k: 4953	n:10000
PCDH17   10000 perm   2 sec   (5544 perm/sec)   p_kst 4.953000e-01   p_cons 9.474000e-01   p_joint 9.878000e-01

Outputting figure to mutsig2_images.part000000000126/PCDH17.2_3496_10000_0.4953_0.9474_0.9878.png
                gene_name: PCDH17
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.95 
      ci_cons_bounds_left: 0.94 
     ci_cons_bounds_right: 0.95 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.99 
    ci_joint_bounds_right: 0.99 

Current progress: 67 percent done.
PCDH9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.590211e-03	ci left: 9.388977e-01	ci right 9.480418e-01	k: 9436	n:10000
Cons ci ratio: 2.459607e-02	ci left: 7.085635e-01	ci right 7.263097e-01	k: 7175	n:10000
KS ci ratio: 5.761920e-02	ci left: 3.071901e-01	ci right 3.255170e-01	k: 3163	n:10000
PCDH9   10000 perm   2 sec   (5470 perm/sec)   p_kst 3.163000e-01   p_cons 7.175000e-01   p_joint 9.436000e-01

Outputting figure to mutsig2_images.part000000000126/PCDH9.2_3730_10000_0.3163_0.7175_0.9436.png
                gene_name: PCDH9
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.73 
                  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.165.3896/
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/181708/iteration1/scatter.0000000126
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 126 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1701>
Subject: Job 1120148: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1701>, 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/181708/iteration1/scatter.0000000127> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:46:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000127.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000127.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 127  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    162.07 sec.
    Max Memory :      1504 MB
    Max Swap   :      3853 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.165.3896/
-whichjob
127
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 127: processing genes 11400 - 11490
Calculating significance of each gene.
Using projection method.
11400	PCDHA3	1
11401	PCDHA4	2.870798e-01
11402	PCDHA5	1
11403	PCDHA6	1
11404	PCDHA7	9.083406e-03
11405	PCDHA8	1
11406	PCDHA9	3.964030e-01
11407	PCDHAC1	1.324320e-04
11408	PCDHAC2	8.636371e-02
11409	PCDHB1	7.720345e-02
11410	PCDHB10	2.625721e-01
11411	PCDHB11	1
11412	PCDHB12	1
11413	PCDHB13	1
11414	PCDHB14	3.537166e-01
11415	PCDHB15	1
11416	PCDHB16	3.299291e-01
11417	PCDHB2	1
11418	PCDHB3	1
11419	PCDHB4	3.169011e-01
11420	PCDHB5	2.599504e-02
11421	PCDHB6	1.317383e-01
11422	PCDHB7	3.512832e-01
11423	PCDHB8	2.915816e-01
11424	PCDHB9	1
11425	PCDHGA1	1
11426	PCDHGA10	1.695499e-01
11427	PCDHGA11	1
11428	PCDHGA12	1
11429	PCDHGA2	1
11430	PCDHGA3	1
11431	PCDHGA4	8.024023e-02
11432	PCDHGA5	3.003393e-01
11433	PCDHGA6	1
11434	PCDHGA7	2.381815e-01
11435	PCDHGA8	1
11436	PCDHGA9	2.584492e-01
11437	PCDHGB1	1
11438	PCDHGB2	2.170231e-01
11439	PCDHGB3	2.857830e-01
11440	PCDHGB4	4.440852e-02
11441	PCDHGB5	1
11442	PCDHGB6	1
11443	PCDHGB7	1
11444	PCDHGC3	3.295714e-01
11445	PCDHGC4	1
11446	PCDHGC5	1.080869e-01
11447	PCDP1	2.565573e-01
11448	PCF11	1
11449	PCGF1	1
11450	PCGF2	1
11451	PCGF3	1
11452	PCGF5	1
11453	PCGF6	1
11454	PCID2	1
11455	PCIF1	1
11456	PCK1	1.317898e-01
11457	PCK2	1
11458	PCLO	6.290481e-01
11459	PCM1	1
11460	PCMT1	1
11461	PCMTD1	1
11462	PCMTD2	1
11463	PCNA	1
11464	PCNP	1
11465	PCNT	4.399190e-01
11466	PCNX	1
11467	PCNXL2	5.381135e-01
11468	PCNXL3	1
11469	PCOLCE	1
11470	PCOLCE2	1
11471	PCOTH	1
11472	PCP2	1
11473	PCP4	1
11474	PCP4L1	1
11475	PCSK1	1
11476	PCSK2	1.812562e-01
11477	PCSK4	1
11478	PCSK5	1
11479	PCSK6	1.605614e-01
11480	PCSK7	1
11481	PCSK9	1
11482	PCTP	1
11483	PCYOX1	1
11484	PCYOX1L	1
11485	PCYT1A	1
11486	PCYT1B	1
11487	PCYT2	1
11488	PDAP1	1
11489	PDC	1
11490	PDCD1	1
Done

Running MutSig 2:
Scatter job 127: processing genes 11400 - 11490
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PCDHAC1
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: 1.891855e-02	ci left: 8.032880e-01	ci right 8.187304e-01	k: 8111	n:10000
KS ci ratio: 2.167809e-02	ci left: 7.573729e-01	ci right 7.740721e-01	k: 7658	n:10000
PCDHAC1   10000 perm   2 sec   (4677 perm/sec)   p_kst 7.658000e-01   p_cons 8.111000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000127/PCDHAC1.4_2932_10000_0.7658_0.8111_1.png
                gene_name: PCDHAC1
               theta_stop: 0.022 
                    nperm: 10000 
                     p_ks: 0.77 
        ci_ks_bounds_left: 0.76 
       ci_ks_bounds_right: 0.77 
                   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: 14 percent done.
PCDHA7
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.046880e-02	ci left: 4.741611e-01	ci right 4.938483e-01	k: 4840	n:10000
Cons ci ratio: 1.610624e-02	ci left: 8.485573e-01	ci right 8.624349e-01	k: 8556	n:10000
KS ci ratio: 6.225664e-02	ci left: 2.749777e-01	ci right 2.927484e-01	k: 2838	n:10000
PCDHA7   10000 perm   2 sec   (5615 perm/sec)   p_kst 2.838000e-01   p_cons 8.556000e-01   p_joint 4.840000e-01

Outputting figure to mutsig2_images.part000000000127/PCDHA7.3_2843_10000_0.2838_0.8556_0.484.png
                gene_name: PCDHA7
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 29 percent done.
PCDHB5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.055197e-01	ci left: 3.148396e-02	ci right 3.879009e-02	k: 350	n:10000
Cons ci ratio: 6.890587e-02	ci left: 2.360028e-01	ci right 2.529463e-01	k: 2444	n:10000
KS ci ratio: 2.037220e-01	ci left: 3.205417e-02	ci right 3.941949e-02	k: 356	n:10000
PCDHB5   10000 perm   2 sec   (4030 perm/sec)   p_kst 3.560000e-02   p_cons 2.444000e-01   p_joint 3.500000e-02

Joint ci ratio: 1.164706e-01	ci left: 5.047003e-02	ci right 5.676054e-02	k: 1071	n:20000
Cons ci ratio: 4.957657e-02	ci left: 2.322105e-01	ci right 2.440657e-01	k: 4762	n:20000
KS ci ratio: 1.450070e-01	ci left: 3.268875e-02	ci right 3.784751e-02	k: 704	n:20000
PCDHB5   20000 perm   5 sec   (3858 perm/sec)   p_kst 3.520000e-02   p_cons 2.381000e-01   p_joint 5.355000e-02

Joint ci ratio: 1.022146e-01	ci left: 4.433973e-02	ci right 4.914854e-02	k: 1401	n:30000
Cons ci ratio: 4.058922e-02	ci left: 2.323294e-01	ci right 2.419882e-01	k: 7114	n:30000
KS ci ratio: 1.181383e-01	ci left: 3.330500e-02	ci right 3.751892e-02	k: 1061	n:30000
PCDHB5   30000 perm   7 sec   (4080 perm/sec)   p_kst 3.536667e-02   p_cons 2.371333e-01   p_joint 4.670000e-02

Joint ci ratio: 1.142265e-01	ci left: 2.696406e-02	ci right 3.025485e-02	k: 1143	n:40000
Cons ci ratio: 3.500304e-02	ci left: 2.345042e-01	ci right 2.428838e-01	k: 9547	n:40000
KS ci ratio: 1.021244e-01	ci left: 3.370793e-02	ci right 3.735990e-02	k: 1420	n:40000
PCDHB5   40000 perm   10 sec   (3847 perm/sec)   p_kst 3.550000e-02   p_cons 2.386750e-01   p_joint 2.857500e-02

Joint ci ratio: 7.419147e-02	ci left: 5.091475e-02	ci right 5.485736e-02	k: 2643	n:50000
Cons ci ratio: 3.142530e-02	ci left: 2.335963e-01	ci right 2.410743e-01	k: 11866	n:50000
KS ci ratio: 9.079460e-02	ci left: 3.430586e-02	ci right 3.758830e-02	k: 1796	n:50000
PCDHB5   50000 perm   13 sec   (3777 perm/sec)   p_kst 3.592000e-02   p_cons 2.373200e-01   p_joint 5.286000e-02

Outputting figure to mutsig2_images.part000000000127/PCDHB5.2_2392_50000_0.03592_0.23732_0.05286.png
                gene_name: PCDHB5
               theta_stop: 0.091 
                    nperm: 50000 
                     p_ks: 0.036 
        ci_ks_bounds_left: 0.034 
       ci_ks_bounds_right: 0.038 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.24 
                  p_joint: 0.053 
     ci_joint_bounds_left: 0.051 
    ci_joint_bounds_right: 0.055 

Current progress: 43 percent done.
PCDHGB4
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: 1.644352e-02	ci left: 8.432573e-01	ci right 8.573380e-01	k: 8504	n:10000
KS ci ratio: 6.106854e-02	ci left: 2.828028e-01	ci right 3.007187e-01	k: 2917	n:10000
PCDHGB4   10000 perm   3 sec   (3993 perm/sec)   p_kst 2.917000e-01   p_cons 8.504000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000127/PCDHGB4.2_2801_10000_0.2917_0.8504_1.png
                gene_name: PCDHGB4
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.85 
      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: 57 percent done.
PCDHGC5
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: 8.639973e-02	ci left: 1.632741e-01	ci right 1.781182e-01	k: 1706	n:10000
KS ci ratio: 1.157396e-01	ci left: 9.691393e-02	ci right 1.089185e-01	k: 1028	n:10000
PCDHGC5   10000 perm   2 sec   (5329 perm/sec)   p_kst 1.028000e-01   p_cons 1.706000e-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: 6.144226e-02	ci left: 1.638791e-01	ci right 1.743173e-01	k: 3381	n:20000
KS ci ratio: 8.260454e-02	ci left: 9.700431e-02	ci right 1.054120e-01	k: 2023	n:20000
PCDHGC5   20000 perm   4 sec   (4586 perm/sec)   p_kst 1.011500e-01   p_cons 1.690500e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000127/PCDHGC5.2_3026_20000_0.10115_0.16905_1.png
                gene_name: PCDHGC5
               theta_stop: 0.083 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.097 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 71 percent done.
PCLO
Processing conservation and coverage...
64% 
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: 2.240852e-02	ci left: 7.451322e-01	ci right 7.621198e-01	k: 7537	n:10000
KS ci ratio: 3.910019e-02	ci left: 4.913511e-01	ci right 5.110482e-01	k: 5012	n:10000
PCLO   10000 perm   3 sec   (2916 perm/sec)   p_kst 5.012000e-01   p_cons 7.537000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000127/PCLO.2_15546_10000_0.5012_0.7537_1.png
                gene_name: PCLO
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.75 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.76 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 86 percent done.
PCNT
Processing conservation and coverage...
98% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.852276e-02	ci left: 6.443816e-01	ci right 6.631288e-01	k: 6538	n:10000
Cons ci ratio: 7.472467e-02	ci left: 2.076722e-01	ci right 2.238937e-01	k: 2157	n:10000
KS ci ratio: 1.650160e-02	ci left: 8.423403e-01	ci right 8.564555e-01	k: 8495	n:10000
PCNT   10000 perm   3 sec   (3708 perm/sec)   p_kst 8.495000e-01   p_cons 2.157000e-01   p_joint 6.538000e-01

Outputting figure to mutsig2_images.part000000000127/PCNT.2_10199_10000_0.8495_0.2157_0.6538.png
                gene_name: PCNT
               theta_stop: 0.075 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.86 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.22 
                  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.165.3896/
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/181708/iteration1/scatter.0000000127
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 127 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1714>
Subject: Job 1120151: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1714>, 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/181708/iteration1/scatter.0000000128> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:46:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000128.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000128.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 128  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    152.96 sec.
    Max Memory :      1353 MB
    Max Swap   :      3838 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.165.3896/
-whichjob
128
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 128: processing genes 11491 - 11580
Calculating significance of each gene.
Using projection method.
11491	PDCD10	1.141085e-01
11492	PDCD11	4.581539e-01
11493	PDCD1LG2	1
11494	PDCD2	1
11495	PDCD2L	5.140929e-02
11496	PDCD4	1
11497	PDCD5	1
11498	PDCD6	1
11499	PDCD6IP	1
11500	PDCD7	1
11501	PDCL	1
11502	PDCL2	1
11503	PDCL3	1
11504	PDDC1	1
11505	PDE10A	1
11506	PDE11A	1
11507	PDE12	2.347784e-01
11508	PDE1A	4.243939e-02
11509	PDE1B	1
11510	PDE1C	7.242838e-03
11511	PDE2A	1
11512	PDE3A	1
11513	PDE3B	1
11514	PDE4A	1.787557e-01
11515	PDE4B	1
11516	PDE4C	3.073752e-02
11517	PDE4D	1
11518	PDE4DIP	2.858048e-01
11519	PDE5A	2.529095e-01
11520	PDE6A	1
11521	PDE6B	2.719865e-01
11522	PDE6C	1
11523	PDE6D	1
11524	PDE6G	1.274812e-02
11525	PDE6H	1
11526	PDE7A	1.921374e-01
11527	PDE7B	1.951515e-01
11528	PDE8A	1
11529	PDE8B	1
11530	PDE9A	1.411100e-01
11531	PDGFA	1
11532	PDGFB	1
11533	PDGFC	1
11534	PDGFD	1
11535	PDGFRA	2.333697e-01
11536	PDGFRB	2.467446e-01
11537	PDGFRL	1
11538	PDHA1	1
11539	PDHA2	1
11540	PDHB	1
11541	PDHX	1
11542	PDIA2	1
11543	PDIA3	1
11544	PDIA4	1
11545	PDIA5	6.015832e-03
11546	PDIA6	1
11547	PDIK1L	1
11548	PDILT	1
11549	PDK1	1
11550	PDK2	1.264625e-01
11551	PDK3	1
11552	PDK4	1
11553	PDLIM1	1
11554	PDLIM2	1
11555	PDLIM3	1.219692e-02
11556	PDLIM4	1
11557	PDLIM5	1
11558	PDLIM7	1.399668e-01
11559	PDP1	1
11560	PDP2	1
11561	PDPK1	1
11562	PDPN	1
11563	PDPR	1
11564	PDRG1	1
11565	PDS5A	2.644817e-01
11566	PDS5B	1
11567	PDSS1	1
11568	PDSS2	1
11569	PDX1	1
11570	PDXDC1	7.523984e-02
11571	PDXK	2.932389e-02
11572	PDXP	1
11573	PDYN	7.395371e-02
11574	PDZD11	1
11575	PDZD2	6.098338e-01
11576	PDZD3	1
11577	PDZD4	1
11578	PDZD7	1.785709e-01
11579	PDZD8	1
11580	PDZD9	1
Done

Running MutSig 2:
Scatter job 128: processing genes 11491 - 11580
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PDE1A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.472561e-02	ci left: 3.297201e-01	ci right 3.483737e-01	k: 3390	n:10000
Cons ci ratio: 9.846546e-02	ci left: 1.300234e-01	ci right 1.435889e-01	k: 1367	n:10000
KS ci ratio: 1.371664e-01	ci left: 7.029921e-02	ci right 8.074967e-02	k: 754	n:10000
PDE1A   10000 perm   2 sec   (4826 perm/sec)   p_kst 7.540000e-02   p_cons 1.367000e-01   p_joint 3.390000e-01

Joint ci ratio: 1.885489e-02	ci left: 6.771535e-01	ci right 6.900931e-01	k: 13673	n:20000
Cons ci ratio: 6.902878e-02	ci left: 1.340362e-01	ci right 1.436691e-01	k: 2776	n:20000
KS ci ratio: 9.855520e-02	ci left: 6.967630e-02	ci right 7.694833e-02	k: 1465	n:20000
PDE1A   20000 perm   7 sec   (2920 perm/sec)   p_kst 7.325000e-02   p_cons 1.388000e-01   p_joint 6.836500e-01

Outputting figure to mutsig2_images.part000000000128/PDE1A.2_1742_20000_0.07325_0.1388_0.68365.png
                gene_name: PDE1A
               theta_stop: 0.099 
                    nperm: 20000 
                     p_ks: 0.073 
        ci_ks_bounds_left: 0.070 
       ci_ks_bounds_right: 0.077 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.68 
     ci_joint_bounds_left: 0.68 
    ci_joint_bounds_right: 0.69 

Current progress: 17 percent done.
PDE1C
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: 3.846421e-02	ci left: 4.995504e-01	ci right 5.192441e-01	k: 5094	n:10000
KS ci ratio: 2.113385e-02	ci left: 7.664836e-01	ci right 7.829561e-01	k: 7748	n:10000
PDE1C   10000 perm   2 sec   (5542 perm/sec)   p_kst 7.748000e-01   p_cons 5.094000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000128/PDE1C.2_1973_10000_0.7748_0.5094_1.png
                gene_name: PDE1C
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.77 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.78 
                   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: 33 percent done.
PDE4C
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: 7.044556e-03	ci left: 9.652030e-01	ci right 9.721204e-01	k: 9688	n:10000
KS ci ratio: 2.670404e-02	ci left: 6.737778e-01	ci right 6.921155e-01	k: 6830	n:10000
PDE4C   10000 perm   2 sec   (4937 perm/sec)   p_kst 6.830000e-01   p_cons 9.688000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000128/PDE4C.2_2349_10000_0.683_0.9688_1.png
                gene_name: PDE4C
               theta_stop: 0.027 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.97 
      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: 50 percent done.
PDE4DIP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.099457e-02	ci left: 7.688127e-01	ci right 7.852256e-01	k: 7771	n:10000
Cons ci ratio: 2.277655e-02	ci left: 7.389648e-01	ci right 7.560908e-01	k: 7476	n:10000
KS ci ratio: 1.876749e-01	ci left: 3.786599e-02	ci right 4.580373e-02	k: 417	n:10000
PDE4DIP   10000 perm   3 sec   (3851 perm/sec)   p_kst 4.170000e-02   p_cons 7.476000e-01   p_joint 7.771000e-01

Joint ci ratio: 3.081223e-02	ci left: 4.403422e-01	ci right 4.541731e-01	k: 8945	n:20000
Cons ci ratio: 1.612481e-02	ci left: 7.410656e-01	ci right 7.531625e-01	k: 14943	n:20000
KS ci ratio: 1.343958e-01	ci left: 3.805187e-02	ci right 4.358264e-02	k: 815	n:20000
PDE4DIP   20000 perm   6 sec   (3431 perm/sec)   p_kst 4.075000e-02   p_cons 7.471500e-01   p_joint 4.472500e-01

Joint ci ratio: 2.603268e-02	ci left: 4.248207e-01	ci right 4.360594e-01	k: 12913	n:30000
Cons ci ratio: 1.326171e-02	ci left: 7.394239e-01	ci right 7.493288e-01	k: 22332	n:30000
KS ci ratio: 1.087654e-01	ci left: 3.923849e-02	ci right 4.378417e-02	k: 1244	n:30000
PDE4DIP   30000 perm   10 sec   (3059 perm/sec)   p_kst 4.146667e-02   p_cons 7.444000e-01   p_joint 4.304333e-01

Joint ci ratio: 2.848652e-02	ci left: 3.166994e-01	ci right 3.258765e-01	k: 12851	n:40000
Cons ci ratio: 1.153329e-02	ci left: 7.384866e-01	ci right 7.470782e-01	k: 29712	n:40000
KS ci ratio: 9.440182e-02	ci left: 3.937086e-02	ci right 4.329608e-02	k: 1652	n:40000
PDE4DIP   40000 perm   15 sec   (2628 perm/sec)   p_kst 4.130000e-02   p_cons 7.428000e-01   p_joint 3.212750e-01

Outputting figure to mutsig2_images.part000000000128/PDE4DIP.2_8813_40000_0.0413_0.7428_0.32127.png
                gene_name: PDE4DIP
               theta_stop: 0.094 
                    nperm: 40000 
                     p_ks: 0.041 
        ci_ks_bounds_left: 0.039 
       ci_ks_bounds_right: 0.043 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.74 
     ci_cons_bounds_right: 0.75 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.33 

Current progress: 67 percent done.
PDIA5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.549987e-03	ci left: 9.843657e-01	ci right 9.889443e-01	k: 9868	n:10000
Cons ci ratio: 5.849639e-02	ci left: 3.007434e-01	ci right 3.189675e-01	k: 3098	n:10000
KS ci ratio: 1.991862e-02	ci left: 7.867494e-01	ci right 8.026785e-01	k: 7948	n:10000
PDIA5   10000 perm   3 sec   (3578 perm/sec)   p_kst 7.948000e-01   p_cons 3.098000e-01   p_joint 9.868000e-01

Outputting figure to mutsig2_images.part000000000128/PDIA5.2_1628_10000_0.7948_0.3098_0.9868.png
                gene_name: PDIA5
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.79 
       ci_ks_bounds_right: 0.80 
                   p_cons: 0.31 
      ci_cons_bounds_left: 0.30 
     ci_cons_bounds_right: 0.32 
                  p_joint: 0.99 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.99 

Current progress: 83 percent done.
PDLIM3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.757356e-02	ci left: 3.946604e-01	ci right 4.139954e-01	k: 4043	n:10000
Cons ci ratio: 5.350728e-03	ci left: 9.789852e-01	ci right 9.843289e-01	k: 9818	n:10000
KS ci ratio: 5.784639e-02	ci left: 3.055038e-01	ci right 3.238042e-01	k: 3146	n:10000
PDLIM3   10000 perm   2 sec   (6501 perm/sec)   p_kst 3.146000e-01   p_cons 9.818000e-01   p_joint 4.043000e-01

Outputting figure to mutsig2_images.part000000000128/PDLIM3.2_1319_10000_0.3146_0.9818_0.4043.png
                gene_name: PDLIM3
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.98 
                  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.165.3896/
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/181708/iteration1/scatter.0000000128
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 128 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1702>
Subject: Job 1120154: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1702>, 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/181708/iteration1/scatter.0000000129> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:46:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000129.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000129.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 129  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    115.81 sec.
    Max Memory :      1067 MB
    Max Swap   :      3869 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.165.3896/
-whichjob
129
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 129: processing genes 11581 - 11671
Calculating significance of each gene.
Using projection method.
11581	PDZK1	1
11582	PDZK1IP1	1
11583	PDZRN3	5.192193e-02
11584	PDZRN4	1
11585	PEA15	1
11586	PEAR1	1
11587	PEBP1	1
11588	PEBP4	1
11589	PECAM1	1
11590	PECI	1
11591	PECR	1
11592	PEF1	1
11593	PEG10	1
11594	PEG3	1
11595	PELI1	1.817464e-01
11596	PELI2	1
11597	PELI3	1
11598	PELO	1
11599	PELP1	1
11600	PEMT	1
11601	PENK	1
11602	PEPD	1
11603	PER1	2.089187e-01
11604	PER2	1
11605	PER3	1
11606	PERP	1
11607	PES1	1
11608	PET112L	1
11609	PEX1	1.477136e-01
11610	PEX10	1
11611	PEX11A	1
11612	PEX11B	1
11613	PEX11G	1
11614	PEX12	1
11615	PEX13	1
11616	PEX14	1
11617	PEX16	1
11618	PEX19	1
11619	PEX2	1
11620	PEX26	1
11621	PEX3	1
11622	PEX5	1
11623	PEX5L	2.558272e-01
11624	PEX6	1
11625	PEX7	1
11626	PF4	1
11627	PF4V1	1
11628	PFAS	1
11629	PFDN1	1
11630	PFDN2	1
11631	PFDN4	1
11632	PFDN5	1
11633	PFDN6	1
11634	PFKFB1	1
11635	PFKFB2	1
11636	PFKFB3	1
11637	PFKFB4	1
11638	PFKL	1
11639	PFKM	1
11640	PFKP	1
11641	PFN1	1
11642	PFN2	1
11643	PFN3	1
11644	PFN4	1
11645	PGA3	1
11646	PGA5	1
11647	PGAM1	1
11648	PGAM2	1
11649	PGAM4	1
11650	PGAM5	1
11651	PGAP1	3.545208e-01
11652	PGAP2	1.139314e-01
11653	PGAP3	1
11654	PGBD1	1
11655	PGBD2	1
11656	PGBD3	1
11657	PGBD4	1
11658	PGBD5	1
11659	PGC	1
11660	PGCP	1
11661	PGD	1
11662	PGF	1
11663	PGGT1B	1
11664	PGK1	1
11665	PGK2	1
11666	PGLS	1
11667	PGLYRP1	1
11668	PGLYRP2	1
11669	PGLYRP3	1
11670	PGLYRP4	1
11671	PGM1	1
Done

Running MutSig 2:
Scatter job 129: processing genes 11581 - 11671
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PDZRN3
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: 2.134564e-02	ci left: 7.629399e-01	ci right 7.795018e-01	k: 7713	n:10000
KS ci ratio: 3.964342e-02	ci left: 4.844537e-01	ci right 5.041496e-01	k: 4943	n:10000
PDZRN3   10000 perm   3 sec   (3080 perm/sec)   p_kst 4.943000e-01   p_cons 7.713000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000129/PDZRN3.2_3241_10000_0.4943_0.7713_1.png
                gene_name: PDZRN3
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.77 
      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: 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.165.3896/
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/181708/iteration1/scatter.0000000129
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 129 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1653>
Subject: Job 1120157: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1653>, 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/181708/iteration1/scatter.0000000130> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:46:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000130.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000130.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 130  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    114.59 sec.
    Max Memory :      1068 MB
    Max Swap   :      3824 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.165.3896/
-whichjob
130
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 130: processing genes 11672 - 11761
Calculating significance of each gene.
Using projection method.
11672	PGM2	1
11673	PGM2L1	1
11674	PGM3	1
11675	PGM5	1
11676	PGP	1
11677	PGPEP1	1
11678	PGPEP1L	1
11679	PGR	1
11680	PGRMC1	1
11681	PGRMC2	1
11682	PGS1	1
11683	PHACTR1	1
11684	PHACTR2	1
11685	PHACTR3	1
11686	PHACTR4	2.467758e-01
11687	PHAX	1
11688	PHB	1
11689	PHB2	1
11690	PHC1	1
11691	PHC2	1
11692	PHC3	1
11693	PHEX	1
11694	PHF1	1
11695	PHF10	1
11696	PHF11	1
11697	PHF12	2.346824e-01
11698	PHF13	1
11699	PHF14	1
11700	PHF15	1
11701	PHF16	1
11702	PHF17	1
11703	PHF19	1
11704	PHF2	1
11705	PHF20	3.907171e-01
11706	PHF20L1	1
11707	PHF21A	1
11708	PHF21B	1
11709	PHF23	1
11710	PHF3	1
11711	PHF5A	1
11712	PHF6	4.634591e-02
11713	PHF7	1
11714	PHF8	1
11715	PHGDH	1
11716	PHIP	4.245103e-02
11717	PHKA1	2.690229e-01
11718	PHKA2	1
11719	PHKB	1
11720	PHKG1	1
11721	PHKG2	1
11722	PHLDA1	1
11723	PHLDA2	1
11724	PHLDA3	1
11725	PHLDB1	1
11726	PHLDB2	1
11727	PHLDB3	1
11728	PHLPP1	1.436704e-01
11729	PHLPP2	1
11730	PHOSPHO1	1
11731	PHOSPHO2	1
11732	PHOX2B	8.948002e-02
11733	PHPT1	1
11734	PHRF1	3.422939e-01
11735	PHTF1	1
11736	PHTF2	1
11737	PHYH	1
11738	PHYHD1	1
11739	PHYHIP	1
11740	PHYHIPL	9.082790e-02
11741	PI15	1
11742	PI16	2.163567e-01
11743	PI3	1
11744	PI4K2A	1
11745	PI4K2B	1
11746	PI4KA	1
11747	PI4KB	1
11748	PIAS1	1
11749	PIAS2	1
11750	PIAS3	1
11751	PIAS4	1
11752	PIBF1	2.721206e-01
11753	PICALM	1
11754	PICK1	1
11755	PID1	1
11756	PIF1	1
11757	PIGA	1
11758	PIGB	1
11759	PIGC	1
11760	PIGF	1
11761	PIGG	1
Done

Running MutSig 2:
Scatter job 130: processing genes 11672 - 11761
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PHIP
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: 2.997394e-02	ci left: 6.214554e-01	ci right 6.404682e-01	k: 6310	n:10000
KS ci ratio: 2.032688e-02	ci left: 7.799572e-01	ci right 7.960747e-01	k: 7881	n:10000
PHIP   10000 perm   2 sec   (4407 perm/sec)   p_kst 7.881000e-01   p_cons 6.310000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000130/PHIP.3_5626_10000_0.7881_0.631_1.png
                gene_name: PHIP
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.80 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000130
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 130 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1706>
Subject: Job 1120160: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1706>, 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/181708/iteration1/scatter.0000000131> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:47:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000131.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000131.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 131  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    194.64 sec.
    Max Memory :      1444 MB
    Max Swap   :      3904 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.165.3896/
-whichjob
131
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 131: processing genes 11762 - 11852
Calculating significance of each gene.
Using projection method.
11762	PIGH	1
11763	PIGK	1
11764	PIGL	1
11765	PIGM	1
11766	PIGN	1
11767	PIGO	1
11768	PIGP	1
11769	PIGQ	1
11770	PIGR	1.878461e-01
11771	PIGS	1
11772	PIGT	1
11773	PIGU	1
11774	PIGV	1
11775	PIGW	1
11776	PIGX	1
11777	PIGY	1
11778	PIGZ	1.049554e-01
11779	PIH1D1	7.687762e-02
11780	PIH1D2	1
11781	PIK3AP1	1
11782	PIK3C2A	4.498633e-01
11783	PIK3C2B	1
11784	PIK3C2G	1
11785	PIK3C3	1.648866e-01
11786	PIK3CA	5.444356e-03
11787	PIK3CB	2.487222e-01
11788	PIK3CD	1
11789	PIK3CG	1
11790	PIK3IP1	1
11791	PIK3R1	1.791314e-01
11792	PIK3R2	1
11793	PIK3R3	1
11794	PIK3R4	5.180836e-01
11795	PIK3R5	1
11796	PIK3R6	1
11797	PIKFYVE	6.380117e-01
11798	PILRA	1.062398e-01
11799	PILRB	1
11800	PIM1	1
11801	PIM2	1
11802	PIM3	1
11803	PIN1	1
11804	PIN4	1
11805	PINK1	1
11806	PINX1	1
11807	PION	1
11808	PIP	1
11809	PIP4K2A	1
11810	PIP4K2B	1
11811	PIP4K2C	4.022770e-02
11812	PIP5K1A	1
11813	PIP5K1B	1
11814	PIP5K1C	1
11815	PIP5KL1	1
11816	PIPOX	1
11817	PIR	1
11818	PIRT	1
11819	PISD	1
11820	PITPNA	1
11821	PITPNB	1
11822	PITPNC1	1
11823	PITPNM1	1
11824	PITPNM2	1
11825	PITPNM3	1
11826	PITRM1	3.427514e-01
11827	PITX1	1
11828	PITX2	1
11829	PITX3	1
11830	PIWIL1	1
11831	PIWIL2	1
11832	PIWIL3	1
11833	PIWIL4	4.269850e-02
11834	PJA1	1
11835	PJA2	1
11836	PKD1	2.499649e-01
11837	PKD1L1	1
11838	PKD1L2	1.694733e-01
11839	PKD2	1
11840	PKD2L1	1
11841	PKD2L2	1
11842	PKDCC	1
11843	PKDREJ	1
11844	PKHD1	1
11845	PKHD1L1	5.588237e-02
11846	PKIA	1
11847	PKIB	1
11848	PKIG	1
11849	PKLR	2.777860e-01
11850	PKM2	1
11851	PKMYT1	1
11852	PKN1	1
Done

Running MutSig 2:
Scatter job 131: processing genes 11762 - 11852
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PIK3CB
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.537862e-01	ci left: 2.033901e-02	ci right 2.634310e-02	k: 232	n:10000
Cons ci ratio: 1.068598e-01	ci left: 1.122272e-01	ci right 1.249959e-01	k: 1185	n:10000
KS ci ratio: 1.296954e-01	ci left: 7.824692e-02	ci right 8.919702e-02	k: 836	n:10000
PIK3CB   10000 perm   2 sec   (4693 perm/sec)   p_kst 8.360000e-02   p_cons 1.185000e-01   p_joint 2.320000e-02

Joint ci ratio: 1.513527e-01	ci left: 2.998929e-02	ci right 3.494786e-02	k: 648	n:20000
Cons ci ratio: 7.540047e-02	ci left: 1.145432e-01	ci right 1.235679e-01	k: 2380	n:20000
KS ci ratio: 9.195033e-02	ci left: 7.945708e-02	ci right 8.716457e-02	k: 1665	n:20000
PIK3CB   20000 perm   7 sec   (3058 perm/sec)   p_kst 8.325000e-02   p_cons 1.190000e-01   p_joint 3.240000e-02

Joint ci ratio: 9.885800e-02	ci left: 4.733292e-02	ci right 5.228806e-02	k: 1493	n:30000
Cons ci ratio: 6.150109e-02	ci left: 1.155866e-01	ci right 1.229540e-01	k: 3577	n:30000
KS ci ratio: 7.519258e-02	ci left: 7.993474e-02	ci right 8.621295e-02	k: 2491	n:30000
PIK3CB   30000 perm   9 sec   (3347 perm/sec)   p_kst 8.303333e-02   p_cons 1.192333e-01   p_joint 4.976667e-02

Outputting figure to mutsig2_images.part000000000131/PIK3CB.4_3299_30000_0.083033_0.11923_0.049767.png
                gene_name: PIK3CB
               theta_stop: 0.099 
                    nperm: 30000 
                     p_ks: 0.083 
        ci_ks_bounds_left: 0.080 
       ci_ks_bounds_right: 0.086 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.050 
     ci_joint_bounds_left: 0.047 
    ci_joint_bounds_right: 0.052 

Current progress: 14 percent done.
PKHD1L1
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: 1.508193e-02	ci left: 8.643742e-01	ci right 8.776089e-01	k: 8711	n:10000
KS ci ratio: 2.062465e-02	ci left: 7.749918e-01	ci right 7.912430e-01	k: 7832	n:10000
PKHD1L1   10000 perm   3 sec   (3220 perm/sec)   p_kst 7.832000e-01   p_cons 8.711000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000131/PKHD1L1.4_13044_10000_0.7832_0.8711_1.png
                gene_name: PKHD1L1
               theta_stop: 0.021 
                    nperm: 10000 
                     p_ks: 0.78 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.79 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.88 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 29 percent done.
PIK3CA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.733613e-02	ci left: 1.964346e-01	ci right 2.123380e-01	k: 2043	n:10000
Cons ci ratio: 1.912852e-01	ci left: 3.643453e-02	ci right 4.423614e-02	k: 402	n:10000
KS ci ratio: 3.795959e-02	ci left: 5.061517e-01	ci right 5.258389e-01	k: 5160	n:10000
PIK3CA   10000 perm   2 sec   (5436 perm/sec)   p_kst 5.160000e-01   p_cons 4.020000e-02   p_joint 2.043000e-01

Joint ci ratio: 8.471597e-02	ci left: 9.258877e-02	ci right 1.008289e-01	k: 1933	n:20000
Cons ci ratio: 1.393670e-01	ci left: 3.539255e-02	ci right 4.074282e-02	k: 760	n:20000
KS ci ratio: 2.712693e-02	ci left: 5.037959e-01	ci right 5.177009e-01	k: 10215	n:20000
PIK3CA   20000 perm   4 sec   (4896 perm/sec)   p_kst 5.107500e-01   p_cons 3.800000e-02   p_joint 9.665000e-02

Joint ci ratio: 4.026657e-02	ci left: 2.352090e-01	ci right 2.449081e-01	k: 7201	n:30000
Cons ci ratio: 1.109208e-01	ci left: 3.774564e-02	ci right 4.221067e-02	k: 1198	n:30000
KS ci ratio: 2.224803e-02	ci left: 5.028590e-01	ci right 5.142060e-01	k: 15256	n:30000
PIK3CA   30000 perm   6 sec   (4679 perm/sec)   p_kst 5.085333e-01   p_cons 3.993333e-02   p_joint 2.400333e-01

Joint ci ratio: 3.475445e-02	ci left: 2.370885e-01	ci right 2.454991e-01	k: 9651	n:40000
Cons ci ratio: 9.561499e-02	ci left: 3.839368e-02	ci right 4.227341e-02	k: 1612	n:40000
KS ci ratio: 1.921979e-02	ci left: 5.048630e-01	ci right 5.146856e-01	k: 20391	n:40000
PIK3CA   40000 perm   9 sec   (4509 perm/sec)   p_kst 5.097750e-01   p_cons 4.030000e-02   p_joint 2.412750e-01

Outputting figure to mutsig2_images.part000000000131/PIK3CA.3_3287_40000_0.50977_0.0403_0.24127.png
                gene_name: PIK3CA
               theta_stop: 0.096 
                    nperm: 40000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.040 
      ci_cons_bounds_left: 0.038 
     ci_cons_bounds_right: 0.042 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.25 

Current progress: 43 percent done.
PITRM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.618281e-01	ci left: 9.503508e-03	ci right 1.378807e-02	k: 115	n:10000
Cons ci ratio: 2.375804e-01	ci left: 2.334629e-02	ci right 2.973355e-02	k: 264	n:10000
KS ci ratio: 3.325900e-01	ci left: 1.142242e-02	ci right 1.606722e-02	k: 136	n:10000
PITRM1   10000 perm   2 sec   (5796 perm/sec)   p_kst 1.360000e-02   p_cons 2.640000e-02   p_joint 1.150000e-02

Joint ci ratio: 3.106165e-01	ci left: 6.673885e-03	ci right 9.172365e-03	k: 157	n:20000
Cons ci ratio: 1.716948e-01	ci left: 2.321577e-02	ci right 2.762368e-02	k: 507	n:20000
KS ci ratio: 2.289106e-01	ci left: 1.279482e-02	ci right 1.614852e-02	k: 288	n:20000
PITRM1   20000 perm   4 sec   (5168 perm/sec)   p_kst 1.440000e-02   p_cons 2.535000e-02   p_joint 7.850000e-03

Joint ci ratio: 3.417378e-01	ci left: 3.621720e-03	ci right 5.143390e-03	k: 130	n:30000
Cons ci ratio: 1.408546e-01	ci left: 2.339150e-02	ci right 2.696793e-02	k: 754	n:30000
KS ci ratio: 1.934640e-01	ci left: 1.219299e-02	ci right 1.483580e-02	k: 404	n:30000
PITRM1   30000 perm   6 sec   (4943 perm/sec)   p_kst 1.346667e-02   p_cons 2.513333e-02   p_joint 4.333333e-03

Joint ci ratio: 3.017950e-01	ci left: 3.566836e-03	ci right 4.856777e-03	k: 167	n:40000
Cons ci ratio: 1.214080e-01	ci left: 2.385590e-02	ci right 2.696352e-02	k: 1015	n:40000
KS ci ratio: 1.738547e-01	ci left: 1.145814e-02	ci right 1.366347e-02	k: 501	n:40000
PITRM1   40000 perm   8 sec   (4814 perm/sec)   p_kst 1.252500e-02   p_cons 2.537500e-02   p_joint 4.175000e-03

Joint ci ratio: 1.286137e-01	ci left: 1.706572e-02	ci right 1.943069e-02	k: 911	n:50000
Cons ci ratio: 8.077810e-02	ci left: 4.316016e-02	ci right 4.681290e-02	k: 2248	n:50000
KS ci ratio: 1.544449e-01	ci left: 1.173687e-02	ci right 1.372030e-02	k: 635	n:50000
PITRM1   50000 perm   11 sec   (4706 perm/sec)   p_kst 1.270000e-02   p_cons 4.496000e-02   p_joint 1.822000e-02

Joint ci ratio: 1.179801e-01	ci left: 1.699977e-02	ci right 1.914721e-02	k: 1083	n:60000
Cons ci ratio: 7.405381e-02	ci left: 4.296202e-02	ci right 4.628221e-02	k: 2676	n:60000
KS ci ratio: 1.415720e-01	ci left: 1.172281e-02	ci right 1.352479e-02	k: 756	n:60000
PITRM1   60000 perm   13 sec   (4565 perm/sec)   p_kst 1.260000e-02   p_cons 4.460000e-02   p_joint 1.805000e-02

Joint ci ratio: 1.134918e-01	ci left: 1.580530e-02	ci right 1.772078e-02	k: 1172	n:70000
Cons ci ratio: 6.839076e-02	ci left: 4.329336e-02	ci right 4.637309e-02	k: 3137	n:70000
KS ci ratio: 1.312335e-01	ci left: 1.175918e-02	ci right 1.342445e-02	k: 880	n:70000
PITRM1   70000 perm   16 sec   (4405 perm/sec)   p_kst 1.257143e-02   p_cons 4.481429e-02   p_joint 1.674286e-02

Joint ci ratio: 1.061850e-01	ci left: 1.585985e-02	ci right 1.765045e-02	k: 1339	n:80000
Cons ci ratio: 6.389253e-02	ci left: 4.349990e-02	ci right 4.638322e-02	k: 3594	n:80000
KS ci ratio: 1.225028e-01	ci left: 1.186279e-02	ci right 1.342286e-02	k: 1010	n:80000
PITRM1   80000 perm   19 sec   (4262 perm/sec)   p_kst 1.262500e-02   p_cons 4.492500e-02   p_joint 1.673750e-02

Joint ci ratio: 8.088475e-02	ci left: 2.440363e-02	ci right 2.647155e-02	k: 2288	n:90000
Cons ci ratio: 6.044515e-02	ci left: 4.329338e-02	ci right 4.600273e-02	k: 4017	n:90000
KS ci ratio: 1.149036e-01	ci left: 1.203259e-02	ci right 1.351017e-02	k: 1148	n:90000
PITRM1   90000 perm   21 sec   (4191 perm/sec)   p_kst 1.275556e-02   p_cons 4.463333e-02   p_joint 2.542222e-02

Joint ci ratio: 7.678570e-02	ci left: 2.442381e-02	ci right 2.638385e-02	k: 2539	n:100000
Cons ci ratio: 5.720562e-02	ci left: 4.356554e-02	ci right 4.614095e-02	k: 4484	n:100000
KS ci ratio: 1.090793e-01	ci left: 1.205406e-02	ci right 1.345442e-02	k: 1274	n:100000
PITRM1   100000 perm   24 sec   (4129 perm/sec)   p_kst 1.274000e-02   p_cons 4.484000e-02   p_joint 2.539000e-02

Joint ci ratio: 7.307825e-02	ci left: 2.455856e-02	ci right 2.643021e-02	k: 2803	n:110000
Cons ci ratio: 5.457529e-02	ci left: 4.357603e-02	ci right 4.602986e-02	k: 4927	n:110000
KS ci ratio: 1.039093e-01	ci left: 1.210860e-02	ci right 1.344454e-02	k: 1404	n:110000
PITRM1   110000 perm   27 sec   (4065 perm/sec)   p_kst 1.276364e-02   p_cons 4.479091e-02   p_joint 2.548182e-02

Joint ci ratio: 6.787723e-02	ci left: 2.612300e-02	ci right 2.796661e-02	k: 3244	n:120000
Cons ci ratio: 5.225697e-02	ci left: 4.361996e-02	ci right 4.596877e-02	k: 5374	n:120000
KS ci ratio: 9.967445e-02	ci left: 1.209033e-02	ci right 1.336671e-02	k: 1526	n:120000
PITRM1   120000 perm   30 sec   (4004 perm/sec)   p_kst 1.271667e-02   p_cons 4.478333e-02   p_joint 2.703333e-02

Outputting figure to mutsig2_images.part000000000131/PITRM1.2_3222_120000_0.012717_0.044783_0.027033.png
                gene_name: PITRM1
               theta_stop: 0.100 
                    nperm: 120000 
                     p_ks: 0.013 
        ci_ks_bounds_left: 0.012 
       ci_ks_bounds_right: 0.013 
                   p_cons: 0.045 
      ci_cons_bounds_left: 0.044 
     ci_cons_bounds_right: 0.046 
                  p_joint: 0.027 
     ci_joint_bounds_left: 0.026 
    ci_joint_bounds_right: 0.028 

Current progress: 57 percent done.
PIWIL4
Processing conservation and coverage...
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: 1.063013e-01	ci left: 1.133015e-01	ci right 1.261210e-01	k: 1196	n:10000
KS ci ratio: 1.028651e-01	ci left: 1.202398e-01	ci right 1.333784e-01	k: 1267	n:10000
PIWIL4   10000 perm   2 sec   (6020 perm/sec)   p_kst 1.267000e-01   p_cons 1.196000e-01   p_joint 8.480000e-02

Joint ci ratio: 5.456815e-02	ci left: 1.994728e-01	ci right 2.107131e-01	k: 4101	n:20000
Cons ci ratio: 7.460246e-02	ci left: 1.167565e-01	ci right 1.258540e-01	k: 2425	n:20000
KS ci ratio: 7.200805e-02	ci left: 1.243836e-01	ci right 1.337245e-01	k: 2580	n:20000
PIWIL4   20000 perm   4 sec   (5390 perm/sec)   p_kst 1.290000e-01   p_cons 1.212500e-01   p_joint 2.050500e-01

Outputting figure to mutsig2_images.part000000000131/PIWIL4.2_2639_20000_0.129_0.12125_0.20505.png
                gene_name: PIWIL4
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.21 

Current progress: 71 percent done.
PKD1
Processing conservation and coverage...
76% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.858751e-02	ci left: 4.979503e-01	ci right 5.176452e-01	k: 5078	n:10000
Cons ci ratio: 5.673863e-02	ci left: 3.138374e-01	ci right 3.322658e-01	k: 3230	n:10000
KS ci ratio: 5.819690e-02	ci left: 3.029251e-01	ci right 3.211845e-01	k: 3120	n:10000
PKD1   10000 perm   3 sec   (3355 perm/sec)   p_kst 3.120000e-01   p_cons 3.230000e-01   p_joint 5.078000e-01

Outputting figure to mutsig2_images.part000000000131/PKD1.2_13096_10000_0.312_0.323_0.5078.png
                gene_name: PKD1
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.51 
     ci_joint_bounds_left: 0.50 
    ci_joint_bounds_right: 0.52 

Current progress: 86 percent done.
PKD1L2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.415377e-02	ci left: 7.159319e-01	ci right 7.335370e-01	k: 7248	n:10000
Cons ci ratio: 2.629793e-02	ci left: 6.804278e-01	ci right 6.986616e-01	k: 6896	n:10000
KS ci ratio: 3.623340e-02	ci left: 5.293701e-01	ci right 5.490070e-01	k: 5392	n:10000
PKD1L2   10000 perm   2 sec   (4368 perm/sec)   p_kst 5.392000e-01   p_cons 6.896000e-01   p_joint 7.248000e-01

Outputting figure to mutsig2_images.part000000000131/PKD1L2.2_7621_10000_0.5392_0.6896_0.7248.png
                gene_name: PKD1L2
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.69 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.70 
                  p_joint: 0.72 
     ci_joint_bounds_left: 0.72 
    ci_joint_bounds_right: 0.73 

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.165.3896/
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/181708/iteration1/scatter.0000000131
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 131 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1541>
Subject: Job 1120163: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1541>, 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/181708/iteration1/scatter.0000000132> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:48:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000132.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000132.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 132  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    270.06 sec.
    Max Memory :      1520 MB
    Max Swap   :      3863 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.165.3896/
-whichjob
132
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 132: processing genes 11853 - 11942
Calculating significance of each gene.
Using projection method.
11853	PKN2	1
11854	PKN3	1
11855	PKNOX1	1
11856	PKNOX2	1.609962e-02
11857	PKP1	1
11858	PKP2	1.342525e-01
11859	PKP3	1
11860	PKP4	1
11861	PLA1A	1
11862	PLA2G10	1
11863	PLA2G12A	1
11864	PLA2G12B	1
11865	PLA2G15	1
11866	PLA2G16	1
11867	PLA2G1B	1
11868	PLA2G2A	1
11869	PLA2G2C	1
11870	PLA2G2D	1
11871	PLA2G2E	4.712107e-02
11872	PLA2G2F	1
11873	PLA2G3	1
11874	PLA2G4A	1
11875	PLA2G4B	1
11876	PLA2G4C	1
11877	PLA2G4D	1
11878	PLA2G4E	1
11879	PLA2G4F	1
11880	PLA2G5	1
11881	PLA2G6	1
11882	PLA2G7	1
11883	PLA2R1	1
11884	PLAA	1
11885	PLAC1	1
11886	PLAC1L	1
11887	PLAC4	1
11888	PLAC8	1
11889	PLAC8L1	1
11890	PLAC9	1
11891	PLAG1	1
11892	PLAGL1	1
11893	PLAGL2	1.721876e-01
11894	PLAT	1
11895	PLAU	1
11896	PLAUR	8.982412e-03
11897	PLB1	1
11898	PLBD1	1
11899	PLBD2	1
11900	PLCB1	3.245116e-01
11901	PLCB2	1
11902	PLCB3	1
11903	PLCB4	1
11904	PLCD1	1
11905	PLCD3	1.602290e-01
11906	PLCD4	2.809058e-02
11907	PLCE1	6.142516e-01
11908	PLCG1	1.117498e-01
11909	PLCG2	1
11910	PLCH1	3.261530e-02
11911	PLCH2	1
11912	PLCL1	2.468908e-01
11913	PLCL2	1
11914	PLCXD1	1
11915	PLCXD2	1
11916	PLCXD3	1
11917	PLCZ1	1
11918	PLD1	1
11919	PLD2	1
11920	PLD3	1
11921	PLD4	1
11922	PLD5	1.600369e-01
11923	PLD6	1
11924	PLDN	1
11925	PLEC	1
11926	PLEK	1
11927	PLEK2	1
11928	PLEKHA1	1
11929	PLEKHA2	1
11930	PLEKHA3	1
11931	PLEKHA4	6.123825e-02
11932	PLEKHA5	3.634719e-01
11933	PLEKHA6	2.296567e-01
11934	PLEKHA7	1
11935	PLEKHA8	1
11936	PLEKHA9	1.372521e-01
11937	PLEKHB1	1
11938	PLEKHB2	1
11939	PLEKHF1	1
11940	PLEKHF2	1
11941	PLEKHG1	1.010281e-01
11942	PLEKHG2	2.234090e-01
Done

Running MutSig 2:
Scatter job 132: processing genes 11853 - 11942
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PLAUR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.093700e-01	ci left: 1.335536e-02	ci right 1.833248e-02	k: 157	n:10000
Cons ci ratio: 5.358556e-02	ci left: 3.391561e-01	ci right 3.579322e-01	k: 3485	n:10000
KS ci ratio: 5.421642e-01	ci left: 3.799572e-03	ci right 6.700171e-03	k: 51	n:10000
PLAUR   10000 perm   2 sec   (6226 perm/sec)   p_kst 5.100000e-03   p_cons 3.485000e-01   p_joint 1.570000e-02

Joint ci ratio: 1.169324e-01	ci left: 5.008111e-02	ci right 5.634959e-02	k: 1063	n:20000
Cons ci ratio: 3.995580e-02	ci left: 3.183604e-01	ci right 3.313906e-01	k: 6497	n:20000
KS ci ratio: 3.693575e-01	ci left: 4.567803e-03	ci right 6.679840e-03	k: 111	n:20000
PLAUR   20000 perm   7 sec   (3039 perm/sec)   p_kst 5.550000e-03   p_cons 3.248500e-01   p_joint 5.315000e-02

Joint ci ratio: 1.454663e-01	ci left: 2.191185e-02	ci right 2.538125e-02	k: 708	n:30000
Cons ci ratio: 3.253969e-02	ci left: 3.206961e-01	ci right 3.313376e-01	k: 9780	n:30000
KS ci ratio: 3.100462e-01	ci left: 4.479162e-03	ci right 6.152174e-03	k: 158	n:30000
PLAUR   30000 perm   9 sec   (3481 perm/sec)   p_kst 5.266667e-03   p_cons 3.260000e-01   p_joint 2.360000e-02

Joint ci ratio: 1.350605e-01	ci left: 1.923041e-02	ci right 2.203979e-02	k: 824	n:40000
Cons ci ratio: 2.659479e-02	ci left: 3.472682e-01	ci right 3.566533e-01	k: 14078	n:40000
KS ci ratio: 2.744276e-01	ci left: 4.378984e-03	ci right 5.794333e-03	k: 202	n:40000
PLAUR   40000 perm   11 sec   (3738 perm/sec)   p_kst 5.050000e-03   p_cons 3.519500e-01   p_joint 2.060000e-02

Joint ci ratio: 1.160241e-01	ci left: 2.102354e-02	ci right 2.363233e-02	k: 1115	n:50000
Cons ci ratio: 2.382652e-02	ci left: 3.470147e-01	ci right 3.554026e-01	k: 17560	n:50000
KS ci ratio: 2.518976e-01	ci left: 4.213085e-03	ci right 5.445488e-03	k: 240	n:50000
PLAUR   50000 perm   13 sec   (3882 perm/sec)   p_kst 4.800000e-03   p_cons 3.512000e-01   p_joint 2.230000e-02

Joint ci ratio: 9.798121e-02	ci left: 2.470877e-02	ci right 2.727069e-02	k: 1558	n:60000
Cons ci ratio: 2.169354e-02	ci left: 3.485764e-01	ci right 3.562379e-01	k: 21144	n:60000
KS ci ratio: 2.316467e-01	ci left: 4.199876e-03	ci right 5.315526e-03	k: 284	n:60000
PLAUR   60000 perm   15 sec   (3962 perm/sec)   p_kst 4.733333e-03   p_cons 3.524000e-01   p_joint 2.596667e-02

Joint ci ratio: 1.484935e-01	ci left: 9.124760e-03	ci right 1.060201e-02	k: 689	n:70000
Cons ci ratio: 2.010770e-02	ci left: 3.483328e-01	ci right 3.554224e-01	k: 24631	n:70000
KS ci ratio: 2.133382e-01	ci left: 4.287942e-03	ci right 5.325191e-03	k: 335	n:70000
PLAUR   70000 perm   17 sec   (4002 perm/sec)   p_kst 4.785714e-03   p_cons 3.518714e-01   p_joint 9.842857e-03

Joint ci ratio: 1.706832e-01	ci left: 5.990754e-03	ci right 7.120478e-03	k: 523	n:80000
Cons ci ratio: 1.877961e-02	ci left: 3.492759e-01	ci right 3.559098e-01	k: 28207	n:80000
KS ci ratio: 2.030426e-01	ci left: 4.166622e-03	ci right 5.119849e-03	k: 370	n:80000
PLAUR   80000 perm   20 sec   (4015 perm/sec)   p_kst 4.625000e-03   p_cons 3.525875e-01   p_joint 6.537500e-03

Joint ci ratio: 1.628089e-01	ci left: 5.878761e-03	ci right 6.931211e-03	k: 575	n:90000
Cons ci ratio: 1.766902e-02	ci left: 3.504092e-01	ci right 3.566669e-01	k: 31818	n:90000
KS ci ratio: 1.903737e-01	ci left: 4.242461e-03	ci right 5.145475e-03	k: 421	n:90000
PLAUR   90000 perm   22 sec   (4008 perm/sec)   p_kst 4.677778e-03   p_cons 3.535333e-01   p_joint 6.388889e-03

Joint ci ratio: 1.617356e-01	ci left: 5.367520e-03	ci right 6.321485e-03	k: 583	n:100000
Cons ci ratio: 1.768027e-02	ci left: 3.266466e-01	ci right 3.324833e-01	k: 32956	n:100000
KS ci ratio: 1.837591e-01	ci left: 4.113675e-03	ci right 4.955461e-03	k: 452	n:100000
PLAUR   100000 perm   25 sec   (3991 perm/sec)   p_kst 4.520000e-03   p_cons 3.295600e-01   p_joint 5.830000e-03

Joint ci ratio: 1.612247e-01	ci left: 4.914364e-03	ci right 5.784757e-03	k: 587	n:110000
Cons ci ratio: 1.683659e-02	ci left: 3.273301e-01	ci right 3.328970e-01	k: 36312	n:110000
KS ci ratio: 1.745577e-01	ci left: 4.165201e-03	ci right 4.970354e-03	k: 501	n:110000
PLAUR   110000 perm   28 sec   (3966 perm/sec)   p_kst 4.554545e-03   p_cons 3.301091e-01   p_joint 5.336364e-03

Joint ci ratio: 1.580514e-01	ci left: 4.696801e-03	ci right 5.510732e-03	k: 611	n:120000
Cons ci ratio: 1.613597e-02	ci left: 3.270069e-01	ci right 3.323347e-01	k: 39560	n:120000
KS ci ratio: 1.663101e-01	ci left: 4.224991e-03	ci right 4.999249e-03	k: 552	n:120000
PLAUR   120000 perm   31 sec   (3928 perm/sec)   p_kst 4.600000e-03   p_cons 3.296667e-01   p_joint 5.091667e-03

Joint ci ratio: 1.480814e-01	ci left: 4.964383e-03	ci right 5.765616e-03	k: 696	n:130000
Cons ci ratio: 1.551637e-02	ci left: 3.267300e-01	ci right 3.318469e-01	k: 42807	n:130000
KS ci ratio: 1.589988e-01	ci left: 4.283725e-03	ci right 5.030942e-03	k: 604	n:130000
PLAUR   130000 perm   33 sec   (3891 perm/sec)   p_kst 4.646154e-03   p_cons 3.292846e-01   p_joint 5.353846e-03

Joint ci ratio: 1.485390e-01	ci left: 4.582206e-03	ci right 5.324240e-03	k: 692	n:140000
Cons ci ratio: 1.495846e-02	ci left: 3.266315e-01	ci right 3.315613e-01	k: 46073	n:140000
KS ci ratio: 1.533972e-01	ci left: 4.286612e-03	ci right 5.005569e-03	k: 649	n:140000
PLAUR   140000 perm   37 sec   (3834 perm/sec)   p_kst 4.635714e-03   p_cons 3.290929e-01   p_joint 4.942857e-03

Joint ci ratio: 1.089698e-01	ci left: 8.087012e-03	ci right 9.025466e-03	k: 1282	n:150000
Cons ci ratio: 1.444013e-02	ci left: 3.270548e-01	ci right 3.318185e-01	k: 49415	n:150000
KS ci ratio: 1.476038e-01	ci left: 4.334461e-03	ci right 5.031565e-03	k: 701	n:150000
PLAUR   150000 perm   40 sec   (3781 perm/sec)   p_kst 4.673333e-03   p_cons 3.294333e-01   p_joint 8.546667e-03

Joint ci ratio: 1.056082e-01	ci left: 8.086404e-03	ci right 8.994040e-03	k: 1365	n:160000
Cons ci ratio: 1.398622e-02	ci left: 3.269848e-01	ci right 3.315964e-01	k: 52686	n:160000
KS ci ratio: 1.432825e-01	ci left: 4.322526e-03	ci right 4.995617e-03	k: 744	n:160000
PLAUR   160000 perm   43 sec   (3737 perm/sec)   p_kst 4.650000e-03   p_cons 3.292875e-01   p_joint 8.531250e-03

Joint ci ratio: 1.035903e-01	ci left: 7.920034e-03	ci right 8.790975e-03	k: 1419	n:170000
Cons ci ratio: 1.357495e-02	ci left: 3.268487e-01	ci right 3.313218e-01	k: 55944	n:170000
KS ci ratio: 1.388778e-01	ci left: 4.340650e-03	ci right 4.994066e-03	k: 792	n:170000
PLAUR   170000 perm   47 sec   (3652 perm/sec)   p_kst 4.658824e-03   p_cons 3.290824e-01   p_joint 8.347059e-03

Joint ci ratio: 1.104439e-01	ci left: 6.565990e-03	ci right 7.338906e-03	k: 1250	n:180000
Cons ci ratio: 1.318814e-02	ci left: 3.270568e-01	ci right 3.314042e-01	k: 59261	n:180000
KS ci ratio: 1.345348e-01	ci left: 4.378518e-03	ci right 5.015373e-03	k: 844	n:180000
PLAUR   180000 perm   50 sec   (3574 perm/sec)   p_kst 4.688889e-03   p_cons 3.292278e-01   p_joint 6.944444e-03

Joint ci ratio: 1.006782e-01	ci left: 7.517081e-03	ci right 8.319095e-03	k: 1503	n:190000
Cons ci ratio: 1.284578e-02	ci left: 3.267927e-01	ci right 3.310230e-01	k: 62492	n:190000
KS ci ratio: 1.311643e-01	ci left: 4.371951e-03	ci right 4.990679e-03	k: 888	n:190000
PLAUR   190000 perm   55 sec   (3478 perm/sec)   p_kst 4.673684e-03   p_cons 3.289053e-01   p_joint 7.910526e-03

Joint ci ratio: 1.211203e-01	ci left: 4.894326e-03	ci right 5.530144e-03	k: 1041	n:200000
Cons ci ratio: 1.252678e-02	ci left: 3.266263e-01	ci right 3.307486e-01	k: 65737	n:200000
KS ci ratio: 1.280350e-01	ci left: 4.366221e-03	ci right 4.968275e-03	k: 932	n:200000
PLAUR   200000 perm   58 sec   (3437 perm/sec)   p_kst 4.660000e-03   p_cons 3.286850e-01   p_joint 5.205000e-03

Joint ci ratio: 1.204978e-01	ci left: 4.712034e-03	ci right 5.320800e-03	k: 1052	n:210000
Cons ci ratio: 1.222936e-02	ci left: 3.265150e-01	ci right 3.305373e-01	k: 68990	n:210000
KS ci ratio: 1.247353e-01	ci left: 4.388876e-03	ci right 4.977305e-03	k: 982	n:210000
PLAUR   210000 perm   62 sec   (3399 perm/sec)   p_kst 4.676190e-03   p_cons 3.285238e-01   p_joint 5.009524e-03

Joint ci ratio: 1.155445e-01	ci left: 4.903719e-03	ci right 5.509430e-03	k: 1144	n:220000
Cons ci ratio: 1.196066e-02	ci left: 3.261017e-01	ci right 3.300301e-01	k: 72174	n:220000
KS ci ratio: 1.216191e-01	ci left: 4.414061e-03	ci right 4.990017e-03	k: 1033	n:220000
PLAUR   220000 perm   66 sec   (3325 perm/sec)   p_kst 4.695455e-03   p_cons 3.280636e-01   p_joint 5.200000e-03

Joint ci ratio: 8.562430e-02	ci left: 8.643596e-03	ci right 9.421026e-03	k: 2076	n:230000
Cons ci ratio: 1.169219e-02	ci left: 3.263548e-01	ci right 3.301973e-01	k: 75503	n:230000
KS ci ratio: 1.183969e-01	ci left: 4.462539e-03	ci right 5.028314e-03	k: 1090	n:230000
PLAUR   230000 perm   71 sec   (3248 perm/sec)   p_kst 4.739130e-03   p_cons 3.282739e-01   p_joint 9.026087e-03

Joint ci ratio: 8.475993e-02	ci left: 8.458762e-03	ci right 9.211506e-03	k: 2119	n:240000
Cons ci ratio: 1.144361e-02	ci left: 3.264878e-01	ci right 3.302496e-01	k: 78808	n:240000
KS ci ratio: 1.160801e-01	ci left: 4.454556e-03	ci right 5.007510e-03	k: 1134	n:240000
PLAUR   240000 perm   76 sec   (3178 perm/sec)   p_kst 4.725000e-03   p_cons 3.283667e-01   p_joint 8.829167e-03

Joint ci ratio: 8.150381e-02	ci left: 8.794172e-03	ci right 9.545273e-03	k: 2291	n:250000
Cons ci ratio: 1.121176e-02	ci left: 3.265511e-01	ci right 3.302369e-01	k: 82098	n:250000
KS ci ratio: 1.137006e-01	ci left: 4.462857e-03	ci right 5.004723e-03	k: 1182	n:250000
PLAUR   250000 perm   80 sec   (3128 perm/sec)   p_kst 4.728000e-03   p_cons 3.283920e-01   p_joint 9.164000e-03

Joint ci ratio: 8.468836e-02	ci left: 7.826803e-03	ci right 8.522689e-03	k: 2124	n:260000
Cons ci ratio: 1.099652e-02	ci left: 3.264873e-01	ci right 3.301012e-01	k: 85356	n:260000
KS ci ratio: 1.118733e-01	ci left: 4.436974e-03	ci right 4.966468e-03	k: 1221	n:260000
PLAUR   260000 perm   85 sec   (3067 perm/sec)   p_kst 4.696154e-03   p_cons 3.282923e-01   p_joint 8.169231e-03

Joint ci ratio: 8.194746e-02	ci left: 8.059183e-03	ci right 8.751432e-03	k: 2268	n:270000
Cons ci ratio: 1.079848e-02	ci left: 3.262143e-01	ci right 3.297597e-01	k: 88556	n:270000
KS ci ratio: 1.097386e-01	ci left: 4.445493e-03	ci right 4.965227e-03	k: 1269	n:270000
PLAUR   270000 perm   89 sec   (3024 perm/sec)   p_kst 4.700000e-03   p_cons 3.279852e-01   p_joint 8.400000e-03

Joint ci ratio: 8.297985e-02	ci left: 7.578899e-03	ci right 8.238490e-03	k: 2213	n:280000
Cons ci ratio: 1.060544e-02	ci left: 3.261826e-01	ci right 3.296638e-01	k: 91818	n:280000
KS ci ratio: 1.076396e-01	ci left: 4.460444e-03	ci right 4.971319e-03	k: 1319	n:280000
PLAUR   280000 perm   94 sec   (2974 perm/sec)   p_kst 4.710714e-03   p_cons 3.279214e-01   p_joint 7.903571e-03

Joint ci ratio: 7.886058e-02	ci left: 8.114978e-03	ci right 8.784556e-03	k: 2449	n:290000
Cons ci ratio: 1.041685e-02	ci left: 3.263877e-01	ci right 3.298088e-01	k: 95148	n:290000
KS ci ratio: 1.064005e-01	ci left: 4.410665e-03	ci right 4.909658e-03	k: 1350	n:290000
PLAUR   290000 perm   99 sec   (2943 perm/sec)   p_kst 4.655172e-03   p_cons 3.280966e-01   p_joint 8.444828e-03

Joint ci ratio: 7.842122e-02	ci left: 7.935948e-03	ci right 8.586939e-03	k: 2477	n:300000
Cons ci ratio: 1.023866e-02	ci left: 3.265497e-01	ci right 3.299136e-01	k: 98469	n:300000
KS ci ratio: 1.041856e-01	ci left: 4.451890e-03	ci right 4.944420e-03	k: 1408	n:300000
PLAUR   300000 perm   103 sec   (2914 perm/sec)   p_kst 4.693333e-03   p_cons 3.282300e-01   p_joint 8.256667e-03

Joint ci ratio: 7.915956e-02	ci left: 7.537587e-03	ci right 8.161989e-03	k: 2432	n:310000
Cons ci ratio: 1.007278e-02	ci left: 3.265503e-01	ci right 3.298594e-01	k: 101743	n:310000
KS ci ratio: 1.025256e-01	ci left: 4.452832e-03	ci right 4.937144e-03	k: 1454	n:310000
PLAUR   310000 perm   108 sec   (2881 perm/sec)   p_kst 4.690323e-03   p_cons 3.282032e-01   p_joint 7.845161e-03

Joint ci ratio: 7.782678e-02	ci left: 7.559388e-03	ci right 8.174575e-03	k: 2516	n:320000
Cons ci ratio: 9.914223e-03	ci left: 3.265731e-01	ci right 3.298300e-01	k: 105024	n:320000
KS ci ratio: 1.013846e-01	ci left: 4.414171e-03	ci right 4.888618e-03	k: 1487	n:320000
PLAUR   320000 perm   112 sec   (2846 perm/sec)   p_kst 4.646875e-03   p_cons 3.282000e-01   p_joint 7.862500e-03

Joint ci ratio: 7.486593e-02	ci left: 7.930809e-03	ci right 8.550600e-03	k: 2718	n:330000
Cons ci ratio: 9.763391e-03	ci left: 3.265737e-01	ci right 3.297808e-01	k: 108298	n:330000
KS ci ratio: 9.978763e-02	ci left: 4.422205e-03	ci right 4.889589e-03	k: 1535	n:330000
PLAUR   330000 perm   117 sec   (2820 perm/sec)   p_kst 4.651515e-03   p_cons 3.281758e-01   p_joint 8.236364e-03

Outputting figure to mutsig2_images.part000000000132/PLAUR.3_1132_330000_0.0046515_0.32818_0.0082364.png
                gene_name: PLAUR
               theta_stop: 0.100 
                    nperm: 330000 
                     p_ks: 0.0047 
        ci_ks_bounds_left: 0.0044 
       ci_ks_bounds_right: 0.0049 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.0082 
     ci_joint_bounds_left: 0.0079 
    ci_joint_bounds_right: 0.0086 

Current progress: 14 percent done.
PLCH1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.752878e-02	ci left: 5.118543e-01	ci right 5.315331e-01	k: 5217	n:10000
Cons ci ratio: 2.923811e-02	ci left: 6.330162e-01	ci right 6.519008e-01	k: 6425	n:10000
KS ci ratio: 4.736681e-02	ci left: 3.967519e-01	ci right 4.161027e-01	k: 4064	n:10000
PLCH1   10000 perm   2 sec   (4132 perm/sec)   p_kst 4.064000e-01   p_cons 6.425000e-01   p_joint 5.217000e-01

Outputting figure to mutsig2_images.part000000000132/PLCH1.3_5189_10000_0.4064_0.6425_0.5217.png
                gene_name: PLCH1
               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: 0.52 
     ci_joint_bounds_left: 0.51 
    ci_joint_bounds_right: 0.53 

Current progress: 29 percent done.
PLEKHG1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.931551e-02	ci left: 3.775373e-01	ci right 3.967285e-01	k: 3871	n:10000
Cons ci ratio: 7.869324e-02	ci left: 1.909179e-01	ci right 2.066579e-01	k: 1987	n:10000
KS ci ratio: 4.902580e-02	ci left: 3.803239e-01	ci right 3.995402e-01	k: 3899	n:10000
PLEKHG1   10000 perm   2 sec   (4144 perm/sec)   p_kst 3.899000e-01   p_cons 1.987000e-01   p_joint 3.871000e-01

Outputting figure to mutsig2_images.part000000000132/PLEKHG1.3_4218_10000_0.3899_0.1987_0.3871.png
                gene_name: PLEKHG1
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 43 percent done.
PKNOX2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.041810e-02	ci left: 7.784370e-01	ci right 7.945958e-01	k: 7866	n:10000
Cons ci ratio: 2.179286e-02	ci left: 7.554502e-01	ci right 7.721959e-01	k: 7639	n:10000
KS ci ratio: 9.021878e-02	ci left: 1.515885e-01	ci right 1.660108e-01	k: 1587	n:10000
PKNOX2   10000 perm   2 sec   (4370 perm/sec)   p_kst 1.587000e-01   p_cons 7.639000e-01   p_joint 7.866000e-01

Outputting figure to mutsig2_images.part000000000132/PKNOX2.2_1459_10000_0.1587_0.7639_0.7866.png
                gene_name: PKNOX2
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.79 

Current progress: 57 percent done.
PLCD4
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: 7.067756e-03	ci left: 9.649925e-01	ci right 9.719311e-01	k: 9686	n:10000
KS ci ratio: 9.971200e-03	ci left: 9.344406e-01	ci right 9.439015e-01	k: 9393	n:10000
PLCD4   10000 perm   2 sec   (4921 perm/sec)   p_kst 9.393000e-01   p_cons 9.686000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000132/PLCD4.2_2349_10000_0.9393_0.9686_1.png
                gene_name: PLCD4
               theta_stop: 0.0100 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.96 
     ci_cons_bounds_right: 0.97 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 71 percent done.
PLCG1
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: 3.841039e-02	ci left: 5.002504e-01	ci right 5.199437e-01	k: 5101	n:10000
KS ci ratio: 4.519813e-02	ci left: 4.194707e-01	ci right 4.389705e-01	k: 4292	n:10000
PLCG1   10000 perm   2 sec   (4651 perm/sec)   p_kst 4.292000e-01   p_cons 5.101000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000132/PLCG1.2_4004_10000_0.4292_0.5101_1.png
                gene_name: PLCG1
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.51 
      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: 86 percent done.
PLEKHA4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.852876e-02	ci left: 8.096859e-01	ci right 8.249288e-01	k: 8174	n:10000
Cons ci ratio: 3.429577e-03	ci left: 9.906076e-01	ci right 9.940963e-01	k: 9925	n:10000
KS ci ratio: 2.598517e-02	ci left: 6.855679e-01	ci right 7.037185e-01	k: 6947	n:10000
PLEKHA4   10000 perm   2 sec   (5641 perm/sec)   p_kst 6.947000e-01   p_cons 9.925000e-01   p_joint 8.174000e-01

Outputting figure to mutsig2_images.part000000000132/PLEKHA4.2_2416_10000_0.6947_0.9925_0.8174.png
                gene_name: PLEKHA4
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.69 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.70 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.82 
     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.165.3896/
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/181708/iteration1/scatter.0000000132
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 132 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120166: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000133> was used as the working directory.
Started at Wed Oct 10 10:44:29 2012
Results reported at Wed Oct 10 10:46:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000133.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000133.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 133  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    127.10 sec.
    Max Memory :      1244 MB
    Max Swap   :      3857 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.165.3896/
-whichjob
133
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 133: processing genes 11943 - 12033
Calculating significance of each gene.
Using projection method.
11943	PLEKHG3	3.662519e-01
11944	PLEKHG4	1
11945	PLEKHG4B	1
11946	PLEKHG5	2.345281e-01
11947	PLEKHG6	1
11948	PLEKHG7	1
11949	PLEKHH1	1
11950	PLEKHH2	4.710226e-01
11951	PLEKHH3	1
11952	PLEKHJ1	1
11953	PLEKHM1	1
11954	PLEKHM2	1
11955	PLEKHM3	1
11956	PLEKHN1	2.313917e-01
11957	PLEKHO1	1
11958	PLEKHO2	1
11959	PLG	1
11960	PLIN1	1
11961	PLIN2	1
11962	PLIN3	1
11963	PLIN4	1
11964	PLIN5	1
11965	PLK1	1
11966	PLK1S1	1
11967	PLK2	1
11968	PLK3	1
11969	PLK4	1
11970	PLLP	1
11971	PLN	1
11972	PLOD1	1
11973	PLOD2	2.110705e-01
11974	PLOD3	1
11975	PLP1	1
11976	PLP2	6.998611e-02
11977	PLRG1	1.970501e-01
11978	PLS1	1
11979	PLS3	1
11980	PLSCR1	1
11981	PLSCR2	1
11982	PLSCR3	1
11983	PLSCR4	7.207576e-02
11984	PLSCR5	1
11985	PLTP	1
11986	PLUNC	1
11987	PLVAP	8.406868e-02
11988	PLXDC1	1
11989	PLXDC2	1
11990	PLXNA1	1
11991	PLXNA2	1
11992	PLXNA3	1
11993	PLXNA4	4.587258e-01
11994	PLXNB1	1
11995	PLXNB2	2.133491e-01
11996	PLXNB3	1.847007e-01
11997	PLXNC1	4.650073e-01
11998	PLXND1	1
11999	PM20D1	1
12000/18094 12000	PM20D2	1
12001	PMAIP1	1
12002	PMCH	1
12003	PMEPA1	1
12004	PMF1	1
12005	PMFBP1	6.206368e-02
12006	PML	1.720929e-02
12007	PMM1	6.438474e-02
12008	PMM2	1
12009	PMP2	1
12010	PMP22	1
12011	PMPCA	9.921651e-02
12012	PMPCB	2.299873e-01
12013	PMS1	1.642625e-01
12014	PMS2	3.454135e-01
12015	PMVK	1
12016	PNCK	1
12017	PNKD	1
12018	PNKP	1
12019	PNLDC1	1
12020	PNLIP	1
12021	PNLIPRP1	1
12022	PNLIPRP2	1
12023	PNLIPRP3	1
12024	PNMA1	1.814803e-01
12025	PNMA2	1
12026	PNMA3	4.831300e-02
12027	PNMA5	1
12028	PNMAL1	1
12029	PNMAL2	1
12030	PNMT	1
12031	PNN	1
12032	PNO1	1
12033	PNOC	1
Done

Running MutSig 2:
Scatter job 133: processing genes 11943 - 12033
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PML
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.721092e-02	ci left: 6.655187e-01	ci right 6.839794e-01	k: 6748	n:10000
Cons ci ratio: 4.917035e-02	ci left: 3.789306e-01	ci right 3.981344e-01	k: 3885	n:10000
KS ci ratio: 1.094871e-02	ci left: 9.224484e-01	ci right 9.327009e-01	k: 9277	n:10000
PML   10000 perm   2 sec   (5023 perm/sec)   p_kst 9.277000e-01   p_cons 3.885000e-01   p_joint 6.748000e-01

Outputting figure to mutsig2_images.part000000000133/PML.3_3702_10000_0.9277_0.3885_0.6748.png
                gene_name: PML
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.67 
     ci_joint_bounds_left: 0.67 
    ci_joint_bounds_right: 0.68 

Current progress: 33 percent done.
PMFBP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.637034e-02	ci left: 4.070126e-01	ci right 4.264360e-01	k: 4167	n:10000
Cons ci ratio: 1.484236e-01	ci left: 6.034192e-02	ci right 7.011322e-02	k: 651	n:10000
KS ci ratio: 8.905301e-03	ci left: 9.465858e-01	ci right 9.551491e-01	k: 9510	n:10000
PMFBP1   10000 perm   2 sec   (5454 perm/sec)   p_kst 9.510000e-01   p_cons 6.510000e-02   p_joint 4.167000e-01

Joint ci ratio: 4.771062e-02	ci left: 2.462919e-01	ci right 2.583802e-01	k: 5046	n:20000
Cons ci ratio: 1.066702e-01	ci left: 5.986647e-02	ci right 6.666118e-02	k: 1264	n:20000
KS ci ratio: 6.185715e-03	ci left: 9.495636e-01	ci right 9.555040e-01	k: 19052	n:20000
PMFBP1   20000 perm   4 sec   (4589 perm/sec)   p_kst 9.526000e-01   p_cons 6.320000e-02   p_joint 2.523000e-01

Joint ci ratio: 3.572440e-02	ci left: 2.812554e-01	ci right 2.915193e-01	k: 8591	n:30000
Cons ci ratio: 8.733012e-02	ci left: 6.017846e-02	ci right 6.570655e-02	k: 1887	n:30000
KS ci ratio: 4.990003e-03	ci left: 9.512270e-01	ci right 9.560180e-01	k: 28610	n:30000
PMFBP1   30000 perm   7 sec   (4299 perm/sec)   p_kst 9.536667e-01   p_cons 6.290000e-02   p_joint 2.863667e-01

Outputting figure to mutsig2_images.part000000000133/PMFBP1.2_3164_30000_0.95367_0.0629_0.28637.png
                gene_name: PMFBP1
               theta_stop: 0.087 
                    nperm: 30000 
                     p_ks: 0.95 
        ci_ks_bounds_left: 0.95 
       ci_ks_bounds_right: 0.96 
                   p_cons: 0.063 
      ci_cons_bounds_left: 0.060 
     ci_cons_bounds_right: 0.066 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.29 

Current progress: 67 percent done.
PNMA1
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: 5.078065e-02	ci left: 3.638081e-01	ci right 3.828658e-01	k: 3733	n:10000
KS ci ratio: 1.713548e-02	ci left: 8.322587e-01	ci right 8.467429e-01	k: 8396	n:10000
PNMA1   10000 perm   1 sec   (6687 perm/sec)   p_kst 8.396000e-01   p_cons 3.733000e-01   p_joint 8.858000e-01

Outputting figure to mutsig2_images.part000000000133/PNMA1.2_1066_10000_0.8396_0.3733_0.8858.png
                gene_name: PNMA1
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.83 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  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.165.3896/
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/181708/iteration1/scatter.0000000133
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 133 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120169: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000134> was used as the working directory.
Started at Wed Oct 10 10:44:33 2012
Results reported at Wed Oct 10 10:46:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000134.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000134.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 134  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    149.71 sec.
    Max Memory :      1289 MB
    Max Swap   :      3853 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.165.3896/
-whichjob
134
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 134: processing genes 12034 - 12123
Calculating significance of each gene.
Using projection method.
12034	PNP	1
12035	PNPLA1	1
12036	PNPLA2	1
12037	PNPLA3	1
12038	PNPLA4	1
12039	PNPLA5	1
12040	PNPLA6	1
12041	PNPLA7	1
12042	PNPLA8	1
12043	PNPO	1.028399e-01
12044	PNPT1	1.071207e-01
12045	PNRC1	1
12046	POC1A	1
12047	POC1B	1
12048	POC5	1
12049	PODN	1
12050	PODNL1	1
12051	PODXL	1
12052	PODXL2	1
12053	POF1B	1
12054	POFUT1	1
12055	POFUT2	1
12056	POGK	2.601008e-01
12057	POGZ	1
12058	POLA1	1.529053e-01
12059	POLA2	2.152813e-01
12060	POLB	1
12061	POLD1	3.066067e-01
12062	POLD2	2.109361e-01
12063	POLD3	1
12064	POLD4	1
12065	POLDIP2	1
12066	POLDIP3	1
12067	POLE	1
12068	POLE2	1.288847e-01
12069	POLE3	1
12070	POLE4	1
12071	POLG	1
12072	POLG2	2.305333e-01
12073	POLH	1
12074	POLI	1.154245e-01
12075	POLK	3.042837e-01
12076	POLL	1
12077	POLM	1
12078	POLN	5.429311e-02
12079	POLQ	3.398297e-01
12080	POLR1A	1
12081	POLR1B	1
12082	POLR1C	1
12083	POLR1D	1
12084	POLR1E	1
12085	POLR2A	1
12086	POLR2B	1
12087	POLR2C	1
12088	POLR2D	1.111384e-02
12089	POLR2E	1
12090	POLR2F	6.853696e-02
12091	POLR2G	1
12092	POLR2H	1
12093	POLR2I	1
12094	POLR2J	1
12095	POLR2J2	1
12096	POLR2K	1
12097	POLR2L	1
12098	POLR3A	2.158842e-01
12099	POLR3B	4.055656e-01
12100	POLR3C	1
12101	POLR3D	1
12102	POLR3E	1.715204e-01
12103	POLR3F	1
12104	POLR3G	1
12105	POLR3GL	1
12106	POLR3H	3.543456e-02
12107	POLR3K	1
12108	POLRMT	1
12109	POM121	1.938990e-01
12110	POM121C	1
12111	POM121L12	1
12112	POMC	1
12113	POMGNT1	1
12114	POMP	1
12115	POMT1	9.132238e-02
12116	POMT2	1
12117	POMZP3	1
12118	PON1	1
12119	PON2	1
12120	PON3	1
12121	POP1	1.905798e-01
12122	POP4	1
12123	POP5	1
Done

Running MutSig 2:
Scatter job 134: processing genes 12034 - 12123
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
POLA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.639181e-02	ci left: 8.440725e-01	ci right 8.581223e-01	k: 8512	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: 2.904114e-02	ci left: 6.361335e-01	ci right 6.549816e-01	k: 6456	n:10000
POLA1   10000 perm   2 sec   (5116 perm/sec)   p_kst 6.456000e-01   p_cons 8.227000e-01   p_joint 8.512000e-01

Outputting figure to mutsig2_images.part000000000134/POLA1.2_4537_10000_0.6456_0.8227_0.8512.png
                gene_name: POLA1
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.83 
                  p_joint: 0.85 
     ci_joint_bounds_left: 0.84 
    ci_joint_bounds_right: 0.86 

Current progress: 33 percent done.
POLN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.607845e-02	ci left: 1.358015e-01	ci right 1.496073e-01	k: 1426	n:10000
Cons ci ratio: 3.737120e-02	ci left: 5.139556e-01	ci right 5.336306e-01	k: 5238	n:10000
KS ci ratio: 3.769094e-01	ci left: 8.686342e-03	ci right 1.280614e-02	k: 106	n:10000
POLN   10000 perm   2 sec   (5967 perm/sec)   p_kst 1.060000e-02   p_cons 5.238000e-01   p_joint 1.426000e-01

Joint ci ratio: 4.558878e-02	ci left: 2.637070e-01	ci right 2.760599e-01	k: 5397	n:20000
Cons ci ratio: 2.629780e-02	ci left: 5.193016e-01	ci right 5.331907e-01	k: 10525	n:20000
KS ci ratio: 2.646529e-01	ci left: 9.413987e-03	ci right 1.233084e-02	k: 216	n:20000
POLN   20000 perm   4 sec   (5288 perm/sec)   p_kst 1.080000e-02   p_cons 5.262500e-01   p_joint 2.698500e-01

Joint ci ratio: 5.125365e-02	ci left: 1.589684e-01	ci right 1.673636e-01	k: 4894	n:30000
Cons ci ratio: 2.137015e-02	ci left: 5.229655e-01	ci right 5.342956e-01	k: 15859	n:30000
KS ci ratio: 2.236817e-01	ci left: 8.999499e-03	ci right 1.129686e-02	k: 303	n:30000
POLN   30000 perm   6 sec   (5054 perm/sec)   p_kst 1.010000e-02   p_cons 5.286333e-01   p_joint 1.631333e-01

Joint ci ratio: 2.921415e-02	ci left: 3.058425e-01	ci right 3.149350e-01	k: 12415	n:40000
Cons ci ratio: 1.845940e-02	ci left: 5.250193e-01	ci right 5.348263e-01	k: 21197	n:40000
KS ci ratio: 1.940375e-01	ci left: 9.119511e-03	ci right 1.110258e-02	k: 403	n:40000
POLN   40000 perm   8 sec   (4782 perm/sec)   p_kst 1.007500e-02   p_cons 5.299250e-01   p_joint 3.103750e-01

Joint ci ratio: 3.690789e-02	ci left: 1.806716e-01	ci right 1.874851e-01	k: 9203	n:50000
Cons ci ratio: 1.583756e-02	ci left: 5.462271e-01	ci right 5.549671e-01	k: 27530	n:50000
KS ci ratio: 1.720111e-01	ci left: 9.395245e-03	ci right 1.118230e-02	k: 513	n:50000
POLN   50000 perm   11 sec   (4698 perm/sec)   p_kst 1.026000e-02   p_cons 5.506000e-01   p_joint 1.840600e-01

Joint ci ratio: 6.437617e-02	ci left: 5.632333e-02	ci right 6.008621e-02	k: 3491	n:60000
Cons ci ratio: 1.503368e-02	ci left: 5.271973e-01	ci right 5.351997e-01	k: 31872	n:60000
KS ci ratio: 1.561062e-01	ci left: 9.587650e-03	ci right 1.122689e-02	k: 623	n:60000
POLN   60000 perm   13 sec   (4614 perm/sec)   p_kst 1.038333e-02   p_cons 5.312000e-01   p_joint 5.818333e-02

Joint ci ratio: 6.407290e-02	ci left: 4.912852e-02	ci right 5.239456e-02	k: 3552	n:70000
Cons ci ratio: 1.390576e-02	ci left: 5.279522e-01	ci right 5.353595e-01	k: 37216	n:70000
KS ci ratio: 1.453355e-01	ci left: 9.537722e-03	ci right 1.104614e-02	k: 719	n:70000
POLN   70000 perm   15 sec   (4540 perm/sec)   p_kst 1.027143e-02   p_cons 5.316571e-01   p_joint 5.074286e-02

Joint ci ratio: 5.911546e-02	ci left: 5.055775e-02	ci right 5.364983e-02	k: 4167	n:80000
Cons ci ratio: 1.301668e-02	ci left: 5.278472e-01	ci right 5.347755e-01	k: 42505	n:80000
KS ci ratio: 1.362721e-01	ci left: 9.539443e-03	ci right 1.094641e-02	k: 818	n:80000
POLN   80000 perm   18 sec   (4460 perm/sec)   p_kst 1.022500e-02   p_cons 5.313125e-01   p_joint 5.208750e-02

Joint ci ratio: 6.573434e-02	ci left: 3.676023e-02	ci right 3.926966e-02	k: 3420	n:90000
Cons ci ratio: 1.226081e-02	ci left: 5.285112e-01	ci right 5.350423e-01	k: 47860	n:90000
KS ci ratio: 1.283643e-01	ci left: 9.596849e-03	ci right 1.092389e-02	k: 922	n:90000
POLN   90000 perm   21 sec   (4385 perm/sec)   p_kst 1.024444e-02   p_cons 5.317778e-01   p_joint 3.800000e-02

Joint ci ratio: 4.750906e-02	ci left: 6.222369e-02	ci right 6.526168e-02	k: 6373	n:100000
Cons ci ratio: 1.163603e-02	ci left: 5.284913e-01	ci right 5.346868e-01	k: 53159	n:100000
KS ci ratio: 1.219910e-01	ci left: 9.596174e-03	ci right 1.085248e-02	k: 1021	n:100000
POLN   100000 perm   23 sec   (4314 perm/sec)   p_kst 1.021000e-02   p_cons 5.315900e-01   p_joint 6.373000e-02

Joint ci ratio: 4.521690e-02	ci left: 6.250662e-02	ci right 6.540733e-02	k: 7034	n:110000
Cons ci ratio: 1.108823e-02	ci left: 5.289186e-01	ci right 5.348251e-01	k: 58506	n:110000
KS ci ratio: 1.159601e-01	ci left: 9.685250e-03	ci right 1.088624e-02	k: 1130	n:110000
POLN   110000 perm   26 sec   (4243 perm/sec)   p_kst 1.027273e-02   p_cons 5.318727e-01   p_joint 6.394545e-02

Joint ci ratio: 4.441399e-02	ci left: 5.960286e-02	ci right 6.231840e-02	k: 7314	n:120000
Cons ci ratio: 1.061934e-02	ci left: 5.288968e-01	ci right 5.345516e-01	k: 63807	n:120000
KS ci ratio: 1.110606e-01	ci left: 9.704022e-03	ci right 1.085316e-02	k: 1232	n:120000
POLN   120000 perm   29 sec   (4177 perm/sec)   p_kst 1.026667e-02   p_cons 5.317250e-01   p_joint 6.095000e-02

Joint ci ratio: 2.569961e-02	ci left: 1.498457e-01	ci right 1.537544e-01	k: 19733	n:130000
Cons ci ratio: 1.020483e-02	ci left: 5.289060e-01	ci right 5.343387e-01	k: 69111	n:130000
KS ci ratio: 1.075096e-01	ci left: 9.578536e-03	ci right 1.067425e-02	k: 1315	n:130000
POLN   130000 perm   32 sec   (4106 perm/sec)   p_kst 1.011538e-02   p_cons 5.316231e-01   p_joint 1.517923e-01

Joint ci ratio: 2.439173e-02	ci left: 1.538470e-01	ci right 1.576530e-01	k: 21804	n:140000
Cons ci ratio: 9.841558e-03	ci left: 5.286032e-01	ci right 5.338383e-01	k: 74371	n:140000
KS ci ratio: 1.035336e-01	ci left: 9.610662e-03	ci right 1.066692e-02	k: 1418	n:140000
POLN   140000 perm   35 sec   (4042 perm/sec)   p_kst 1.012857e-02   p_cons 5.312214e-01   p_joint 1.557429e-01

Joint ci ratio: 3.657089e-02	ci left: 6.984409e-02	ci right 7.245251e-02	k: 10671	n:150000
Cons ci ratio: 9.510810e-03	ci left: 5.285373e-01	ci right 5.335948e-01	k: 79660	n:150000
KS ci ratio: 9.953982e-02	ci left: 9.723677e-03	ci right 1.074872e-02	k: 1534	n:150000
POLN   150000 perm   38 sec   (3977 perm/sec)   p_kst 1.022667e-02   p_cons 5.310667e-01   p_joint 7.114000e-02

Outputting figure to mutsig2_images.part000000000134/POLN.2_2799_150000_0.010227_0.53107_0.07114.png
                gene_name: POLN
               theta_stop: 0.100 
                    nperm: 150000 
                     p_ks: 0.010 
        ci_ks_bounds_left: 0.0097 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.071 
     ci_joint_bounds_left: 0.070 
    ci_joint_bounds_right: 0.072 

Current progress: 67 percent done.
POLQ
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: 4.841319e-02	ci left: 3.862964e-01	ci right 4.055643e-01	k: 3959	n:10000
KS ci ratio: 1.050099e-01	ci left: 1.158415e-01	ci right 1.287794e-01	k: 1222	n:10000
POLQ   10000 perm   2 sec   (4012 perm/sec)   p_kst 1.222000e-01   p_cons 3.959000e-01   p_joint 7.171000e-01

Joint ci ratio: 7.239501e-02	ci left: 1.232023e-01	ci right 1.325062e-01	k: 2556	n:20000
Cons ci ratio: 3.408678e-02	ci left: 3.912064e-01	ci right 4.048232e-01	k: 7960	n:20000
KS ci ratio: 7.527493e-02	ci left: 1.148875e-01	ci right 1.239235e-01	k: 2387	n:20000
POLQ   20000 perm   5 sec   (3785 perm/sec)   p_kst 1.193500e-01   p_cons 3.980000e-01   p_joint 1.278000e-01

Outputting figure to mutsig2_images.part000000000134/POLQ.2_7893_20000_0.11935_0.398_0.1278.png
                gene_name: POLQ
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.11 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.40 
                  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.165.3896/
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/181708/iteration1/scatter.0000000134
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 134 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120172: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000135> was used as the working directory.
Started at Wed Oct 10 10:44:33 2012
Results reported at Wed Oct 10 10:47:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000135.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000135.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 135  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    190.86 sec.
    Max Memory :      1113 MB
    Max Swap   :      3867 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.165.3896/
-whichjob
135
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 135: processing genes 12124 - 12213
Calculating significance of each gene.
Using projection method.
12124	POP7	1
12125	POPDC2	1
12126	POPDC3	1
12127	POR	1
12128	PORCN	1
12129	POSTN	1
12130	POT1	1
12131	POTEA	1
12132	POTEC	2.805430e-04
12133	POTEE	1
12134	POTEF	1
12135	POTEG	1
12136	POTEH	1
12137	POTEM	1
12138	POU1F1	1
12139	POU2AF1	1
12140	POU2F1	1
12141	POU2F2	1
12142	POU2F3	1
12143	POU3F1	1
12144	POU3F2	1
12145	POU3F3	1
12146	POU3F4	1
12147	POU4F1	1
12148	POU4F2	1
12149	POU4F3	1
12150	POU5F1	8.771092e-02
12151	POU5F1B	1
12152	POU5F2	1
12153	POU6F1	1
12154	POU6F2	1
12155	PPA1	1
12156	PPA2	1
12157	PPAN	1
12158	PPAN-P2RY11	1
12159	PPAP2A	1
12160	PPAP2B	1.205399e-01
12161	PPAP2C	1
12162	PPAPDC1A	1
12163	PPAPDC1B	1
12164	PPAPDC2	1
12165	PPAPDC3	1
12166	PPARA	1
12167	PPARD	1
12168	PPARG	1
12169	PPARGC1A	1
12170	PPARGC1B	1
12171	PPAT	1
12172	PPBP	1.149093e-04
12173	PPCDC	1
12174	PPCS	1
12175	PPDPF	1
12176	PPEF1	1
12177	PPEF2	5.583015e-02
12178	PPFIA1	2.334743e-01
12179	PPFIA2	1
12180	PPFIA3	1.514496e-01
12181	PPFIA4	1
12182	PPFIBP1	1
12183	PPFIBP2	1.569758e-01
12184	PPHLN1	1
12185	PPIA	6.763301e-02
12186	PPIAL4E	1
12187	PPIAL4G	1
12188	PPIB	1
12189	PPIC	2.246929e-02
12190	PPID	1
12191	PPIE	6.990241e-02
12192	PPIF	1
12193	PPIG	1
12194	PPIH	1
12195	PPIL1	1
12196	PPIL2	1
12197	PPIL3	1
12198	PPIL4	1.353445e-01
12199	PPIL5	1
12200	PPIL6	1
12201	PPIP5K1	1
12202	PPIP5K2	3.547585e-01
12203	PPL	5.476555e-01
12204	PPM1A	1
12205	PPM1B	1
12206	PPM1D	1
12207	PPM1E	1
12208	PPM1F	1
12209	PPM1G	2.317216e-01
12210	PPM1H	1
12211	PPM1J	1
12212	PPM1K	3.982656e-02
12213	PPM1L	1
Done

Running MutSig 2:
Scatter job 135: processing genes 12124 - 12213
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
POTEC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.152427e-01	ci left: 2.863733e-02	ci right 3.563870e-02	k: 320	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: 4.846095e-01	ci left: 4.932166e-03	ci right 8.165407e-03	k: 64	n:10000
POTEC   10000 perm   2 sec   (5197 perm/sec)   p_kst 6.400000e-03   p_cons 8.568000e-01   p_joint 3.200000e-02

Joint ci ratio: 1.409142e-01	ci left: 3.461962e-02	ci right 3.991600e-02	k: 744	n:20000
Cons ci ratio: 1.047047e-02	ci left: 8.704893e-01	ci right 8.797013e-01	k: 17503	n:20000
KS ci ratio: 3.086535e-01	ci left: 6.766163e-03	ci right 9.280034e-03	k: 159	n:20000
POTEC   20000 perm   7 sec   (2745 perm/sec)   p_kst 7.950000e-03   p_cons 8.751500e-01   p_joint 3.720000e-02

Joint ci ratio: 8.902807e-02	ci left: 5.799134e-02	ci right 6.342745e-02	k: 1820	n:30000
Cons ci ratio: 9.133177e-03	ci left: 8.559883e-01	ci right 8.638752e-01	k: 25799	n:30000
KS ci ratio: 2.530818e-01	ci left: 6.929423e-03	ci right 8.967601e-03	k: 237	n:30000
POTEC   30000 perm   10 sec   (3114 perm/sec)   p_kst 7.900000e-03   p_cons 8.599667e-01   p_joint 6.066667e-02

Joint ci ratio: 1.090819e-01	ci left: 2.956650e-02	ci right 3.300199e-02	k: 1250	n:40000
Cons ci ratio: 7.899339e-03	ci left: 8.568387e-01	ci right 8.636589e-01	k: 34411	n:40000
KS ci ratio: 2.155539e-01	ci left: 7.315922e-03	ci right 9.106577e-03	k: 327	n:40000
POTEC   40000 perm   12 sec   (3360 perm/sec)   p_kst 8.175000e-03   p_cons 8.602750e-01   p_joint 3.125000e-02

Joint ci ratio: 8.791672e-02	ci left: 3.655632e-02	ci right 3.993756e-02	k: 1911	n:50000
Cons ci ratio: 7.043423e-03	ci left: 8.579569e-01	ci right 8.640411e-01	k: 43051	n:50000
KS ci ratio: 1.925611e-01	ci left: 7.428193e-03	ci right 9.029691e-03	k: 410	n:50000
POTEC   50000 perm   14 sec   (3503 perm/sec)   p_kst 8.200000e-03   p_cons 8.610200e-01   p_joint 3.822000e-02

Joint ci ratio: 6.550914e-02	ci left: 5.446881e-02	ci right 5.817425e-02	k: 3378	n:60000
Cons ci ratio: 6.424420e-03	ci left: 8.584246e-01	ci right 8.639738e-01	k: 51673	n:60000
KS ci ratio: 1.737006e-01	ci left: 7.685258e-03	ci right 9.162882e-03	k: 504	n:60000
POTEC   60000 perm   17 sec   (3567 perm/sec)   p_kst 8.400000e-03   p_cons 8.612167e-01   p_joint 5.630000e-02

Joint ci ratio: 7.397072e-02	ci left: 3.714285e-02	ci right 4.000985e-02	k: 2699	n:70000
Cons ci ratio: 5.943984e-03	ci left: 8.587894e-01	ci right 8.639234e-01	k: 60296	n:70000
KS ci ratio: 1.607012e-01	ci left: 7.750918e-03	ci right 9.118870e-03	k: 589	n:70000
POTEC   70000 perm   19 sec   (3613 perm/sec)   p_kst 8.414286e-03   p_cons 8.613714e-01   p_joint 3.855714e-02

Joint ci ratio: 5.558059e-02	ci left: 5.690819e-02	ci right 6.017392e-02	k: 4682	n:80000
Cons ci ratio: 5.545723e-03	ci left: 8.595780e-01	ci right 8.643707e-01	k: 68959	n:80000
KS ci ratio: 1.499065e-01	ci left: 7.839369e-03	ci right 9.121659e-03	k: 677	n:80000
POTEC   80000 perm   22 sec   (3633 perm/sec)   p_kst 8.462500e-03   p_cons 8.619875e-01   p_joint 5.852500e-02

Joint ci ratio: 5.454820e-02	ci left: 5.278447e-02	ci right 5.575545e-02	k: 4883	n:90000
Cons ci ratio: 5.224121e-03	ci left: 8.599197e-01	ci right 8.644348e-01	k: 77597	n:90000
KS ci ratio: 1.410306e-01	ci left: 7.910561e-03	ci right 9.121438e-03	k: 765	n:90000
POTEC   90000 perm   25 sec   (3620 perm/sec)   p_kst 8.500000e-03   p_cons 8.621889e-01   p_joint 5.425556e-02

Joint ci ratio: 5.281040e-02	ci left: 5.083927e-02	ci right 5.360678e-02	k: 5221	n:100000
Cons ci ratio: 4.950581e-03	ci left: 8.602997e-01	ci right 8.645792e-01	k: 86245	n:100000
KS ci ratio: 1.351706e-01	ci left: 7.775978e-03	ci right 8.912816e-03	k: 833	n:100000
POTEC   100000 perm   28 sec   (3613 perm/sec)   p_kst 8.330000e-03   p_cons 8.624500e-01   p_joint 5.221000e-02

Joint ci ratio: 5.113329e-02	ci left: 4.941984e-02	ci right 5.202210e-02	k: 5578	n:110000
Cons ci ratio: 4.728412e-03	ci left: 8.599843e-01	ci right 8.640693e-01	k: 94824	n:110000
KS ci ratio: 1.288377e-01	ci left: 7.807506e-03	ci right 8.891383e-03	k: 917	n:110000
POTEC   110000 perm   31 sec   (3599 perm/sec)   p_kst 8.336364e-03   p_cons 8.620364e-01   p_joint 5.070909e-02

Joint ci ratio: 5.073879e-02	ci left: 4.617981e-02	ci right 4.859212e-02	k: 5685	n:120000
Cons ci ratio: 4.523514e-03	ci left: 8.602620e-01	ci right 8.641705e-01	k: 103467	n:120000
KS ci ratio: 1.236929e-01	ci left: 7.786348e-03	ci right 8.820959e-03	k: 995	n:120000
POTEC   120000 perm   34 sec   (3580 perm/sec)   p_kst 8.291667e-03   p_cons 8.622250e-01   p_joint 4.737500e-02

Joint ci ratio: 4.419915e-02	ci left: 5.579143e-02	ci right 5.832068e-02	k: 7416	n:130000
Cons ci ratio: 4.350865e-03	ci left: 8.600745e-01	ci right 8.638324e-01	k: 112055	n:130000
KS ci ratio: 1.184535e-01	ci left: 7.858761e-03	ci right 8.855664e-03	k: 1085	n:130000
POTEC   130000 perm   37 sec   (3551 perm/sec)   p_kst 8.346154e-03   p_cons 8.619615e-01   p_joint 5.704615e-02

Joint ci ratio: 4.307834e-02	ci left: 5.463863e-02	ci right 5.705123e-02	k: 7817	n:140000
Cons ci ratio: 4.184112e-03	ci left: 8.606276e-01	ci right 8.642431e-01	k: 120742	n:140000
KS ci ratio: 1.138280e-01	ci left: 7.921620e-03	ci right 8.884621e-03	k: 1175	n:140000
POTEC   140000 perm   40 sec   (3523 perm/sec)   p_kst 8.392857e-03   p_cons 8.624429e-01   p_joint 5.583571e-02

Joint ci ratio: 4.130372e-02	ci left: 5.547547e-02	ci right 5.782171e-02	k: 8496	n:150000
Cons ci ratio: 4.048866e-03	ci left: 8.602979e-01	ci right 8.637948e-01	k: 129308	n:150000
KS ci ratio: 1.100565e-01	ci left: 7.924874e-03	ci right 8.854279e-03	k: 1257	n:150000
POTEC   150000 perm   43 sec   (3468 perm/sec)   p_kst 8.380000e-03   p_cons 8.620533e-01   p_joint 5.664000e-02

Joint ci ratio: 4.214350e-02	ci left: 5.021786e-02	ci right 5.238593e-02	k: 8207	n:160000
Cons ci ratio: 3.916126e-03	ci left: 8.606082e-01	ci right 8.639912e-01	k: 137969	n:160000
KS ci ratio: 1.069185e-01	ci left: 7.885592e-03	ci right 8.782361e-03	k: 1332	n:160000
POTEC   160000 perm   47 sec   (3436 perm/sec)   p_kst 8.325000e-03   p_cons 8.623063e-01   p_joint 5.129375e-02

Joint ci ratio: 4.049033e-02	ci left: 5.119396e-02	ci right 5.331546e-02	k: 8882	n:170000
Cons ci ratio: 3.803438e-03	ci left: 8.603927e-01	ci right 8.636772e-01	k: 146547	n:170000
KS ci ratio: 1.039601e-01	ci left: 7.862726e-03	ci right 8.730639e-03	k: 1409	n:170000
POTEC   170000 perm   50 sec   (3402 perm/sec)   p_kst 8.288235e-03   p_cons 8.620412e-01   p_joint 5.224706e-02

Joint ci ratio: 3.933746e-02	ci left: 5.125394e-02	ci right 5.331607e-02	k: 9410	n:180000
Cons ci ratio: 3.695015e-03	ci left: 8.605209e-01	ci right 8.637119e-01	k: 155182	n:180000
KS ci ratio: 1.011658e-01	ci left: 7.853536e-03	ci right 8.695749e-03	k: 1488	n:180000
POTEC   180000 perm   53 sec   (3365 perm/sec)   p_kst 8.266667e-03   p_cons 8.621222e-01   p_joint 5.227778e-02

Joint ci ratio: 3.923905e-02	ci left: 4.892519e-02	ci right 5.088857e-02	k: 9481	n:190000
Cons ci ratio: 3.592976e-03	ci left: 8.607953e-01	ci right 8.638989e-01	k: 163847	n:190000
KS ci ratio: 9.852203e-02	ci left: 7.855863e-03	ci right 8.675036e-03	k: 1569	n:190000
POTEC   190000 perm   57 sec   (3322 perm/sec)   p_kst 8.257895e-03   p_cons 8.623526e-01   p_joint 4.990000e-02

Outputting figure to mutsig2_images.part000000000135/POTEC.3_1673_190000_0.0082579_0.86235_0.0499.png
                gene_name: POTEC
               theta_stop: 0.099 
                    nperm: 190000 
                     p_ks: 0.0083 
        ci_ks_bounds_left: 0.0079 
       ci_ks_bounds_right: 0.0087 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.050 
     ci_joint_bounds_left: 0.049 
    ci_joint_bounds_right: 0.051 

Current progress: 33 percent done.
PPBP
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: 5.495838e-02	ci left: 3.278334e-01	ci right 3.464615e-01	k: 3371	n:10000
KS ci ratio: 4.122148e-02	ci left: 4.649712e-01	ci right 4.846435e-01	k: 4748	n:10000
PPBP   10000 perm   1 sec   (6793 perm/sec)   p_kst 4.748000e-01   p_cons 3.371000e-01   p_joint 3.819000e-01

Outputting figure to mutsig2_images.part000000000135/PPBP.2_399_10000_0.4748_0.3371_0.3819.png
                gene_name: PPBP
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.35 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 67 percent done.
PPEF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.552846e-02	ci left: 8.575336e-01	ci right 8.710534e-01	k: 8644	n:10000
Cons ci ratio: 1.673316e-02	ci left: 8.386731e-01	ci right 8.529249e-01	k: 8459	n:10000
KS ci ratio: 3.120255e-02	ci left: 6.024681e-01	ci right 6.216665e-01	k: 6121	n:10000
PPEF2   10000 perm   2 sec   (5551 perm/sec)   p_kst 6.121000e-01   p_cons 8.459000e-01   p_joint 8.644000e-01

Outputting figure to mutsig2_images.part000000000135/PPEF2.2_2326_10000_0.6121_0.8459_0.8644.png
                gene_name: PPEF2
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.85 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

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.165.3896/
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/181708/iteration1/scatter.0000000135
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 135 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120175: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000136> was used as the working directory.
Started at Wed Oct 10 10:44:33 2012
Results reported at Wed Oct 10 10:46:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000136.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000136.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 136  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    131.50 sec.
    Max Memory :      1153 MB
    Max Swap   :      3777 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.165.3896/
-whichjob
136
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 136: processing genes 12214 - 12304
Calculating significance of each gene.
Using projection method.
12214	PPM1M	1
12215	PPM1N	1
12216	PPME1	1
12217	PPOX	1.654616e-01
12218	PPP1CA	1.782296e-01
12219	PPP1CB	1
12220	PPP1CC	1
12221	PPP1R10	1
12222	PPP1R11	1
12223	PPP1R12A	1
12224	PPP1R12B	2.839006e-01
12225	PPP1R12C	1
12226	PPP1R13B	1
12227	PPP1R13L	2.130004e-01
12228	PPP1R14A	1
12229	PPP1R14B	1
12230	PPP1R14C	1
12231	PPP1R14D	1
12232	PPP1R15A	3.139028e-01
12233	PPP1R15B	3.374234e-01
12234	PPP1R16A	1
12235	PPP1R16B	1
12236	PPP1R1A	1
12237	PPP1R1B	1
12238	PPP1R1C	1
12239	PPP1R2	9.900677e-03
12240	PPP1R3A	1
12241	PPP1R3B	1
12242	PPP1R3C	1
12243	PPP1R3D	7.307656e-02
12244	PPP1R3F	1
12245	PPP1R7	1
12246	PPP1R8	1
12247	PPP1R9A	2.932988e-02
12248	PPP1R9B	1
12249	PPP2CA	1
12250	PPP2CB	1
12251	PPP2R1A	1
12252	PPP2R1B	4.053678e-02
12253	PPP2R2A	1
12254	PPP2R2B	1
12255	PPP2R2C	5.250572e-02
12256	PPP2R2D	1
12257	PPP2R3A	3.875192e-01
12258	PPP2R3B	1
12259	PPP2R3C	1
12260	PPP2R4	1
12261	PPP2R5A	1
12262	PPP2R5B	1
12263	PPP2R5C	1
12264	PPP2R5D	2.176614e-01
12265	PPP2R5E	1
12266	PPP3CA	5.552075e-02
12267	PPP3CB	2.070396e-01
12268	PPP3CC	1
12269	PPP3R1	1
12270	PPP3R2	1
12271	PPP4C	1
12272	PPP4R1	1
12273	PPP4R2	5.277703e-02
12274	PPP4R4	1
12275	PPP5C	1
12276	PPP6C	1
12277	PPPDE1	1
12278	PPPDE2	1
12279	PPRC1	1
12280	PPT1	1
12281	PPT2	1.192523e-01
12282	PPTC7	1
12283	PPWD1	1
12284	PPY	1
12285	PPYR1	1
12286	PQBP1	1
12287	PQLC1	1
12288	PQLC2	1.311695e-01
12289	PQLC3	1
12290	PRAC	1
12291	PRAF2	1
12292	PRAM1	1
12293	PRAME	1
12294	PRAMEF1	1
12295	PRAMEF10	1
12296	PRAMEF11	1
12297	PRAMEF12	1
12298	PRAMEF13	1
12299	PRAMEF14	1
12300	PRAMEF16	1
12301	PRAMEF17	1
12302	PRAMEF18	1
12303	PRAMEF19	1
12304	PRAMEF2	1
Done

Running MutSig 2:
Scatter job 136: processing genes 12214 - 12304
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PPP1CA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.865137e-01	ci left: 3.834345e-02	ci right 4.632594e-02	k: 422	n:10000
Cons ci ratio: 3.823649e-01	ci left: 8.414755e-03	ci right 1.247803e-02	k: 103	n:10000
KS ci ratio: 1.323893e-01	ci left: 7.524035e-02	ci right 8.600545e-02	k: 805	n:10000
PPP1CA   10000 perm   2 sec   (5744 perm/sec)   p_kst 8.050000e-02   p_cons 1.030000e-02   p_joint 4.220000e-02

Joint ci ratio: 1.014209e-01	ci left: 6.596456e-02	ci right 7.306121e-02	k: 1389	n:20000
Cons ci ratio: 2.822767e-01	ci left: 8.202300e-03	ci right 1.094312e-02	k: 190	n:20000
KS ci ratio: 9.513196e-02	ci left: 7.451555e-02	ci right 8.200761e-02	k: 1564	n:20000
PPP1CA   20000 perm   6 sec   (3245 perm/sec)   p_kst 7.820000e-02   p_cons 9.500000e-03   p_joint 6.945000e-02

Joint ci ratio: 7.623155e-02	ci left: 7.790390e-02	ci right 8.411086e-02	k: 2429	n:30000
Cons ci ratio: 2.274923e-01	ci left: 8.684843e-03	ci right 1.094494e-02	k: 293	n:30000
KS ci ratio: 7.764855e-02	ci left: 7.525161e-02	ci right 8.136369e-02	k: 2348	n:30000
PPP1CA   30000 perm   8 sec   (3747 perm/sec)   p_kst 7.826667e-02   p_cons 9.766667e-03   p_joint 8.096667e-02

Joint ci ratio: 8.303548e-02	ci left: 5.057944e-02	ci right 5.498577e-02	k: 2110	n:40000
Cons ci ratio: 1.942806e-01	ci left: 9.095716e-03	ci right 1.107638e-02	k: 402	n:40000
KS ci ratio: 6.640977e-02	ci left: 7.745791e-02	ci right 8.280323e-02	k: 3204	n:40000
PPP1CA   40000 perm   10 sec   (4037 perm/sec)   p_kst 8.010000e-02   p_cons 1.005000e-02   p_joint 5.275000e-02

Joint ci ratio: 7.398489e-02	ci left: 5.118984e-02	ci right 5.514224e-02	k: 2657	n:50000
Cons ci ratio: 1.735529e-01	ci left: 9.222959e-03	ci right 1.099461e-02	k: 504	n:50000
KS ci ratio: 5.951397e-02	ci left: 7.745894e-02	ci right 8.222998e-02	k: 3991	n:50000
PPP1CA   50000 perm   12 sec   (4206 perm/sec)   p_kst 7.982000e-02   p_cons 1.008000e-02   p_joint 5.314000e-02

Joint ci ratio: 5.981450e-02	ci left: 6.479844e-02	ci right 6.881025e-02	k: 4007	n:60000
Cons ci ratio: 1.575152e-01	ci left: 9.411444e-03	ci right 1.103645e-02	k: 612	n:60000
KS ci ratio: 5.456668e-02	ci left: 7.703478e-02	ci right 8.137269e-02	k: 4751	n:60000
PPP1CA   60000 perm   14 sec   (4297 perm/sec)   p_kst 7.918333e-02   p_cons 1.020000e-02   p_joint 6.678333e-02

Joint ci ratio: 4.668598e-02	ci left: 8.935983e-02	ci right 9.364553e-02	k: 6404	n:70000
Cons ci ratio: 1.449293e-01	ci left: 9.592809e-03	ci right 1.110534e-02	k: 723	n:70000
KS ci ratio: 5.031719e-02	ci left: 7.777463e-02	ci right 8.180315e-02	k: 5584	n:70000
PPP1CA   70000 perm   16 sec   (4330 perm/sec)   p_kst 7.977143e-02   p_cons 1.032857e-02   p_joint 9.148571e-02

Joint ci ratio: 3.487477e-02	ci left: 1.340038e-01	ci right 1.387726e-01	k: 10910	n:80000
Cons ci ratio: 1.352744e-01	ci left: 9.684396e-03	ci right 1.110145e-02	k: 830	n:80000
KS ci ratio: 4.713111e-02	ci left: 7.770866e-02	ci right 8.147190e-02	k: 6366	n:80000
PPP1CA   80000 perm   18 sec   (4327 perm/sec)   p_kst 7.957500e-02   p_cons 1.037500e-02   p_joint 1.363750e-01

Joint ci ratio: 4.156327e-02	ci left: 8.807195e-02	ci right 9.182119e-02	k: 8094	n:90000
Cons ci ratio: 1.277366e-01	ci left: 9.693676e-03	ci right 1.102706e-02	k: 931	n:90000
KS ci ratio: 4.446897e-02	ci left: 7.770767e-02	ci right 8.125282e-02	k: 7152	n:90000
PPP1CA   90000 perm   21 sec   (4314 perm/sec)   p_kst 7.946667e-02   p_cons 1.034444e-02   p_joint 8.993333e-02

Joint ci ratio: 3.986152e-02	ci left: 8.641958e-02	ci right 8.994435e-02	k: 8817	n:100000
Cons ci ratio: 1.209197e-01	ci left: 9.770757e-03	ci right 1.103788e-02	k: 1039	n:100000
KS ci ratio: 4.228468e-02	ci left: 7.746414e-02	ci right 8.082032e-02	k: 7913	n:100000
PPP1CA   100000 perm   23 sec   (4289 perm/sec)   p_kst 7.913000e-02   p_cons 1.039000e-02   p_joint 8.817000e-02

Joint ci ratio: 3.069299e-02	ci left: 1.271508e-01	ci right 1.311233e-01	k: 14204	n:110000
Cons ci ratio: 8.907898e-02	ci left: 1.652879e-02	ci right 1.807863e-02	k: 1902	n:110000
KS ci ratio: 4.031788e-02	ci left: 7.753864e-02	ci right 8.073814e-02	k: 8704	n:110000
PPP1CA   110000 perm   26 sec   (4256 perm/sec)   p_kst 7.912727e-02   p_cons 1.729091e-02   p_joint 1.291273e-01

Outputting figure to mutsig2_images.part000000000136/PPP1CA.3_1054_110000_0.079127_0.017291_0.12913.png
                gene_name: PPP1CA
               theta_stop: 0.089 
                    nperm: 110000 
                     p_ks: 0.079 
        ci_ks_bounds_left: 0.078 
       ci_ks_bounds_right: 0.081 
                   p_cons: 0.017 
      ci_cons_bounds_left: 0.017 
     ci_cons_bounds_right: 0.018 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.13 

Current progress: 25 percent done.
PPP1R9A
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: 1.423304e-01	ci left: 6.546168e-02	ci right 7.559023e-02	k: 704	n:10000
KS ci ratio: 3.175713e-02	ci left: 5.940342e-01	ci right 6.133054e-01	k: 6037	n:10000
PPP1R9A   10000 perm   2 sec   (4646 perm/sec)   p_kst 6.037000e-01   p_cons 7.040000e-02   p_joint 3.701000e-01

Joint ci ratio: 3.681032e-02	ci left: 3.551359e-01	ci right 3.685043e-01	k: 7236	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: 2.247565e-02	ci left: 5.964804e-01	ci right 6.100896e-01	k: 12066	n:20000
PPP1R9A   20000 perm   4 sec   (4469 perm/sec)   p_kst 6.033000e-01   p_cons 7.115000e-02   p_joint 3.618000e-01

Joint ci ratio: 4.118898e-02	ci left: 2.271006e-01	ci right 2.366847e-01	k: 6956	n:30000
Cons ci ratio: 8.429725e-02	ci left: 6.439222e-02	ci right 7.009194e-02	k: 2016	n:30000
KS ci ratio: 1.842711e-02	ci left: 5.957666e-01	ci right 6.068805e-01	k: 18040	n:30000
PPP1R9A   30000 perm   7 sec   (4358 perm/sec)   p_kst 6.013333e-01   p_cons 6.720000e-02   p_joint 2.318667e-01

Outputting figure to mutsig2_images.part000000000136/PPP1R9A.3_4229_30000_0.60133_0.0672_0.23187.png
                gene_name: PPP1R9A
               theta_stop: 0.084 
                    nperm: 30000 
                     p_ks: 0.60 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.067 
      ci_cons_bounds_left: 0.064 
     ci_cons_bounds_right: 0.070 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.24 

Current progress: 50 percent done.
PPP1R15B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.072075e-02	ci left: 4.710641e-01	ci right 4.907470e-01	k: 4809	n:10000
Cons ci ratio: 5.197341e-02	ci left: 3.530692e-01	ci right 3.720109e-01	k: 3625	n:10000
KS ci ratio: 8.814885e-02	ci left: 1.577733e-01	ci right 1.724223e-01	k: 1650	n:10000
PPP1R15B   10000 perm   2 sec   (6455 perm/sec)   p_kst 1.650000e-01   p_cons 3.625000e-01   p_joint 4.809000e-01

Outputting figure to mutsig2_images.part000000000136/PPP1R15B.2_2150_10000_0.165_0.3625_0.4809.png
                gene_name: PPP1R15B
               theta_stop: 0.088 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.36 
      ci_cons_bounds_left: 0.35 
     ci_cons_bounds_right: 0.37 
                  p_joint: 0.48 
     ci_joint_bounds_left: 0.47 
    ci_joint_bounds_right: 0.49 

Current progress: 75 percent done.
PPP2R1B
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: 4.816114e-02	ci left: 3.887854e-01	ci right 4.080738e-01	k: 3984	n:10000
KS ci ratio: 1.364354e-02	ci left: 8.857521e-01	ci right 8.980186e-01	k: 8920	n:10000
PPP2R1B   10000 perm   2 sec   (6216 perm/sec)   p_kst 8.920000e-01   p_cons 3.984000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000136/PPP2R1B.2_2089_10000_0.892_0.3984_1.png
                gene_name: PPP2R1B
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000136
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 136 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120179: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000137> was used as the working directory.
Started at Wed Oct 10 10:44:39 2012
Results reported at Wed Oct 10 10:46:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000137.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000137.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 137  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    129.61 sec.
    Max Memory :       943 MB
    Max Swap   :      3747 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.165.3896/
-whichjob
137
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 137: processing genes 12305 - 12394
Calculating significance of each gene.
Using projection method.
12305	PRAMEF4	1
12306	PRAP1	1
12307	PRB1	1
12308	PRB2	8.794497e-02
12309	PRB3	1
12310	PRB4	1
12311	PRC1	7.537074e-02
12312	PRCC	1
12313	PRCD	1
12314	PRCP	1.026532e-01
12315	PRDM1	2.472855e-01
12316	PRDM10	1
12317	PRDM11	1
12318	PRDM12	1
12319	PRDM13	1
12320	PRDM14	7.269071e-02
12321	PRDM15	3.972830e-01
12322	PRDM16	2.272672e-02
12323	PRDM2	2.240398e-01
12324	PRDM4	1
12325	PRDM5	1.442390e-01
12326	PRDM7	1
12327	PRDM8	1
12328	PRDM9	1
12329	PRDX1	1
12330	PRDX2	1
12331	PRDX3	1
12332	PRDX4	1
12333	PRDX5	1
12334	PRDX6	2.227260e-02
12335	PREB	1
12336	PRELID1	1
12337	PRELID2	1
12338	PRELP	1
12339	PREP	1
12340	PREPL	1
12341	PREX1	4.417616e-01
12342	PREX2	1.524577e-01
12343	PRF1	1.071262e-03
12344	PRG2	1.063981e-01
12345	PRG3	1
12346	PRG4	4.156853e-01
12347	PRH1	1
12348	PRH2	1
12349	PRHOXNB	1
12350	PRIC285	4.861770e-01
12351	PRICKLE1	2.453835e-01
12352	PRICKLE2	1
12353	PRICKLE3	1
12354	PRICKLE4	1
12355	PRIM1	1
12356	PRIM2	1
12357	PRIMA1	1
12358	PRKAA1	1
12359	PRKAA2	1
12360	PRKAB1	1
12361	PRKAB2	1
12362	PRKACA	1
12363	PRKACB	1
12364	PRKACG	1
12365	PRKAG1	1
12366	PRKAG2	1
12367	PRKAG3	1
12368	PRKAR1A	1
12369	PRKAR1B	1
12370	PRKAR2A	1
12371	PRKAR2B	1
12372	PRKCA	1
12373	PRKCB	1.458093e-01
12374	PRKCD	1
12375	PRKCDBP	1
12376	PRKCE	1
12377	PRKCG	1.527945e-01
12378	PRKCH	1
12379	PRKCI	1
12380	PRKCQ	1
12381	PRKCSH	1
12382	PRKCZ	1
12383	PRKD1	3.163900e-02
12384	PRKD2	3.376919e-01
12385	PRKD3	1
12386	PRKDC	1
12387	PRKG1	1
12388	PRKG2	1
12389	PRKRA	1
12390	PRKRIP1	1
12391	PRKRIR	1
12392	PRKX	1
12393	PRL	1
12394	PRLH	1
Done

Running MutSig 2:
Scatter job 137: processing genes 12305 - 12394
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PRDM16
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.326853e-02	ci left: 3.418387e-01	ci right 3.606481e-01	k: 3512	n:10000
Cons ci ratio: 1.210554e-01	ci left: 8.912712e-02	ci right 1.007101e-01	k: 948	n:10000
KS ci ratio: 3.270783e-02	ci left: 5.797835e-01	ci right 5.991643e-01	k: 5895	n:10000
PRDM16   10000 perm   3 sec   (3573 perm/sec)   p_kst 5.895000e-01   p_cons 9.480000e-02   p_joint 3.512000e-01

Joint ci ratio: 4.259916e-02	ci left: 2.910697e-01	ci right 3.037893e-01	k: 5948	n:20000
Cons ci ratio: 8.296989e-02	ci left: 9.621914e-02	ci right 1.045974e-01	k: 2007	n:20000
KS ci ratio: 2.329687e-02	ci left: 5.791367e-01	ci right 5.928383e-01	k: 11720	n:20000
PRDM16   20000 perm   7 sec   (2745 perm/sec)   p_kst 5.860000e-01   p_cons 1.003500e-01   p_joint 2.974000e-01

Outputting figure to mutsig2_images.part000000000137/PRDM16.3_3899_20000_0.586_0.10035_0.2974.png
                gene_name: PRDM16
               theta_stop: 0.083 
                    nperm: 20000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.59 
                   p_cons: 0.10 
      ci_cons_bounds_left: 0.096 
     ci_cons_bounds_right: 0.10 
                  p_joint: 0.30 
     ci_joint_bounds_left: 0.29 
    ci_joint_bounds_right: 0.30 

Current progress: 25 percent done.
PRF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.584152e-02	ci left: 5.347774e-01	ci right 5.543966e-01	k: 5446	n:10000
Cons ci ratio: 2.689535e-02	ci left: 6.706551e-01	ci right 6.890400e-01	k: 6799	n:10000
KS ci ratio: 4.873855e-02	ci left: 3.831109e-01	ci right 4.023516e-01	k: 3927	n:10000
PRF1   10000 perm   2 sec   (5140 perm/sec)   p_kst 3.927000e-01   p_cons 6.799000e-01   p_joint 5.446000e-01

Outputting figure to mutsig2_images.part000000000137/PRF1.3_1676_10000_0.3927_0.6799_0.5446.png
                gene_name: PRF1
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 50 percent done.
PREX2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.415534e-02	ci left: 2.102365e-01	ci right 2.265279e-01	k: 2183	n:10000
Cons ci ratio: 8.783046e-02	ci left: 1.587554e-01	ci right 1.734397e-01	k: 1660	n:10000
KS ci ratio: 1.988809e-02	ci left: 7.872564e-01	ci right 8.031712e-01	k: 7953	n:10000
PREX2   10000 perm   2 sec   (4923 perm/sec)   p_kst 7.953000e-01   p_cons 1.660000e-01   p_joint 2.183000e-01

Outputting figure to mutsig2_images.part000000000137/PREX2.2_5210_10000_0.7953_0.166_0.2183.png
                gene_name: PREX2
               theta_stop: 0.088 
                    nperm: 10000 
                     p_ks: 0.80 
        ci_ks_bounds_left: 0.79 
       ci_ks_bounds_right: 0.80 
                   p_cons: 0.17 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.23 

Current progress: 75 percent done.
PRKD1
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: 3.677630e-02	ci left: 5.219620e-01	ci right 5.416195e-01	k: 5318	n:10000
KS ci ratio: 2.814575e-02	ci left: 6.504187e-01	ci right 6.690882e-01	k: 6598	n:10000
PRKD1   10000 perm   2 sec   (5731 perm/sec)   p_kst 6.598000e-01   p_cons 5.318000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000137/PRKD1.2_2811_10000_0.6598_0.5318_1.png
                gene_name: PRKD1
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   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.165.3896/
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/181708/iteration1/scatter.0000000137
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 137 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120182: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000138> was used as the working directory.
Started at Wed Oct 10 10:44:39 2012
Results reported at Wed Oct 10 10:46:28 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000138.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000138.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 138  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    104.64 sec.
    Max Memory :       916 MB
    Max Swap   :      3678 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.165.3896/
-whichjob
138
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 138: processing genes 12395 - 12485
Calculating significance of each gene.
Using projection method.
12395	PRLHR	1
12396	PRLR	1
12397	PRM1	1
12398	PRM2	1
12399	PRM3	1
12400	PRMT1	1
12401	PRMT10	1
12402	PRMT2	1
12403	PRMT3	1
12404	PRMT5	1
12405	PRMT6	1.356444e-01
12406	PRMT7	1
12407	PRMT8	1
12408	PRND	1
12409	PRNP	1
12410	PROC	1
12411	PROCA1	2.463532e-02
12412	PROCR	1
12413	PRODH	1
12414	PRODH2	1
12415	PROK1	1
12416	PROK2	1
12417	PROKR1	1
12418	PROKR2	1
12419	PROL1	1
12420	PROM1	1
12421	PROM2	2.429438e-01
12422	PROP1	1
12423	PROS1	1.710952e-01
12424	PROSC	1
12425	PROX1	1
12426	PROX2	1
12427	PROZ	1
12428	PRPF18	1
12429	PRPF19	1.929909e-01
12430	PRPF3	2.692761e-01
12431	PRPF31	1.191484e-01
12432	PRPF38A	1
12433	PRPF38B	1
12434	PRPF39	1
12435	PRPF4	1
12436	PRPF40A	2.891542e-01
12437	PRPF40B	1
12438	PRPF4B	1
12439	PRPF6	1
12440	PRPF8	1
12441	PRPH	1
12442	PRPH2	1
12443	PRPS1	1
12444	PRPS1L1	1
12445	PRPS2	1
12446	PRPSAP1	1
12447	PRPSAP2	1
12448	PRR11	1
12449	PRR12	4.490185e-01
12450	PRR13	4.061263e-02
12451	PRR14	1
12452	PRR15	1
12453	PRR15L	1
12454	PRR16	9.566271e-02
12455	PRR18	1
12456	PRR19	1
12457	PRR21	1
12458	PRR22	5.963095e-02
12459	PRR23A	1
12460	PRR23B	6.959161e-02
12461	PRR23C	1
12462	PRR25	1
12463	PRR3	1
12464	PRR4	1
12465	PRR5	1
12466	PRR5-ARHGAP8	1
12467	PRR5L	1
12468	PRR7	1
12469	PRRC1	1
12470	PRRG1	1
12471	PRRG2	1
12472	PRRG3	1
12473	PRRG4	1.050395e-01
12474	PRRT1	1
12475	PRRT2	1
12476	PRRT3	1
12477	PRRX1	1
12478	PRRX2	1
12479	PRSS1	1
12480	PRSS12	7.214064e-02
12481	PRSS16	1
12482	PRSS2	1
12483	PRSS21	1
12484	PRSS22	1
12485	PRSS23	1
Done

Running MutSig 2:
Scatter job 138: processing genes 12395 - 12485
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.165.3896/
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/181708/iteration1/scatter.0000000138
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 138 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120184: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000139> was used as the working directory.
Started at Wed Oct 10 10:44:39 2012
Results reported at Wed Oct 10 10:46:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000139.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000139.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 139  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    118.46 sec.
    Max Memory :       881 MB
    Max Swap   :      3672 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.165.3896/
-whichjob
139
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 139: processing genes 12486 - 12575
Calculating significance of each gene.
Using projection method.
12486	PRSS27	1
12487	PRSS3	1
12488	PRSS33	1
12489	PRSS35	1
12490	PRSS36	1
12491	PRSS37	1
12492	PRSS38	1
12493	PRSS42	1
12494	PRSS45	1
12495	PRSS48	2.302370e-02
12496	PRSS50	1
12497	PRSS53	1
12498	PRSS54	1.891021e-01
12499	PRSS55	1
12500	PRSS8	1
12501	PRSSL1	1
12502	PRTFDC1	1
12503	PRTG	1
12504	PRTN3	4.711731e-02
12505	PRUNE	1
12506	PRUNE2	1
12507	PRX	1.535321e-02
12508	PSAP	1
12509	PSAT1	1
12510	PSCA	1
12511	PSD	1
12512	PSD2	1
12513	PSD3	4.205939e-01
12514	PSD4	4.189773e-01
12515	PSEN1	2.232769e-01
12516	PSEN2	1
12517	PSENEN	1
12518	PSG1	1
12519	PSG11	1
12520	PSG2	1
12521	PSG3	2.083627e-01
12522	PSG4	1
12523	PSG5	1
12524	PSG6	8.512960e-02
12525	PSG7	1
12526	PSG8	1
12527	PSG9	1
12528	PSIP1	1
12529	PSKH1	1
12530	PSKH2	1.648244e-01
12531	PSMA1	1
12532	PSMA2	1
12533	PSMA3	1
12534	PSMA4	1
12535	PSMA5	1
12536	PSMA6	1.216303e-01
12537	PSMA7	1
12538	PSMA8	1
12539	PSMB1	1
12540	PSMB10	1
12541	PSMB11	1
12542	PSMB2	1
12543	PSMB3	1
12544	PSMB4	1
12545	PSMB5	1
12546	PSMB6	1
12547	PSMB7	1
12548	PSMB8	5.796878e-02
12549	PSMB9	1
12550	PSMC1	1
12551	PSMC2	1
12552	PSMC3	1.735623e-01
12553	PSMC3IP	1
12554	PSMC4	1
12555	PSMC5	1
12556	PSMC6	1
12557	PSMD1	1
12558	PSMD10	1
12559	PSMD11	1
12560	PSMD12	6.403308e-02
12561	PSMD13	1
12562	PSMD14	1
12563	PSMD2	1
12564	PSMD3	1
12565	PSMD4	1
12566	PSMD5	1
12567	PSMD6	1
12568	PSMD7	1
12569	PSMD8	1
12570	PSMD9	1
12571	PSME1	1.271761e-01
12572	PSME2	1
12573	PSME3	1
12574	PSME4	3.050375e-01
12575	PSMF1	1
Done

Running MutSig 2:
Scatter job 139: processing genes 12486 - 12575
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PRX
Processing conservation and coverage...
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: 1.845427e-02	ci left: 8.109049e-01	ci right 8.261091e-01	k: 8186	n:10000
KS ci ratio: 9.349504e-02	ci left: 1.424659e-01	ci right 1.565389e-01	k: 1494	n:10000
PRX   10000 perm   2 sec   (4178 perm/sec)   p_kst 1.494000e-01   p_cons 8.186000e-01   p_joint 2.437000e-01

Outputting figure to mutsig2_images.part000000000139/PRX.9_4465_10000_0.1494_0.8186_0.2437.png
                gene_name: PRX
               theta_stop: 0.093 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.82 
      ci_cons_bounds_left: 0.81 
     ci_cons_bounds_right: 0.83 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.25 

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.165.3896/
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/181708/iteration1/scatter.0000000139
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 139 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120188: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000140> was used as the working directory.
Started at Wed Oct 10 10:44:39 2012
Results reported at Wed Oct 10 10:47:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000140.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000140.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 140  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    165.09 sec.
    Max Memory :      1351 MB
    Max Swap   :      3853 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.165.3896/
-whichjob
140
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 140: processing genes 12576 - 12666
Calculating significance of each gene.
Using projection method.
12576	PSMG1	5.669244e-02
12577	PSMG2	1
12578	PSMG3	1
12579	PSORS1C1	1
12580	PSORS1C2	1
12581	PSPC1	3.237281e-02
12582	PSPH	1
12583	PSPN	1
12584	PSRC1	1
12585	PSTK	1
12586	PSTPIP1	1
12587	PSTPIP2	1
12588	PTAFR	1
12589	PTAR1	1
12590	PTBP1	1
12591	PTBP2	1
12592	PTCD1	1
12593	PTCD2	1
12594	PTCD3	1
12595	PTCH1	1.834369e-01
12596	PTCH2	1
12597	PTCHD1	1.729105e-01
12598	PTCHD2	1
12599	PTCHD3	1
12600	PTCRA	1
12601	PTDSS1	1
12602	PTDSS2	1
12603	PTEN	1
12604	PTER	1
12605	PTF1A	1
12606	PTGDR	6.553418e-02
12607	PTGDS	1
12608	PTGER2	1
12609	PTGER3	1
12610	PTGER4	2.456097e-02
12611	PTGES	1
12612	PTGES2	1
12613	PTGES3	1
12614	PTGFR	1
12615	PTGFRN	1
12616	PTGIR	7.479946e-02
12617	PTGIS	1
12618	PTGR1	1
12619	PTGR2	1
12620	PTGS1	1
12621	PTGS2	1
12622	PTH	1
12623	PTH1R	2.382271e-02
12624	PTH2	1
12625	PTH2R	1
12626	PTHLH	1
12627	PTK2	3.980064e-01
12628	PTK2B	1
12629	PTK6	1
12630	PTK7	1
12631	PTMA	1
12632	PTMS	1
12633	PTN	8.965776e-02
12634	PTOV1	1
12635	PTP4A1	1
12636	PTP4A2	3.245709e-02
12637	PTP4A3	1
12638	PTPDC1	3.592609e-01
12639	PTPLA	1
12640	PTPLAD1	1
12641	PTPLAD2	1
12642	PTPLB	1
12643	PTPMT1	1
12644	PTPN1	1
12645	PTPN11	1
12646	PTPN12	2.113823e-01
12647	PTPN13	5.795884e-01
12648	PTPN14	1.624843e-01
12649	PTPN18	1
12650	PTPN2	1
12651	PTPN21	4.410269e-01
12652	PTPN22	1.373632e-01
12653	PTPN23	1
12654	PTPN3	3.087793e-01
12655	PTPN4	2.489591e-01
12656	PTPN5	1
12657	PTPN6	1
12658	PTPN7	5.189697e-02
12659	PTPN9	2.207267e-01
12660	PTPRA	1
12661	PTPRB	6.035381e-01
12662	PTPRC	1.210235e-01
12663	PTPRCAP	1
12664	PTPRD	1
12665	PTPRE	1
12666	PTPRF	1
Done

Running MutSig 2:
Scatter job 140: processing genes 12576 - 12666
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PSMG1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.326693e-02	ci left: 2.685418e-01	ci right 2.861881e-01	k: 2773	n:10000
Cons ci ratio: 1.535590e-02	ci left: 8.601875e-01	ci right 8.735980e-01	k: 8670	n:10000
KS ci ratio: 1.640648e-01	ci left: 4.955445e-02	ci right 5.850759e-02	k: 539	n:10000
PSMG1   10000 perm   2 sec   (5014 perm/sec)   p_kst 5.390000e-02   p_cons 8.670000e-01   p_joint 2.773000e-01

Joint ci ratio: 4.764749e-02	ci left: 2.467879e-01	ci right 2.588840e-01	k: 5056	n:20000
Cons ci ratio: 1.089262e-02	ci left: 8.614544e-01	ci right 8.709389e-01	k: 17325	n:20000
KS ci ratio: 1.142902e-01	ci left: 5.236672e-02	ci right 5.876326e-02	k: 1110	n:20000
PSMG1   20000 perm   7 sec   (2847 perm/sec)   p_kst 5.550000e-02   p_cons 8.662500e-01   p_joint 2.528000e-01

Joint ci ratio: 3.922768e-02	ci left: 2.448098e-01	ci right 2.546387e-01	k: 7491	n:30000
Cons ci ratio: 8.963125e-03	ci left: 8.605076e-01	ci right 8.682883e-01	k: 25933	n:30000
KS ci ratio: 9.444866e-02	ci left: 5.172973e-02	ci right 5.689034e-02	k: 1628	n:30000
PSMG1   30000 perm   9 sec   (3188 perm/sec)   p_kst 5.426667e-02   p_cons 8.644333e-01   p_joint 2.497000e-01

Outputting figure to mutsig2_images.part000000000140/PSMG1.2_895_30000_0.054267_0.86443_0.2497.png
                gene_name: PSMG1
               theta_stop: 0.094 
                    nperm: 30000 
                     p_ks: 0.054 
        ci_ks_bounds_left: 0.052 
       ci_ks_bounds_right: 0.057 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.87 
                  p_joint: 0.25 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.25 

Current progress: 17 percent done.
PSPC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.579244e-02	ci left: 3.211817e-01	ci right 3.397172e-01	k: 3304	n:10000
Cons ci ratio: 5.574205e-02	ci left: 3.215787e-01	ci right 3.401199e-01	k: 3308	n:10000
KS ci ratio: 7.909067e-02	ci left: 1.893422e-01	ci right 2.050346e-01	k: 1971	n:10000
PSPC1   10000 perm   2 sec   (5539 perm/sec)   p_kst 1.971000e-01   p_cons 3.308000e-01   p_joint 3.304000e-01

Outputting figure to mutsig2_images.part000000000140/PSPC1.2_1608_10000_0.1971_0.3308_0.3304.png
                gene_name: PSPC1
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.33 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.34 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 33 percent done.
PTCH1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.320203e-02	ci left: 1.432503e-01	ci right 1.573541e-01	k: 1502	n:10000
Cons ci ratio: 8.260373e-02	ci left: 1.761532e-01	ci right 1.914315e-01	k: 1837	n:10000
KS ci ratio: 1.292744e-01	ci left: 7.873206e-02	ci right 8.971158e-02	k: 841	n:10000
PTCH1   10000 perm   2 sec   (4624 perm/sec)   p_kst 8.410000e-02   p_cons 1.837000e-01   p_joint 1.502000e-01

Joint ci ratio: 5.715669e-02	ci left: 1.849296e-01	ci right 1.958606e-01	k: 3807	n:20000
Cons ci ratio: 5.657024e-02	ci left: 1.880944e-01	ci right 1.990948e-01	k: 3871	n:20000
KS ci ratio: 8.973561e-02	ci left: 8.317825e-02	ci right 9.104227e-02	k: 1741	n:20000
PTCH1   20000 perm   5 sec   (4145 perm/sec)   p_kst 8.705000e-02   p_cons 1.935500e-01   p_joint 1.903500e-01

Outputting figure to mutsig2_images.part000000000140/PTCH1.2_4645_20000_0.08705_0.19355_0.19035.png
                gene_name: PTCH1
               theta_stop: 0.090 
                    nperm: 20000 
                     p_ks: 0.087 
        ci_ks_bounds_left: 0.083 
       ci_ks_bounds_right: 0.091 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.20 

Current progress: 50 percent done.
PTGER4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.314164e-01	ci left: 7.630693e-02	ci right 8.713821e-02	k: 816	n:10000
Cons ci ratio: 8.971560e-02	ci left: 1.530607e-01	ci right 1.675377e-01	k: 1602	n:10000
KS ci ratio: 6.213439e-02	ci left: 2.757699e-01	ci right 2.935557e-01	k: 2846	n:10000
PTGER4   10000 perm   2 sec   (6168 perm/sec)   p_kst 2.846000e-01   p_cons 1.602000e-01   p_joint 8.160000e-02

Joint ci ratio: 4.386048e-02	ci left: 2.790981e-01	ci right 2.916644e-01	k: 5707	n:20000
Cons ci ratio: 6.339240e-02	ci left: 1.553880e-01	ci right 1.656109e-01	k: 3209	n:20000
KS ci ratio: 4.328688e-02	ci left: 2.844623e-01	ci right 2.970986e-01	k: 5815	n:20000
PTGER4   20000 perm   4 sec   (5145 perm/sec)   p_kst 2.907500e-01   p_cons 1.604500e-01   p_joint 2.853500e-01

Outputting figure to mutsig2_images.part000000000140/PTGER4.2_1475_20000_0.29075_0.16045_0.28535.png
                gene_name: PTGER4
               theta_stop: 0.063 
                    nperm: 20000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.30 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.16 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.29 

Current progress: 67 percent done.
PTH1R
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.457943e-02	ci left: 3.309118e-01	ci right 3.495813e-01	k: 3402	n:10000
Cons ci ratio: 1.141993e-01	ci left: 9.934967e-02	ci right 1.114813e-01	k: 1053	n:10000
KS ci ratio: 5.389372e-02	ci left: 3.365732e-01	ci right 3.553166e-01	k: 3459	n:10000
PTH1R   10000 perm   2 sec   (5846 perm/sec)   p_kst 3.459000e-01   p_cons 1.053000e-01   p_joint 3.402000e-01

Joint ci ratio: 4.046215e-02	ci left: 3.128902e-01	ci right 3.258623e-01	k: 6387	n:20000
Cons ci ratio: 8.047557e-02	ci left: 1.017662e-01	ci right 1.103488e-01	k: 2120	n:20000
KS ci ratio: 3.851194e-02	ci left: 3.346277e-01	ci right 3.478185e-01	k: 6824	n:20000
PTH1R   20000 perm   4 sec   (5184 perm/sec)   p_kst 3.412000e-01   p_cons 1.060000e-01   p_joint 3.193500e-01

Outputting figure to mutsig2_images.part000000000140/PTH1R.2_1838_20000_0.3412_0.106_0.31935.png
                gene_name: PTH1R
               theta_stop: 0.080 
                    nperm: 20000 
                     p_ks: 0.34 
        ci_ks_bounds_left: 0.33 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.33 

Current progress: 83 percent done.
PTPRC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.128017e-02	ci left: 1.485467e-01	ci right 1.628545e-01	k: 1556	n:10000
Cons ci ratio: 1.010034e-01	ci left: 1.242496e-01	ci right 1.375662e-01	k: 1308	n:10000
KS ci ratio: 4.307694e-02	ci left: 4.431087e-01	ci right 4.627188e-01	k: 4529	n:10000
PTPRC   10000 perm   2 sec   (4773 perm/sec)   p_kst 4.529000e-01   p_cons 1.308000e-01   p_joint 1.556000e-01

Joint ci ratio: 5.763387e-02	ci left: 1.824080e-01	ci right 1.932829e-01	k: 3756	n:20000
Cons ci ratio: 7.137438e-02	ci left: 1.263528e-01	ci right 1.357547e-01	k: 2620	n:20000
KS ci ratio: 3.005705e-02	ci left: 4.526245e-01	ci right 4.664873e-01	k: 9191	n:20000
PTPRC   20000 perm   5 sec   (4310 perm/sec)   p_kst 4.595500e-01   p_cons 1.310000e-01   p_joint 1.878000e-01

Outputting figure to mutsig2_images.part000000000140/PTPRC.2_4054_20000_0.45955_0.131_0.1878.png
                gene_name: PTPRC
               theta_stop: 0.071 
                    nperm: 20000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  p_joint: 0.19 
     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.165.3896/
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/181708/iteration1/scatter.0000000140
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 140 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1708>
Subject: Job 1120192: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, 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/181708/iteration1/scatter.0000000141> was used as the working directory.
Started at Wed Oct 10 10:44:40 2012
Results reported at Wed Oct 10 10:46:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000141.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000141.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 141  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    124.61 sec.
    Max Memory :      1218 MB
    Max Swap   :      3841 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.165.3896/
-whichjob
141
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 141: processing genes 12667 - 12756
Calculating significance of each gene.
Using projection method.
12667	PTPRG	3.238446e-01
12668	PTPRH	3.013342e-01
12669	PTPRJ	4.672835e-01
12670	PTPRK	3.147351e-01
12671	PTPRM	1
12672	PTPRN	9.116211e-02
12673	PTPRN2	1
12674	PTPRO	1
12675	PTPRR	1
12676	PTPRS	1
12677	PTPRT	5.592461e-02
12678	PTPRU	1.533396e-01
12679	PTPRZ1	5.596932e-01
12680	PTRF	1.746831e-01
12681	PTRH1	1
12682	PTRH2	1
12683	PTS	1
12684	PTTG1	1
12685	PTTG1IP	1
12686	PTTG2	1
12687	PTX3	1
12688	PTX4	1
12689	PUF60	1
12690	PUM1	3.894815e-01
12691	PUM2	1.123292e-01
12692	PURA	1
12693	PURB	1
12694	PURG	1.352579e-01
12695	PUS1	1
12696	PUS10	1
12697	PUS3	1
12698	PUS7	1
12699	PUS7L	1
12700	PUSL1	1
12701	PVALB	1
12702	PVR	1
12703	PVRIG	1
12704	PVRL1	2.464861e-01
12705	PVRL2	1
12706	PVRL3	1
12707	PVRL4	1.028755e-01
12708	PWP1	1.261784e-01
12709	PWP2	1
12710	PWWP2A	1
12711	PWWP2B	1.581265e-01
12712	PXDN	1.305330e-02
12713	PXDNL	1
12714	PXK	9.602262e-02
12715	PXMP2	1
12716	PXMP4	1
12717	PXN	1
12718	PXT1	1
12719	PYCARD	1
12720	PYCR1	1
12721	PYCR2	1
12722	PYCRL	1
12723	PYDC1	1
12724	PYDC2	1
12725	PYGB	1
12726	PYGL	1
12727	PYGM	1
12728	PYGO1	2.152647e-04
12729	PYGO2	8.771653e-02
12730	PYHIN1	2.436620e-01
12731	PYROXD1	1
12732	PYROXD2	1
12733	PYY	1
12734	PZP	1
12735	ProSAPiP1	1
12736	QARS	1
12737	QDPR	1
12738	QKI	1.581206e-01
12739	QPCT	1
12740	QPCTL	1
12741	QPRT	1
12742	QRFP	1
12743	QRFPR	1
12744	QRICH1	1
12745	QRICH2	1
12746	QRSL1	1
12747	QSER1	4.696308e-01
12748	QSOX1	1
12749	QSOX2	1
12750	QTRT1	1.558456e-01
12751	QTRTD1	1
12752	R3HDM1	1.162481e-01
12753	R3HDM2	1.438636e-01
12754	R3HDML	1
12755	RAB10	1
12756	RAB11A	1
Done

Running MutSig 2:
Scatter job 141: processing genes 12667 - 12756
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
PXDN
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.583216e-02	ci left: 6.880881e-01	ci right 7.061970e-01	k: 6972	n:10000
Cons ci ratio: 3.826467e-02	ci left: 5.021507e-01	ci right 5.218423e-01	k: 5120	n:10000
KS ci ratio: 3.002544e-02	ci left: 6.206514e-01	ci right 6.396727e-01	k: 6302	n:10000
PXDN   10000 perm   2 sec   (4950 perm/sec)   p_kst 6.302000e-01   p_cons 5.120000e-01   p_joint 6.972000e-01

Outputting figure to mutsig2_images.part000000000141/PXDN.3_4532_10000_0.6302_0.512_0.6972.png
                gene_name: PXDN
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.51 
      ci_cons_bounds_left: 0.50 
     ci_cons_bounds_right: 0.52 
                  p_joint: 0.70 
     ci_joint_bounds_left: 0.69 
    ci_joint_bounds_right: 0.71 

Current progress: 20 percent done.
PYGO1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.010034e-01	ci left: 1.242496e-01	ci right 1.375662e-01	k: 1308	n:10000
Cons ci ratio: 3.058833e-02	ci left: 6.119096e-01	ci right 6.310196e-01	k: 6215	n:10000
KS ci ratio: 1.240382e-01	ci left: 8.514113e-02	ci right 9.649855e-02	k: 907	n:10000
PYGO1   10000 perm   2 sec   (5354 perm/sec)   p_kst 9.070000e-02   p_cons 6.215000e-01   p_joint 1.308000e-01

Joint ci ratio: 6.584042e-02	ci left: 1.455706e-01	ci right 1.555312e-01	k: 3010	n:20000
Cons ci ratio: 2.166247e-02	ci left: 6.140336e-01	ci right 6.275313e-01	k: 12416	n:20000
KS ci ratio: 8.884463e-02	ci left: 8.474573e-02	ci right 9.267431e-02	k: 1773	n:20000
PYGO1   20000 perm   4 sec   (4820 perm/sec)   p_kst 8.865000e-02   p_cons 6.208000e-01   p_joint 1.505000e-01

Outputting figure to mutsig2_images.part000000000141/PYGO1.3_1272_20000_0.08865_0.6208_0.1505.png
                gene_name: PYGO1
               theta_stop: 0.089 
                    nperm: 20000 
                     p_ks: 0.089 
        ci_ks_bounds_left: 0.085 
       ci_ks_bounds_right: 0.093 
                   p_cons: 0.62 
      ci_cons_bounds_left: 0.61 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.15 
    ci_joint_bounds_right: 0.16 

Current progress: 40 percent done.
PTPRT
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.223756e-03	ci left: 9.722779e-01	ci right 9.784409e-01	k: 9755	n:10000
Cons ci ratio: 8.056948e-02	ci left: 1.836317e-01	ci right 1.991485e-01	k: 1913	n:10000
KS ci ratio: 1.510876e-02	ci left: 8.639656e-01	ci right 8.772177e-01	k: 8707	n:10000
PTPRT   10000 perm   2 sec   (5132 perm/sec)   p_kst 8.707000e-01   p_cons 1.913000e-01   p_joint 9.755000e-01

Outputting figure to mutsig2_images.part000000000141/PTPRT.2_4511_10000_0.8707_0.1913_0.9755.png
                gene_name: PTPRT
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.88 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.98 

Current progress: 60 percent done.
PTPRU
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.328347e-02	ci left: 7.304755e-01	ci right 7.477850e-01	k: 7392	n:10000
Cons ci ratio: 1.368725e-01	ci left: 7.058968e-02	ci right 8.105902e-02	k: 757	n:10000
KS ci ratio: 2.127305e-02	ci left: 7.641548e-01	ci right 7.806862e-01	k: 7725	n:10000
PTPRU   10000 perm   2 sec   (5104 perm/sec)   p_kst 7.725000e-01   p_cons 7.570000e-02   p_joint 7.392000e-01

Joint ci ratio: 1.636806e-02	ci left: 7.353222e-01	ci right 7.475076e-01	k: 14829	n:20000
Cons ci ratio: 9.490190e-02	ci left: 7.485789e-02	ci right 8.236516e-02	k: 1571	n:20000
KS ci ratio: 1.504014e-02	ci left: 7.666761e-01	ci right 7.783446e-01	k: 15451	n:20000
PTPRU   20000 perm   4 sec   (4629 perm/sec)   p_kst 7.725500e-01   p_cons 7.855000e-02   p_joint 7.414500e-01

Outputting figure to mutsig2_images.part000000000141/PTPRU.2_4487_20000_0.77255_0.07855_0.74145.png
                gene_name: PTPRU
               theta_stop: 0.095 
                    nperm: 20000 
                     p_ks: 0.77 
        ci_ks_bounds_left: 0.77 
       ci_ks_bounds_right: 0.78 
                   p_cons: 0.079 
      ci_cons_bounds_left: 0.075 
     ci_cons_bounds_right: 0.082 
                  p_joint: 0.74 
     ci_joint_bounds_left: 0.74 
    ci_joint_bounds_right: 0.75 

Current progress: 80 percent done.
R3HDM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.309951e-02	ci left: 8.935428e-01	ci right 9.054233e-01	k: 8996	n:10000
Cons ci ratio: 2.166601e-02	ci left: 7.575753e-01	ci right 7.742695e-01	k: 7660	n:10000
KS ci ratio: 2.300583e-02	ci left: 7.351239e-01	ci right 7.523339e-01	k: 7438	n:10000
R3HDM1   10000 perm   2 sec   (5137 perm/sec)   p_kst 7.438000e-01   p_cons 7.660000e-01   p_joint 8.996000e-01

Outputting figure to mutsig2_images.part000000000141/R3HDM1.2_3396_10000_0.7438_0.766_0.8996.png
                gene_name: R3HDM1
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.75 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.90 
     ci_joint_bounds_left: 0.89 
    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.165.3896/
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/181708/iteration1/scatter.0000000141
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 141 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120194: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000142> was used as the working directory.
Started at Wed Oct 10 10:44:42 2012
Results reported at Wed Oct 10 10:46:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000142.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000142.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 142  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    127.67 sec.
    Max Memory :       906 MB
    Max Swap   :      3656 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.165.3896/
-whichjob
142
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 142: processing genes 12757 - 12847
Calculating significance of each gene.
Using projection method.
12757	RAB11B	1
12758	RAB11FIP1	1.096264e-01
12759	RAB11FIP2	1
12760	RAB11FIP3	1
12761	RAB11FIP4	4.607352e-02
12762	RAB11FIP5	1
12763	RAB12	1
12764	RAB13	1
12765	RAB14	1
12766	RAB15	1
12767	RAB17	1
12768	RAB18	1
12769	RAB19	1
12770	RAB1A	1
12771	RAB1B	1
12772	RAB20	1
12773	RAB21	1
12774	RAB22A	1
12775	RAB23	1
12776	RAB24	1
12777	RAB25	1
12778	RAB26	1
12779	RAB27A	1
12780	RAB27B	1
12781	RAB28	1
12782	RAB2A	1
12783	RAB2B	1
12784	RAB30	1
12785	RAB31	1
12786	RAB32	1
12787	RAB33A	1
12788	RAB33B	1
12789	RAB34	1
12790	RAB35	1
12791	RAB36	6.646005e-02
12792	RAB37	1
12793	RAB38	1
12794	RAB39	1
12795	RAB39B	1
12796	RAB3A	1
12797	RAB3B	1
12798	RAB3C	1
12799	RAB3D	1
12800	RAB3GAP1	3.194969e-01
12801	RAB3GAP2	2.711965e-01
12802	RAB3IL1	4.481450e-02
12803	RAB3IP	1
12804	RAB40A	1
12805	RAB40AL	1
12806	RAB40B	9.340156e-03
12807	RAB40C	1
12808	RAB41	1
12809	RAB42	1
12810	RAB43	1
12811	RAB4A	1
12812	RAB4B	1
12813	RAB5A	2.674643e-02
12814	RAB5B	1
12815	RAB5C	1
12816	RAB6A	1
12817	RAB6B	1
12818	RAB6C	1
12819	RAB7A	9.019182e-02
12820	RAB7L1	9.202549e-02
12821	RAB8A	1
12822	RAB8B	1
12823	RAB9A	1
12824	RAB9B	1
12825	RABAC1	1
12826	RABEP1	1
12827	RABEP2	1
12828	RABEPK	6.232908e-02
12829	RABGAP1	1
12830	RABGAP1L	1
12831	RABGEF1	1
12832	RABGGTA	1
12833	RABGGTB	1
12834	RABIF	1
12835	RABL2A	1
12836	RABL2B	1
12837	RABL3	1
12838	RABL5	1
12839	RAC1	1
12840	RAC2	1
12841	RAC3	1
12842	RACGAP1	1
12843	RAD1	1.224345e-01
12844	RAD17	1
12845	RAD18	1
12846	RAD21	1
12847	RAD23A	1
Done

Running MutSig 2:
Scatter job 142: processing genes 12757 - 12847
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RAB11FIP1
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: 1.800553e-02	ci left: 8.182217e-01	ci right 8.331881e-01	k: 8258	n:10000
KS ci ratio: 2.999969e-02	ci left: 6.210534e-01	ci right 6.400704e-01	k: 6306	n:10000
RAB11FIP1   10000 perm   2 sec   (4528 perm/sec)   p_kst 6.306000e-01   p_cons 8.258000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000142/RAB11FIP1.2_3876_10000_0.6306_0.8258_1.png
                gene_name: RAB11FIP1
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.83 
      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.
RAB40B
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: 4.909800e-02	ci left: 3.796273e-01	ci right 3.988373e-01	k: 3892	n:10000
KS ci ratio: 1.585526e-01	ci left: 5.301669e-02	ci right 6.224312e-02	k: 575	n:10000
RAB40B   10000 perm   1 sec   (6707 perm/sec)   p_kst 5.750000e-02   p_cons 3.892000e-01   p_joint 3.083000e-01

Joint ci ratio: 9.862781e-02	ci left: 6.957859e-02	ci right 7.684608e-02	k: 1463	n:20000
Cons ci ratio: 3.488212e-02	ci left: 3.802416e-01	ci right 3.937913e-01	k: 7740	n:20000
KS ci ratio: 1.128455e-01	ci left: 5.368046e-02	ci right 6.014911e-02	k: 1137	n:20000
RAB40B   20000 perm   3 sec   (5772 perm/sec)   p_kst 5.685000e-02   p_cons 3.870000e-01   p_joint 7.315000e-02

Joint ci ratio: 8.007826e-02	ci left: 7.099709e-02	ci right 7.695239e-02	k: 2218	n:30000
Cons ci ratio: 2.852013e-02	ci left: 3.808513e-01	ci right 3.919040e-01	k: 11591	n:30000
KS ci ratio: 9.176870e-02	ci left: 5.469633e-02	ci right 5.998981e-02	k: 1719	n:30000
RAB40B   30000 perm   6 sec   (5453 perm/sec)   p_kst 5.730000e-02   p_cons 3.863667e-01   p_joint 7.393333e-02

Outputting figure to mutsig2_images.part000000000142/RAB40B.2_861_30000_0.0573_0.38637_0.073933.png
                gene_name: RAB40B
               theta_stop: 0.092 
                    nperm: 30000 
                     p_ks: 0.057 
        ci_ks_bounds_left: 0.055 
       ci_ks_bounds_right: 0.060 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.074 
     ci_joint_bounds_left: 0.071 
    ci_joint_bounds_right: 0.077 

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.165.3896/
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/181708/iteration1/scatter.0000000142
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 142 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120198: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000143> was used as the working directory.
Started at Wed Oct 10 10:44:49 2012
Results reported at Wed Oct 10 10:48:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000143.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000143.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 143  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    238.81 sec.
    Max Memory :      1545 MB
    Max Swap   :      3997 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.165.3896/
-whichjob
143
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 143: processing genes 12848 - 12937
Calculating significance of each gene.
Using projection method.
12848	RAD23B	1
12849	RAD50	3.487744e-01
12850	RAD51	1
12851	RAD51AP1	1
12852	RAD51AP2	1.083798e-01
12853	RAD51C	1.242978e-01
12854	RAD51L1	1
12855	RAD51L3	1.760793e-01
12856	RAD52	1.492980e-02
12857	RAD54B	1.680340e-01
12858	RAD54L	1
12859	RAD54L2	1
12860	RAD9A	1
12861	RAD9B	1
12862	RADIL	2.099976e-01
12863	RAE1	1
12864	RAET1E	1
12865	RAET1G	3.059274e-02
12866	RAET1L	1
12867	RAF1	1
12868	RAG1	2.020693e-01
12869	RAG1AP1	1
12870	RAG2	1
12871	RAGE	1
12872	RAI1	1
12873	RAI14	2.822530e-01
12874	RAI2	1
12875	RALA	1
12876	RALB	1
12877	RALBP1	1
12878	RALGAPA1	4.416773e-01
12879	RALGAPA2	1
12880	RALGAPB	1
12881	RALGDS	1.117274e-01
12882	RALGPS1	2.513993e-01
12883	RALGPS2	9.650323e-02
12884	RALY	1.342093e-01
12885	RALYL	1
12886	RAMP1	1
12887	RAMP2	1
12888	RAMP3	1
12889	RAN	1
12890	RANBP1	1
12891	RANBP10	1
12892	RANBP17	1
12893	RANBP2	7.855210e-01
12894	RANBP3	1
12895	RANBP3L	1.984545e-01
12896	RANBP6	1
12897	RANBP9	1
12898	RANGAP1	5.151231e-02
12899	RANGRF	1
12900	RAP1A	1
12901	RAP1B	2.907468e-03
12902	RAP1GAP	1
12903	RAP1GAP2	1
12904	RAP1GDS1	1
12905	RAP2A	1
12906	RAP2B	1
12907	RAP2C	1
12908	RAPGEF1	1
12909	RAPGEF2	1.378088e-01
12910	RAPGEF3	1
12911	RAPGEF4	1.649790e-01
12912	RAPGEF5	1
12913	RAPGEF6	1
12914	RAPGEFL1	1
12915	RAPH1	4.803798e-01
12916	RAPSN	1
12917	RARA	2.538545e-02
12918	RARB	1
12919	RARG	5.871947e-02
12920	RARRES1	1
12921	RARRES2	1
12922	RARRES3	1
12923	RARS	1
12924	RARS2	1
12925	RASA1	1.813209e-01
12926	RASA2	1
12927	RASA3	1
12928	RASAL1	1
12929	RASAL2	1
12930	RASAL3	1
12931	RASD1	1
12932	RASD2	1
12933	RASEF	1
12934	RASGEF1A	7.799056e-02
12935	RASGEF1B	1
12936	RASGEF1C	1
12937	RASGRF1	4.368707e-01
Done

Running MutSig 2:
Scatter job 143: processing genes 12848 - 12937
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RAI1
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: 1.783640e-02	ci left: 8.209666e-01	ci right 8.358415e-01	k: 8285	n:10000
KS ci ratio: 4.184154e-01	ci left: 6.884481e-03	ci right 1.061018e-02	k: 86	n:10000
RAI1   10000 perm   2 sec   (4640 perm/sec)   p_kst 8.600000e-03   p_cons 8.285000e-01   p_joint 4.800000e-02

Joint ci ratio: 1.132152e-01	ci left: 5.333981e-02	ci right 5.978987e-02	k: 1130	n:20000
Cons ci ratio: 1.255178e-02	ci left: 8.245694e-01	ci right 8.350345e-01	k: 16597	n:20000
KS ci ratio: 2.984783e-01	ci left: 7.274556e-03	ci right 9.871356e-03	k: 170	n:20000
RAI1   20000 perm   7 sec   (3006 perm/sec)   p_kst 8.500000e-03   p_cons 8.298500e-01   p_joint 5.650000e-02

Joint ci ratio: 1.266724e-01	ci left: 2.897069e-02	ci right 3.292083e-02	k: 927	n:30000
Cons ci ratio: 1.027555e-02	ci left: 8.247920e-01	ci right 8.333442e-01	k: 24873	n:30000
KS ci ratio: 2.449152e-01	ci left: 7.429710e-03	ci right 9.533810e-03	k: 253	n:30000
RAI1   30000 perm   9 sec   (3233 perm/sec)   p_kst 8.433333e-03   p_cons 8.291000e-01   p_joint 3.090000e-02

Joint ci ratio: 1.308321e-01	ci left: 2.051221e-02	ci right 2.340777e-02	k: 877	n:40000
Cons ci ratio: 8.901178e-03	ci left: 8.252991e-01	ci right 8.327030e-01	k: 33161	n:40000
KS ci ratio: 2.059566e-01	ci left: 8.050337e-03	ci right 9.921990e-03	k: 358	n:40000
RAI1   40000 perm   12 sec   (3343 perm/sec)   p_kst 8.950000e-03   p_cons 8.290250e-01   p_joint 2.192500e-02

Joint ci ratio: 9.001805e-02	ci left: 3.489277e-02	ci right 3.820132e-02	k: 1826	n:50000
Cons ci ratio: 7.964371e-03	ci left: 8.255901e-01	ci right 8.322116e-01	k: 41446	n:50000
KS ci ratio: 1.811333e-01	ci left: 8.439034e-03	ci right 1.013867e-02	k: 463	n:50000
RAI1   50000 perm   15 sec   (3385 perm/sec)   p_kst 9.260000e-03   p_cons 8.289200e-01   p_joint 3.652000e-02

Joint ci ratio: 7.931613e-02	ci left: 3.756304e-02	ci right 4.068174e-02	k: 2346	n:60000
Cons ci ratio: 7.266236e-03	ci left: 8.260470e-01	ci right 8.320878e-01	k: 49745	n:60000
KS ci ratio: 1.691970e-01	ci left: 8.116098e-03	ci right 9.631980e-03	k: 531	n:60000
RAI1   60000 perm   18 sec   (3408 perm/sec)   p_kst 8.850000e-03   p_cons 8.290833e-01   p_joint 3.910000e-02

Joint ci ratio: 8.794316e-02	ci left: 2.638489e-02	ci right 2.882591e-02	k: 1931	n:70000
Cons ci ratio: 6.740039e-03	ci left: 8.257300e-01	ci right 8.313285e-01	k: 57998	n:70000
KS ci ratio: 1.571151e-01	ci left: 8.121413e-03	ci right 9.519759e-03	k: 616	n:70000
RAI1   70000 perm   20 sec   (3415 perm/sec)   p_kst 8.800000e-03   p_cons 8.285429e-01   p_joint 2.758571e-02

Joint ci ratio: 9.192572e-02	ci left: 2.120237e-02	ci right 2.325748e-02	k: 1777	n:80000
Cons ci ratio: 6.297348e-03	ci left: 8.262471e-01	ci right 8.314791e-01	k: 66310	n:80000
KS ci ratio: 1.488037e-01	ci left: 7.959734e-03	ci right 9.251282e-03	k: 687	n:80000
RAI1   80000 perm   23 sec   (3410 perm/sec)   p_kst 8.587500e-03   p_cons 8.288750e-01   p_joint 2.221250e-02

Joint ci ratio: 7.310803e-02	ci left: 2.982269e-02	ci right 3.209656e-02	k: 2785	n:90000
Cons ci ratio: 5.931783e-03	ci left: 8.266581e-01	ci right 8.315873e-01	k: 74622	n:90000
KS ci ratio: 1.393881e-01	ci left: 8.103600e-03	ci right 9.328381e-03	k: 783	n:90000
RAI1   90000 perm   27 sec   (3396 perm/sec)   p_kst 8.700000e-03   p_cons 8.291333e-01   p_joint 3.094444e-02

Joint ci ratio: 7.760467e-02	ci left: 2.391360e-02	ci right 2.585409e-02	k: 2487	n:100000
Cons ci ratio: 5.628636e-03	ci left: 8.267223e-01	ci right 8.313986e-01	k: 82907	n:100000
KS ci ratio: 1.324741e-01	ci left: 8.104685e-03	ci right 9.264083e-03	k: 867	n:100000
RAI1   100000 perm   30 sec   (3377 perm/sec)   p_kst 8.670000e-03   p_cons 8.290700e-01   p_joint 2.487000e-02

Joint ci ratio: 8.267685e-02	ci left: 1.919861e-02	ci right 2.086320e-02	k: 2202	n:110000
Cons ci ratio: 5.357858e-03	ci left: 8.273009e-01	ci right 8.317544e-01	k: 91249	n:110000
KS ci ratio: 1.258314e-01	ci left: 8.194866e-03	ci right 9.303996e-03	k: 961	n:110000
RAI1   110000 perm   33 sec   (3339 perm/sec)   p_kst 8.736364e-03   p_cons 8.295364e-01   p_joint 2.001818e-02

Joint ci ratio: 6.832214e-02	ci left: 2.578700e-02	ci right 2.761930e-02	k: 3203	n:120000
Cons ci ratio: 5.134495e-03	ci left: 8.271340e-01	ci right 8.314001e-01	k: 99513	n:120000
KS ci ratio: 1.204429e-01	ci left: 8.222717e-03	ci right 9.284561e-03	k: 1049	n:120000
RAI1   120000 perm   36 sec   (3310 perm/sec)   p_kst 8.741667e-03   p_cons 8.292750e-01   p_joint 2.669167e-02

Joint ci ratio: 6.984958e-02	ci left: 2.282698e-02	ci right 2.448667e-02	k: 3074	n:130000
Cons ci ratio: 4.929676e-03	ci left: 8.274136e-01	ci right 8.315102e-01	k: 107831	n:130000
KS ci ratio: 1.153857e-01	ci left: 8.291972e-03	ci right 9.314735e-03	k: 1143	n:130000
RAI1   130000 perm   40 sec   (3279 perm/sec)   p_kst 8.792308e-03   p_cons 8.294692e-01   p_joint 2.364615e-02

Joint ci ratio: 7.073766e-02	ci left: 2.070446e-02	ci right 2.222973e-02	k: 3004	n:140000
Cons ci ratio: 4.753554e-03	ci left: 8.272972e-01	ci right 8.312463e-01	k: 116099	n:140000
KS ci ratio: 1.113710e-01	ci left: 8.282672e-03	ci right 9.266407e-03	k: 1227	n:140000
RAI1   140000 perm   43 sec   (3240 perm/sec)   p_kst 8.764286e-03   p_cons 8.292786e-01   p_joint 2.145714e-02

Joint ci ratio: 7.098245e-02	ci left: 1.921886e-02	ci right 2.063978e-02	k: 2988	n:150000
Cons ci ratio: 4.592885e-03	ci left: 8.273327e-01	ci right 8.311479e-01	k: 124387	n:150000
KS ci ratio: 1.079559e-01	ci left: 8.242706e-03	ci right 9.189764e-03	k: 1306	n:150000
RAI1   150000 perm   47 sec   (3209 perm/sec)   p_kst 8.706667e-03   p_cons 8.292467e-01   p_joint 1.992000e-02

Joint ci ratio: 6.312937e-02	ci left: 2.278787e-02	ci right 2.427946e-02	k: 3764	n:160000
Cons ci ratio: 4.452286e-03	ci left: 8.270582e-01	ci right 8.307549e-01	k: 132626	n:160000
KS ci ratio: 1.038957e-01	ci left: 8.360345e-03	ci right 9.282586e-03	k: 1410	n:160000
RAI1   160000 perm   50 sec   (3178 perm/sec)   p_kst 8.812500e-03   p_cons 8.289125e-01   p_joint 2.352500e-02

Joint ci ratio: 6.239885e-02	ci left: 2.197980e-02	ci right 2.340125e-02	k: 3856	n:170000
Cons ci ratio: 4.321064e-03	ci left: 8.270008e-01	ci right 8.305879e-01	k: 140896	n:170000
KS ci ratio: 1.006646e-01	ci left: 8.395901e-03	ci right 9.291557e-03	k: 1502	n:170000
RAI1   170000 perm   54 sec   (3147 perm/sec)   p_kst 8.835294e-03   p_cons 8.288000e-01   p_joint 2.268235e-02

Joint ci ratio: 5.455512e-02	ci left: 2.712211e-02	ci right 2.864870e-02	k: 5018	n:180000
Cons ci ratio: 4.063611e-03	ci left: 8.362116e-01	ci right 8.396220e-01	k: 150826	n:180000
KS ci ratio: 9.747105e-02	ci left: 8.471270e-03	ci right 9.344657e-03	k: 1602	n:180000
RAI1   180000 perm   58 sec   (3115 perm/sec)   p_kst 8.900000e-03   p_cons 8.379222e-01   p_joint 2.787778e-02

Outputting figure to mutsig2_images.part000000000143/RAI1.4_5737_180000_0.0089_0.83792_0.027878.png
                gene_name: RAI1
               theta_stop: 0.097 
                    nperm: 180000 
                     p_ks: 0.0089 
        ci_ks_bounds_left: 0.0085 
       ci_ks_bounds_right: 0.0093 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.84 
     ci_cons_bounds_right: 0.84 
                  p_joint: 0.028 
     ci_joint_bounds_left: 0.027 
    ci_joint_bounds_right: 0.029 

Current progress: 11 percent done.
RAD50
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.006058e-01	ci left: 1.251301e-01	ci right 1.384852e-01	k: 1317	n:10000
Cons ci ratio: 1.404114e-01	ci left: 6.720239e-02	ci right 7.744844e-02	k: 722	n:10000
KS ci ratio: 1.044753e-01	ci left: 1.169164e-01	ci right 1.299039e-01	k: 1233	n:10000
RAD50   10000 perm   2 sec   (5511 perm/sec)   p_kst 1.233000e-01   p_cons 7.220000e-02   p_joint 1.317000e-01

Joint ci ratio: 5.677031e-02	ci left: 1.870064e-01	ci right 1.979831e-01	k: 3849	n:20000
Cons ci ratio: 9.723735e-02	ci left: 7.148437e-02	ci right 7.883971e-02	k: 1502	n:20000
KS ci ratio: 7.401342e-02	ci left: 1.184290e-01	ci right 1.275809e-01	k: 2459	n:20000
RAD50   20000 perm   4 sec   (4906 perm/sec)   p_kst 1.229500e-01   p_cons 7.510000e-02   p_joint 1.924500e-01

Outputting figure to mutsig2_images.part000000000143/RAD50.2_4039_20000_0.12295_0.0751_0.19245.png
                gene_name: RAD50
               theta_stop: 0.097 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.075 
      ci_cons_bounds_left: 0.071 
     ci_cons_bounds_right: 0.079 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.20 

Current progress: 22 percent done.
RAD51AP2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.732748e-02	ci left: 3.093726e-01	ci right 3.277332e-01	k: 3185	n:10000
Cons ci ratio: 7.443885e-02	ci left: 2.089543e-01	ci right 2.252108e-01	k: 2170	n:10000
KS ci ratio: 3.631366e-02	ci left: 5.282688e-01	ci right 5.479090e-01	k: 5381	n:10000
RAD51AP2   10000 perm   2 sec   (5638 perm/sec)   p_kst 5.381000e-01   p_cons 2.170000e-01   p_joint 3.185000e-01

Outputting figure to mutsig2_images.part000000000143/RAD51AP2.2_3492_10000_0.5381_0.217_0.3185.png
                gene_name: RAD51AP2
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.33 

Current progress: 33 percent done.
RAD52
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.272134e-02	ci left: 5.795829e-01	ci right 5.989651e-01	k: 5893	n:10000
Cons ci ratio: 6.548479e-02	ci left: 2.550834e-01	ci right 2.724544e-01	k: 2637	n:10000
KS ci ratio: 3.923333e-02	ci left: 4.896515e-01	ci right 5.093488e-01	k: 4995	n:10000
RAD52   10000 perm   2 sec   (6488 perm/sec)   p_kst 4.995000e-01   p_cons 2.637000e-01   p_joint 5.893000e-01

Outputting figure to mutsig2_images.part000000000143/RAD52.2_1301_10000_0.4995_0.2637_0.5893.png
                gene_name: RAD52
               theta_stop: 0.065 
                    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: 0.26 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.59 
     ci_joint_bounds_left: 0.58 
    ci_joint_bounds_right: 0.60 

Current progress: 44 percent done.
RAD54B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.596939e-02	ci left: 3.197920e-01	ci right 3.383077e-01	k: 3290	n:10000
Cons ci ratio: 4.622758e-02	ci left: 4.085072e-01	ci right 4.279405e-01	k: 4182	n:10000
KS ci ratio: 2.284450e-01	ci left: 2.532660e-02	ci right 3.195180e-02	k: 285	n:10000
RAD54B   10000 perm   2 sec   (5906 perm/sec)   p_kst 2.850000e-02   p_cons 4.182000e-01   p_joint 3.290000e-01

Joint ci ratio: 9.444622e-02	ci left: 7.554264e-02	ci right 8.308021e-02	k: 1585	n:20000
Cons ci ratio: 3.456446e-02	ci left: 3.845773e-01	ci right 3.981543e-01	k: 7827	n:20000
KS ci ratio: 1.609604e-01	ci left: 2.647782e-02	ci right 3.116050e-02	k: 575	n:20000
RAD54B   20000 perm   4 sec   (5262 perm/sec)   p_kst 2.875000e-02   p_cons 3.913500e-01   p_joint 7.925000e-02

Joint ci ratio: 9.793022e-02	ci left: 4.821186e-02	ci right 5.320894e-02	k: 1520	n:30000
Cons ci ratio: 2.821972e-02	ci left: 3.858712e-01	ci right 3.969498e-01	k: 11742	n:30000
KS ci ratio: 1.301886e-01	ci left: 2.742065e-02	ci right 3.127122e-02	k: 879	n:30000
RAD54B   30000 perm   6 sec   (5025 perm/sec)   p_kst 2.930000e-02   p_cons 3.914000e-01   p_joint 5.066667e-02

Joint ci ratio: 5.926143e-02	ci left: 9.567048e-02	ci right 1.015379e-01	k: 3943	n:40000
Cons ci ratio: 2.440352e-02	ci left: 3.873110e-01	ci right 3.969046e-01	k: 15684	n:40000
KS ci ratio: 1.111153e-01	ci left: 2.849591e-02	ci right 3.187275e-02	k: 1206	n:40000
RAD54B   40000 perm   8 sec   (4863 perm/sec)   p_kst 3.015000e-02   p_cons 3.921000e-01   p_joint 9.857500e-02

Joint ci ratio: 2.761393e-02	ci left: 2.832764e-01	ci right 2.912283e-01	k: 14362	n:50000
Cons ci ratio: 2.177528e-02	ci left: 3.889548e-01	ci right 3.975376e-01	k: 19662	n:50000
KS ci ratio: 9.944430e-02	ci left: 2.863920e-02	ci right 3.165568e-02	k: 1506	n:50000
RAD54B   50000 perm   11 sec   (4740 perm/sec)   p_kst 3.012000e-02   p_cons 3.932400e-01   p_joint 2.872400e-01

Outputting figure to mutsig2_images.part000000000143/RAD54B.2_2789_50000_0.03012_0.39324_0.28724.png
                gene_name: RAD54B
               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: 0.39 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.29 

Current progress: 56 percent done.
RALY
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.895970e-02	ci left: 4.931507e-01	ci right 5.128476e-01	k: 5030	n:10000
Cons ci ratio: 4.474909e-02	ci left: 4.243561e-01	ci right 4.438824e-01	k: 4341	n:10000
KS ci ratio: 2.662392e-02	ci left: 6.750875e-01	ci right 6.934051e-01	k: 6843	n:10000
RALY   10000 perm   1 sec   (7201 perm/sec)   p_kst 6.843000e-01   p_cons 4.341000e-01   p_joint 5.030000e-01

Outputting figure to mutsig2_images.part000000000143/RALY.2_949_10000_0.6843_0.4341_0.503.png
                gene_name: RALY
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    ci_joint_bounds_right: 0.51 

Current progress: 67 percent done.
RAP1B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.737275e-01	ci left: 5.196070e-03	ci right 8.501060e-03	k: 67	n:10000
Cons ci ratio: 4.090336e-01	ci left: 7.243098e-03	ci right 1.105110e-02	k: 90	n:10000
KS ci ratio: 5.347955e-02	ci left: 3.400502e-01	ci right 3.588375e-01	k: 3494	n:10000
RAP1B   10000 perm   1 sec   (7131 perm/sec)   p_kst 3.494000e-01   p_cons 9.000000e-03   p_joint 6.700000e-03

Joint ci ratio: 3.677103e-01	ci left: 4.613191e-03	ci right 6.734416e-03	k: 112	n:20000
Cons ci ratio: 2.876468e-01	ci left: 7.877125e-03	ci right 1.056846e-02	k: 183	n:20000
KS ci ratio: 3.780321e-02	ci left: 3.429887e-01	ci right 3.562551e-01	k: 6992	n:20000
RAP1B   20000 perm   3 sec   (6233 perm/sec)   p_kst 3.496000e-01   p_cons 9.150000e-03   p_joint 5.600000e-03

Joint ci ratio: 3.043262e-01	ci left: 4.663813e-03	ci right 6.367437e-03	k: 164	n:30000
Cons ci ratio: 2.374838e-01	ci left: 7.931051e-03	ci right 1.009897e-02	k: 269	n:30000
KS ci ratio: 3.091260e-02	ci left: 3.435380e-01	ci right 3.543579e-01	k: 10468	n:30000
RAP1B   30000 perm   5 sec   (5877 perm/sec)   p_kst 3.489333e-01   p_cons 8.966667e-03   p_joint 5.466667e-03

Joint ci ratio: 2.347101e-01	ci left: 6.112239e-03	ci right 7.760564e-03	k: 276	n:40000
Cons ci ratio: 2.039596e-01	ci left: 8.216425e-03	ci right 1.010586e-02	k: 365	n:40000
KS ci ratio: 2.662250e-02	ci left: 3.467947e-01	ci right 3.561769e-01	k: 14059	n:40000
RAP1B   40000 perm   7 sec   (5671 perm/sec)   p_kst 3.514750e-01   p_cons 9.125000e-03   p_joint 6.900000e-03

Joint ci ratio: 2.234025e-01	ci left: 5.436306e-03	ci right 6.821974e-03	k: 305	n:50000
Cons ci ratio: 1.811333e-01	ci left: 8.439034e-03	ci right 1.013867e-02	k: 463	n:50000
KS ci ratio: 2.384640e-02	ci left: 3.466358e-01	ci right 3.550216e-01	k: 17541	n:50000
RAP1B   50000 perm   9 sec   (5504 perm/sec)   p_kst 3.508200e-01   p_cons 9.260000e-03   p_joint 6.100000e-03

Joint ci ratio: 2.138933e-01	ci left: 4.971242e-03	ci right 6.177340e-03	k: 333	n:60000
Cons ci ratio: 1.657728e-01	ci left: 8.467520e-03	ci right 1.001384e-02	k: 553	n:60000
KS ci ratio: 2.182007e-02	ci left: 3.459332e-01	ci right 3.535814e-01	k: 20985	n:60000
RAP1B   60000 perm   11 sec   (5362 perm/sec)   p_kst 3.497500e-01   p_cons 9.216667e-03   p_joint 5.550000e-03

Joint ci ratio: 1.974334e-01	ci left: 5.047041e-03	ci right 6.165969e-03	k: 391	n:70000
Cons ci ratio: 1.533962e-01	ci left: 8.533471e-03	ci right 9.964795e-03	k: 646	n:70000
KS ci ratio: 2.017083e-02	ci left: 3.469076e-01	ci right 3.539905e-01	k: 24531	n:70000
RAP1B   70000 perm   13 sec   (5236 perm/sec)   p_kst 3.504429e-01   p_cons 9.228571e-03   p_joint 5.585714e-03

Joint ci ratio: 1.834508e-01	ci left: 5.154278e-03	ci right 6.207058e-03	k: 453	n:80000
Cons ci ratio: 1.423690e-01	ci left: 8.718794e-03	ci right 1.006714e-02	k: 750	n:80000
KS ci ratio: 1.888185e-02	ci left: 3.468063e-01	ci right 3.534296e-01	k: 28009	n:80000
RAP1B   80000 perm   16 sec   (5118 perm/sec)   p_kst 3.501125e-01   p_cons 9.375000e-03   p_joint 5.662500e-03

Joint ci ratio: 1.688123e-01	ci left: 5.452653e-03	ci right 6.468475e-03	k: 535	n:90000
Cons ci ratio: 1.347004e-01	ci left: 8.693936e-03	ci right 9.960215e-03	k: 838	n:90000
KS ci ratio: 1.780818e-02	ci left: 3.468388e-01	ci right 3.530820e-01	k: 31496	n:90000
RAP1B   90000 perm   18 sec   (5007 perm/sec)   p_kst 3.499556e-01   p_cons 9.311111e-03   p_joint 5.944444e-03

Joint ci ratio: 1.620149e-01	ci left: 5.348326e-03	ci right 6.300681e-03	k: 581	n:100000
Cons ci ratio: 1.290675e-01	ci left: 8.549761e-03	ci right 9.738972e-03	k: 913	n:100000
KS ci ratio: 1.688789e-02	ci left: 3.471729e-01	ci right 3.530958e-01	k: 35013	n:100000
RAP1B   100000 perm   20 sec   (4905 perm/sec)   p_kst 3.501300e-01   p_cons 9.130000e-03   p_joint 5.810000e-03

Joint ci ratio: 1.547429e-01	ci left: 5.351035e-03	ci right 6.257137e-03	k: 637	n:110000
Cons ci ratio: 1.228394e-01	ci left: 8.608960e-03	ci right 9.744417e-03	k: 1008	n:110000
KS ci ratio: 1.609149e-02	ci left: 3.476072e-01	ci right 3.532552e-01	k: 38547	n:110000
RAP1B   110000 perm   23 sec   (4806 perm/sec)   p_kst 3.504273e-01   p_cons 9.163636e-03   p_joint 5.790909e-03

Joint ci ratio: 1.486932e-01	ci left: 5.330014e-03	ci right 6.194134e-03	k: 690	n:120000
Cons ci ratio: 1.178655e-01	ci left: 8.594721e-03	ci right 9.679201e-03	k: 1095	n:120000
KS ci ratio: 1.540173e-02	ci left: 3.478665e-01	ci right 3.532741e-01	k: 42068	n:120000
RAP1B   120000 perm   25 sec   (4717 perm/sec)   p_kst 3.505667e-01   p_cons 9.125000e-03   p_joint 5.750000e-03

Joint ci ratio: 1.414027e-01	ci left: 5.461207e-03	ci right 6.299525e-03	k: 763	n:130000
Cons ci ratio: 1.125421e-01	ci left: 8.725516e-03	ci right 9.773473e-03	k: 1201	n:130000
KS ci ratio: 1.480720e-02	ci left: 3.476755e-01	ci right 3.528696e-01	k: 45535	n:130000
RAP1B   130000 perm   28 sec   (4630 perm/sec)   p_kst 3.502692e-01   p_cons 9.238462e-03   p_joint 5.869231e-03

Joint ci ratio: 1.356608e-01	ci left: 5.526227e-03	ci right 6.337298e-03	k: 829	n:140000
Cons ci ratio: 1.078387e-01	ci left: 8.845520e-03	ci right 9.860671e-03	k: 1308	n:140000
KS ci ratio: 1.427524e-02	ci left: 3.475581e-01	ci right 3.525624e-01	k: 49008	n:140000
RAP1B   140000 perm   31 sec   (4545 perm/sec)   p_kst 3.500571e-01   p_cons 9.342857e-03   p_joint 5.921429e-03

Joint ci ratio: 1.310820e-01	ci left: 5.538025e-03	ci right 6.321258e-03	k: 888	n:150000
Cons ci ratio: 1.040885e-01	ci left: 8.878866e-03	ci right 9.860239e-03	k: 1404	n:150000
KS ci ratio: 1.378547e-02	ci left: 3.478321e-01	ci right 3.526670e-01	k: 52537	n:150000
RAP1B   150000 perm   34 sec   (4465 perm/sec)   p_kst 3.502467e-01   p_cons 9.360000e-03   p_joint 5.920000e-03

Joint ci ratio: 1.267360e-01	ci left: 5.566909e-03	ci right 6.326161e-03	k: 950	n:160000
Cons ci ratio: 1.009421e-01	ci left: 8.865923e-03	ci right 9.814485e-03	k: 1493	n:160000
KS ci ratio: 1.332896e-02	ci left: 3.485486e-01	ci right 3.532318e-01	k: 56142	n:160000
RAP1B   160000 perm   36 sec   (4389 perm/sec)   p_kst 3.508875e-01   p_cons 9.331250e-03   p_joint 5.937500e-03

Joint ci ratio: 1.237203e-01	ci left: 5.507243e-03	ci right 6.239174e-03	k: 997	n:170000
Cons ci ratio: 9.850537e-02	ci left: 8.774550e-03	ci right 9.689363e-03	k: 1568	n:170000
KS ci ratio: 1.292998e-02	ci left: 3.486544e-01	ci right 3.531977e-01	k: 59657	n:170000
RAP1B   170000 perm   39 sec   (4314 perm/sec)   p_kst 3.509235e-01   p_cons 9.223529e-03   p_joint 5.864706e-03

Joint ci ratio: 1.203323e-01	ci left: 5.508286e-03	ci right 6.218881e-03	k: 1054	n:180000
Cons ci ratio: 9.582596e-02	ci left: 8.769503e-03	ci right 9.657523e-03	k: 1657	n:180000
KS ci ratio: 1.257508e-02	ci left: 3.483787e-01	ci right 3.527928e-01	k: 63105	n:180000
RAP1B   180000 perm   42 sec   (4241 perm/sec)   p_kst 3.505833e-01   p_cons 9.205556e-03   p_joint 5.855556e-03

Joint ci ratio: 1.176882e-01	ci left: 5.463480e-03	ci right 6.151730e-03	k: 1102	n:190000
Cons ci ratio: 9.367921e-02	ci left: 8.703596e-03	ci right 9.564113e-03	k: 1734	n:190000
KS ci ratio: 1.225057e-02	ci left: 3.480337e-01	ci right 3.523288e-01	k: 66534	n:190000
RAP1B   190000 perm   46 sec   (4171 perm/sec)   p_kst 3.501789e-01   p_cons 9.126316e-03   p_joint 5.800000e-03

Joint ci ratio: 1.140703e-01	ci left: 5.535029e-03	ci right 6.209414e-03	k: 1173	n:200000
Cons ci ratio: 9.076497e-02	ci left: 8.820410e-03	ci right 9.663906e-03	k: 1847	n:200000
KS ci ratio: 1.194062e-02	ci left: 3.480791e-01	ci right 3.522653e-01	k: 70034	n:200000
RAP1B   200000 perm   49 sec   (4105 perm/sec)   p_kst 3.501700e-01   p_cons 9.235000e-03   p_joint 5.865000e-03

Joint ci ratio: 1.114441e-01	ci left: 5.530601e-03	ci right 6.187913e-03	k: 1229	n:210000
Cons ci ratio: 8.872535e-02	ci left: 8.800719e-03	ci right 9.622438e-03	k: 1933	n:210000
KS ci ratio: 1.164758e-02	ci left: 3.483354e-01	ci right 3.524211e-01	k: 73579	n:210000
RAP1B   210000 perm   52 sec   (4039 perm/sec)   p_kst 3.503762e-01   p_cons 9.204762e-03   p_joint 5.852381e-03

Joint ci ratio: 1.089912e-01	ci left: 5.526738e-03	ci right 6.168205e-03	k: 1285	n:220000
Cons ci ratio: 8.668748e-02	ci left: 8.809697e-03	ci right 9.612405e-03	k: 2025	n:220000
KS ci ratio: 1.137737e-02	ci left: 3.484787e-01	ci right 3.524707e-01	k: 77104	n:220000
RAP1B   220000 perm   55 sec   (3976 perm/sec)   p_kst 3.504727e-01   p_cons 9.204545e-03   p_joint 5.840909e-03

Joint ci ratio: 1.064147e-01	ci left: 5.552983e-03	ci right 6.181307e-03	k: 1348	n:230000
Cons ci ratio: 8.458257e-02	ci left: 8.860657e-03	ci right 9.647437e-03	k: 2127	n:230000
KS ci ratio: 1.112461e-02	ci left: 3.486323e-01	ci right 3.525367e-01	k: 80634	n:230000
RAP1B   230000 perm   59 sec   (3913 perm/sec)   p_kst 3.505826e-01   p_cons 9.247826e-03   p_joint 5.860870e-03

Joint ci ratio: 1.039018e-01	ci left: 5.589382e-03	ci right 6.205976e-03	k: 1414	n:240000
Cons ci ratio: 8.271755e-02	ci left: 8.887180e-03	ci right 9.658074e-03	k: 2224	n:240000
KS ci ratio: 1.089196e-02	ci left: 3.486075e-01	ci right 3.524294e-01	k: 84124	n:240000
RAP1B   240000 perm   62 sec   (3853 perm/sec)   p_kst 3.505167e-01   p_cons 9.266667e-03   p_joint 5.891667e-03

Joint ci ratio: 1.019054e-01	ci left: 5.584040e-03	ci right 6.187502e-03	k: 1470	n:250000
Cons ci ratio: 8.109416e-02	ci left: 8.884318e-03	ci right 9.639125e-03	k: 2314	n:250000
KS ci ratio: 1.067108e-02	ci left: 3.486814e-01	ci right 3.524261e-01	k: 87638	n:250000
RAP1B   250000 perm   66 sec   (3797 perm/sec)   p_kst 3.505520e-01   p_cons 9.256000e-03   p_joint 5.880000e-03

Joint ci ratio: 1.000859e-01	ci left: 5.571714e-03	ci right 6.162460e-03	k: 1524	n:260000
Cons ci ratio: 7.962961e-02	ci left: 8.866732e-03	ci right 9.605808e-03	k: 2400	n:260000
KS ci ratio: 1.045789e-02	ci left: 3.489769e-01	ci right 3.526495e-01	k: 91211	n:260000
RAP1B   260000 perm   69 sec   (3744 perm/sec)   p_kst 3.508115e-01   p_cons 9.230769e-03   p_joint 5.861538e-03

Joint ci ratio: 9.795567e-02	ci left: 5.607362e-03	ci right 6.188506e-03	k: 1591	n:270000
Cons ci ratio: 7.805181e-02	ci left: 8.894146e-03	ci right 9.620150e-03	k: 2498	n:270000
KS ci ratio: 1.025950e-02	ci left: 3.491403e-01	ci right 3.527444e-01	k: 94754	n:270000
RAP1B   270000 perm   73 sec   (3690 perm/sec)   p_kst 3.509407e-01   p_cons 9.251852e-03   p_joint 5.892593e-03

Outputting figure to mutsig2_images.part000000000143/RAP1B.2_579_270000_0.35094_0.0092519_0.0058926.png
                gene_name: RAP1B
               theta_stop: 0.098 
                    nperm: 270000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.0093 
      ci_cons_bounds_left: 0.0089 
     ci_cons_bounds_right: 0.0096 
                  p_joint: 0.0059 
     ci_joint_bounds_left: 0.0056 
    ci_joint_bounds_right: 0.0062 

Current progress: 78 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: 4.960770e-02	ci left: 3.747510e-01	ci right 3.939164e-01	k: 3843	n:10000
KS ci ratio: 3.669516e-02	ci left: 5.230630e-01	ci right 5.427178e-01	k: 5329	n:10000
RAPGEF2   10000 perm   2 sec   (5290 perm/sec)   p_kst 5.329000e-01   p_cons 3.843000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000143/RAPGEF2.2_4596_10000_0.5329_0.3843_1.png
                gene_name: RAPGEF2
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.53 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.54 
                   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: 89 percent done.
RARA
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: 4.426074e-02	ci left: 4.297410e-01	ci right 4.492943e-01	k: 4395	n:10000
KS ci ratio: 4.569972e-02	ci left: 4.140880e-01	ci right 4.335564e-01	k: 4238	n:10000
RARA   10000 perm   2 sec   (6504 perm/sec)   p_kst 4.238000e-01   p_cons 4.395000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000143/RARA.2_1588_10000_0.4238_0.4395_1.png
                gene_name: RARA
               theta_stop: 0.046 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.44 
      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: 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.165.3896/
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/181708/iteration1/scatter.0000000143
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 143 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120202: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000144> was used as the working directory.
Started at Wed Oct 10 10:44:49 2012
Results reported at Wed Oct 10 10:46:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000144.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000144.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 144  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    115.50 sec.
    Max Memory :      1181 MB
    Max Swap   :      3932 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.165.3896/
-whichjob
144
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 144: processing genes 12938 - 13028
Calculating significance of each gene.
Using projection method.
12938	RASGRF2	1
12939	RASGRP1	2.969738e-01
12940	RASGRP2	1
12941	RASGRP3	8.580010e-02
12942	RASGRP4	1
12943	RASIP1	1
12944	RASL10A	1
12945	RASL10B	1
12946	RASL11A	1
12947	RASL11B	1
12948	RASL12	1.118575e-01
12949	RASSF1	9.417853e-02
12950	RASSF10	1
12951	RASSF2	1
12952	RASSF3	1
12953	RASSF4	1
12954	RASSF5	1
12955	RASSF6	1
12956	RASSF7	1
12957	RASSF8	3.137282e-02
12958	RASSF9	1
12959	RAVER1	5.225165e-02
12960	RAVER2	8.342609e-02
12961	RAX	1
12962	RAX2	1
12963	RB1	5.962871e-03
12964	RB1CC1	1
12965	RBAK	1.791389e-01
12966	RBBP4	1
12967	RBBP5	1
12968	RBBP6	3.026205e-01
12969	RBBP7	1
12970	RBBP8	1
12971	RBBP9	1
12972	RBCK1	1
12973	RBKS	1
12974	RBL1	1
12975	RBL2	2.344914e-01
12976	RBM10	6.093454e-03
12977	RBM11	1
12978	RBM12	1
12979	RBM12B	1
12980	RBM14	1
12981	RBM15	1.229397e-01
12982	RBM15B	1
12983	RBM16	1
12984	RBM17	5.787526e-02
12985	RBM18	1
12986	RBM19	1
12987	RBM22	1
12988	RBM23	1
12989	RBM24	1
12990	RBM25	1
12991	RBM26	1
12992	RBM27	1.460093e-01
12993	RBM28	1
12994	RBM3	1
12995	RBM33	1
12996	RBM34	1
12997	RBM38	1
12998	RBM39	1
12999	RBM4	1
13000/18094 13000	RBM41	1
13001	RBM42	1
13002	RBM43	1
13003	RBM44	5.219061e-02
13004	RBM45	1
13005	RBM46	1.217576e-01
13006	RBM47	1
13007	RBM4B	9.730710e-03
13008	RBM5	1
13009	RBM6	1
13010	RBM7	1
13011	RBM8A	1
13012	RBM9	1
13013	RBMS1	1
13014	RBMS2	1
13015	RBMS3	1
13016	RBMX	2.671253e-02
13017	RBMX2	1.306770e-01
13018	RBMXL1	1
13019	RBMXL2	1
13020	RBP1	1
13021	RBP2	8.820097e-03
13022	RBP3	3.639069e-01
13023	RBP4	1
13024	RBP5	1
13025	RBP7	1
13026	RBPJ	1
13027	RBPJL	7.614257e-02
13028	RBPMS	1
Done

Running MutSig 2:
Scatter job 144: processing genes 12938 - 13028
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RB1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.909574e-02	ci left: 1.285551e-01	ci right 1.420581e-01	k: 1352	n:10000
Cons ci ratio: 2.363374e-02	ci left: 7.246163e-01	ci right 7.420476e-01	k: 7334	n:10000
KS ci ratio: 3.618281e-01	ci left: 9.503508e-03	ci right 1.378807e-02	k: 115	n:10000
RB1   10000 perm   2 sec   (5791 perm/sec)   p_kst 1.150000e-02   p_cons 7.334000e-01   p_joint 1.352000e-01

Joint ci ratio: 6.774517e-02	ci left: 1.385205e-01	ci right 1.482834e-01	k: 2867	n:20000
Cons ci ratio: 1.650254e-02	ci left: 7.321488e-01	ci right 7.443819e-01	k: 14766	n:20000
KS ci ratio: 2.717025e-01	ci left: 8.900643e-03	ci right 1.174443e-02	k: 205	n:20000
RB1   20000 perm   6 sec   (3487 perm/sec)   p_kst 1.025000e-02   p_cons 7.383000e-01   p_joint 1.433500e-01

Joint ci ratio: 4.605200e-02	ci left: 1.900341e-01	ci right 1.990251e-01	k: 5835	n:30000
Cons ci ratio: 1.341274e-02	ci left: 7.350638e-01	ci right 7.450230e-01	k: 22202	n:30000
KS ci ratio: 2.155883e-01	ci left: 9.724379e-03	ci right 1.210509e-02	k: 326	n:30000
RB1   30000 perm   8 sec   (3816 perm/sec)   p_kst 1.086667e-02   p_cons 7.400667e-01   p_joint 1.945000e-01

Joint ci ratio: 4.515693e-02	ci left: 1.549334e-01	ci right 1.621162e-01	k: 6340	n:40000
Cons ci ratio: 1.221656e-02	ci left: 7.157725e-01	ci right 7.245955e-01	k: 28808	n:40000
KS ci ratio: 1.914221e-01	ci left: 9.381360e-03	ci right 1.139067e-02	k: 414	n:40000
RB1   40000 perm   10 sec   (3986 perm/sec)   p_kst 1.035000e-02   p_cons 7.202000e-01   p_joint 1.585000e-01

Joint ci ratio: 4.138780e-02	ci left: 1.489625e-01	ci right 1.552779e-01	k: 7605	n:50000
Cons ci ratio: 1.093281e-02	ci left: 7.160216e-01	ci right 7.239128e-01	k: 35999	n:50000
KS ci ratio: 1.716739e-01	ci left: 9.433540e-03	ci right 1.122400e-02	k: 515	n:50000
RB1   50000 perm   12 sec   (4063 perm/sec)   p_kst 1.030000e-02   p_cons 7.199800e-01   p_joint 1.521000e-01

Joint ci ratio: 2.362125e-02	ci left: 3.108685e-01	ci right 3.183161e-01	k: 18875	n:60000
Cons ci ratio: 9.985539e-03	ci left: 7.161542e-01	ci right 7.233579e-01	k: 43186	n:60000
KS ci ratio: 1.549807e-01	ci left: 9.731866e-03	ci right 1.138266e-02	k: 632	n:60000
RB1   60000 perm   15 sec   (4089 perm/sec)   p_kst 1.053333e-02   p_cons 7.197667e-01   p_joint 3.145833e-01

Joint ci ratio: 1.994128e-02	ci left: 3.521240e-01	ci right 3.592308e-01	k: 24897	n:70000
Cons ci ratio: 9.244058e-03	ci left: 7.164569e-01	ci right 7.231249e-01	k: 50386	n:70000
KS ci ratio: 1.433374e-01	ci left: 9.813216e-03	ci right 1.134205e-02	k: 739	n:70000
RB1   70000 perm   17 sec   (4087 perm/sec)   p_kst 1.055714e-02   p_cons 7.198000e-01   p_joint 3.556714e-01

Joint ci ratio: 2.079587e-02	ci left: 3.043405e-01	ci right 3.107485e-01	k: 24603	n:80000
Cons ci ratio: 8.648102e-03	ci left: 7.166236e-01	ci right 7.228604e-01	k: 57580	n:80000
KS ci ratio: 1.349466e-01	ci left: 9.732722e-03	ci right 1.115312e-02	k: 834	n:80000
RB1   80000 perm   20 sec   (4070 perm/sec)   p_kst 1.042500e-02   p_cons 7.197500e-01   p_joint 3.075375e-01

Joint ci ratio: 1.959248e-02	ci left: 3.048294e-01	ci right 3.108719e-01	k: 27706	n:90000
Cons ci ratio: 8.158566e-03	ci left: 7.165524e-01	ci right 7.224334e-01	k: 64755	n:90000
KS ci ratio: 1.263735e-01	ci left: 9.908903e-03	ci right 1.125626e-02	k: 951	n:90000
RB1   90000 perm   22 sec   (4042 perm/sec)   p_kst 1.056667e-02   p_cons 7.195000e-01   p_joint 3.078444e-01

Joint ci ratio: 2.681004e-02	ci left: 1.737635e-01	ci right 1.784953e-01	k: 17612	n:100000
Cons ci ratio: 7.739132e-03	ci left: 7.167444e-01	ci right 7.223229e-01	k: 71954	n:100000
KS ci ratio: 1.191945e-01	ci left: 1.006184e-02	ci right 1.134678e-02	k: 1069	n:100000
RB1   100000 perm   25 sec   (4007 perm/sec)   p_kst 1.069000e-02   p_cons 7.195400e-01   p_joint 1.761200e-01

Joint ci ratio: 2.578176e-02	ci left: 1.714200e-01	ci right 1.759063e-01	k: 19102	n:110000
Cons ci ratio: 7.375054e-03	ci left: 7.170902e-01	ci right 7.224073e-01	k: 79173	n:110000
KS ci ratio: 1.132591e-01	ci left: 1.016222e-02	ci right 1.139105e-02	k: 1184	n:110000
RB1   110000 perm   28 sec   (3970 perm/sec)   p_kst 1.076364e-02   p_cons 7.197545e-01   p_joint 1.736545e-01

Joint ci ratio: 2.468318e-02	ci left: 1.715271e-01	ci right 1.758221e-01	k: 20840	n:120000
Cons ci ratio: 7.057074e-03	ci left: 7.174334e-01	ci right 7.225226e-01	k: 86398	n:120000
KS ci ratio: 1.084258e-01	ci left: 1.019043e-02	ci right 1.136672e-02	k: 1292	n:120000
RB1   120000 perm   31 sec   (3928 perm/sec)   p_kst 1.076667e-02   p_cons 7.199833e-01   p_joint 1.736667e-01

Joint ci ratio: 2.371977e-02	ci left: 1.715522e-01	ci right 1.756778e-01	k: 22569	n:130000
Cons ci ratio: 6.775283e-03	ci left: 7.178282e-01	ci right 7.227158e-01	k: 93636	n:130000
KS ci ratio: 1.042004e-01	ci left: 1.020775e-02	ci right 1.133731e-02	k: 1399	n:130000
RB1   130000 perm   33 sec   (3884 perm/sec)   p_kst 1.076154e-02   p_cons 7.202769e-01   p_joint 1.736077e-01

Joint ci ratio: 2.282806e-02	ci left: 1.719889e-01	ci right 1.759675e-01	k: 24356	n:140000
Cons ci ratio: 6.528685e-03	ci left: 7.179264e-01	ci right 7.226359e-01	k: 100840	n:140000
KS ci ratio: 1.000648e-01	ci left: 1.029998e-02	ci right 1.139185e-02	k: 1517	n:140000
RB1   140000 perm   36 sec   (3840 perm/sec)   p_kst 1.083571e-02   p_cons 7.202857e-01   p_joint 1.739714e-01

Joint ci ratio: 2.186547e-02	ci left: 1.745271e-01	ci right 1.783920e-01	k: 26468	n:150000
Cons ci ratio: 6.310426e-03	ci left: 7.178071e-01	ci right 7.223577e-01	k: 108013	n:150000
KS ci ratio: 9.653474e-02	ci left: 1.034814e-02	ci right 1.140422e-02	k: 1630	n:150000
RB1   150000 perm   40 sec   (3794 perm/sec)   p_kst 1.086667e-02   p_cons 7.200867e-01   p_joint 1.764533e-01

Outputting figure to mutsig2_images.part000000000144/RB1.2_2895_150000_0.010867_0.72009_0.17645.png
                gene_name: RB1
               theta_stop: 0.097 
                    nperm: 150000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.010 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 20 percent done.
RBM10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.440970e-02	ci left: 3.323022e-01	ci right 3.509901e-01	k: 3416	n:10000
Cons ci ratio: 7.398202e-02	ci left: 2.110256e-01	ci right 2.273383e-01	k: 2191	n:10000
KS ci ratio: 4.432366e-02	ci left: 4.290429e-01	ci right 4.485928e-01	k: 4388	n:10000
RBM10   10000 perm   2 sec   (5842 perm/sec)   p_kst 4.388000e-01   p_cons 2.191000e-01   p_joint 3.416000e-01

Outputting figure to mutsig2_images.part000000000144/RBM10.2_2885_10000_0.4388_0.2191_0.3416.png
                gene_name: RBM10
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   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: 40 percent done.
RBM15
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.297085e-03	ci left: 9.530476e-01	ci right 9.610834e-01	k: 9572	n:10000
Cons ci ratio: 3.716947e-02	ci left: 5.166574e-01	ci right 5.363271e-01	k: 5265	n:10000
KS ci ratio: 9.697687e-03	ci left: 9.376532e-01	ci right 9.468871e-01	k: 9424	n:10000
RBM15   10000 perm   2 sec   (6062 perm/sec)   p_kst 9.424000e-01   p_cons 5.265000e-01   p_joint 9.572000e-01

Outputting figure to mutsig2_images.part000000000144/RBM15.2_2942_10000_0.9424_0.5265_0.9572.png
                gene_name: RBM15
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.94 
       ci_ks_bounds_right: 0.95 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.96 

Current progress: 60 percent done.
RBM44
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.089156e-02	ci left: 7.705345e-01	ci right 7.869028e-01	k: 7788	n:10000
Cons ci ratio: 2.125490e-02	ci left: 7.644585e-01	ci right 7.809823e-01	k: 7728	n:10000
KS ci ratio: 6.871987e-02	ci left: 2.369909e-01	ci right 2.539576e-01	k: 2454	n:10000
RBM44   10000 perm   2 sec   (5703 perm/sec)   p_kst 2.454000e-01   p_cons 7.728000e-01   p_joint 7.788000e-01

Outputting figure to mutsig2_images.part000000000144/RBM44.2_3215_10000_0.2454_0.7728_0.7788.png
                gene_name: RBM44
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.77 
      ci_cons_bounds_left: 0.76 
     ci_cons_bounds_right: 0.78 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.79 

Current progress: 80 percent done.
RBM4B
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: 3.210996e-02	ci left: 5.887143e-01	ci right 6.080283e-01	k: 5984	n:10000
KS ci ratio: 1.169719e-02	ci left: 9.127588e-01	ci right 9.235961e-01	k: 9183	n:10000
RBM4B   10000 perm   1 sec   (7070 perm/sec)   p_kst 9.183000e-01   p_cons 5.984000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000144/RBM4B.2_1088_10000_0.9183_0.5984_1.png
                gene_name: RBM4B
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.91 
       ci_ks_bounds_right: 0.92 
                   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.165.3896/
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/181708/iteration1/scatter.0000000144
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 144 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120206: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000145> was used as the working directory.
Started at Wed Oct 10 10:44:49 2012
Results reported at Wed Oct 10 10:46:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000145.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000145.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 145  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     85.34 sec.
    Max Memory :      1429 MB
    Max Swap   :      3919 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.165.3896/
-whichjob
145
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 145: processing genes 13029 - 13118
Calculating significance of each gene.
Using projection method.
13029	RBPMS2	1
13030	RBX1	1
13031	RC3H1	2.363085e-01
13032	RC3H2	1
13033	RCAN1	1
13034	RCAN2	1
13035	RCAN3	1
13036	RCBTB1	3.808324e-02
13037	RCBTB2	1
13038	RCC1	1
13039	RCC2	1
13040	RCCD1	1
13041	RCE1	1
13042	RCHY1	1
13043	RCL1	1
13044	RCN1	1
13045	RCN2	1
13046	RCN3	1
13047	RCOR1	1
13048	RCOR2	1
13049	RCOR3	1
13050	RCSD1	5.966248e-02
13051	RCVRN	1
13052	RD3	1
13053	RDBP	1
13054	RDH10	1
13055	RDH11	1
13056	RDH12	1
13057	RDH13	1
13058	RDH14	1
13059	RDH16	1
13060	RDH5	1
13061	RDH8	1
13062	RDM1	1
13063	RDX	1.589297e-01
13064	REC8	1.362861e-01
13065	RECK	1
13066	RECQL	1.288945e-01
13067	RECQL4	1
13068	RECQL5	3.436419e-02
13069	REEP1	1
13070	REEP2	5.861983e-02
13071	REEP3	1
13072	REEP4	6.936311e-02
13073	REEP5	1
13074	REEP6	1
13075	REG1A	1
13076	REG1B	1
13077	REG3A	1
13078	REG3G	6.471420e-02
13079	REG4	1
13080	REL	1
13081	RELA	2.158285e-01
13082	RELB	1
13083	RELL1	1
13084	RELL2	1
13085	RELN	3.865343e-01
13086	RELT	1
13087	REM1	1
13088	REM2	1
13089	REN	1
13090	RENBP	1
13091	REP15	1
13092	REPIN1	1
13093	REPS1	1
13094	REPS2	1.306989e-01
13095	RER1	1
13096	RERE	1.329920e-01
13097	RERG	1
13098	RERGL	3.448638e-02
13099	REST	1
13100	RET	1
13101	RETN	1
13102	RETNLB	1
13103	RETSAT	1.452951e-01
13104	REV1	1
13105	REV3L	1
13106	REXO1	1
13107	REXO2	1
13108	REXO4	1
13109	RFC1	1.062096e-01
13110	RFC2	1
13111	RFC3	1
13112	RFC4	1.837902e-01
13113	RFC5	1
13114	RFESD	5.310121e-02
13115	RFFL	1
13116	RFK	7.374952e-02
13117	RFNG	1
13118	RFPL1	1
Done

Running MutSig 2:
Scatter job 145: processing genes 13029 - 13118
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: 5.281585e-02	ci left: 3.457140e-01	ci right 3.645704e-01	k: 3551	n:10000
Cons ci ratio: 2.191967e-02	ci left: 7.533254e-01	ci right 7.701219e-01	k: 7618	n:10000
KS ci ratio: 8.112025e-02	ci left: 1.815648e-01	ci right 1.970166e-01	k: 1892	n:10000
RECQL5   10000 perm   2 sec   (4780 perm/sec)   p_kst 1.892000e-01   p_cons 7.618000e-01   p_joint 3.551000e-01

Outputting figure to mutsig2_images.part000000000145/RECQL5.5_3139_10000_0.1892_0.7618_0.3551.png
                gene_name: RECQL5
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.77 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.36 

Current progress: 20 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: 2.399645e-02	ci left: 7.185570e-01	ci right 7.361104e-01	k: 7274	n:10000
KS ci ratio: 3.516050e-02	ci left: 5.442931e-01	ci right 5.638753e-01	k: 5541	n:10000
RELN   10000 perm   3 sec   (3897 perm/sec)   p_kst 5.541000e-01   p_cons 7.274000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000145/RELN.2_10643_10000_0.5541_0.7274_1.png
                gene_name: RELN
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.74 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 40 percent done.
RERE
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.327990e-02	ci left: 8.909790e-01	ci right 9.029887e-01	k: 8971	n:10000
Cons ci ratio: 1.071161e-01	ci left: 1.117389e-01	ci right 1.244845e-01	k: 1180	n:10000
KS ci ratio: 1.096501e-02	ci left: 9.222420e-01	ci right 9.325074e-01	k: 9275	n:10000
RERE   10000 perm   2 sec   (4849 perm/sec)   p_kst 9.275000e-01   p_cons 1.180000e-01   p_joint 8.971000e-01

Joint ci ratio: 4.799040e-02	ci left: 2.441097e-01	ci right 2.561630e-01	k: 5002	n:20000
Cons ci ratio: 7.698740e-02	ci left: 1.103149e-01	ci right 1.191974e-01	k: 2294	n:20000
KS ci ratio: 7.725599e-03	ci left: 9.242789e-01	ci right 9.314961e-01	k: 18559	n:20000
RERE   20000 perm   5 sec   (4323 perm/sec)   p_kst 9.279500e-01   p_cons 1.147000e-01   p_joint 2.501000e-01

Outputting figure to mutsig2_images.part000000000145/RERE.2_4789_20000_0.92795_0.1147_0.2501.png
                gene_name: RERE
               theta_stop: 0.077 
                    nperm: 20000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.25 
     ci_joint_bounds_left: 0.24 
    ci_joint_bounds_right: 0.26 

Current progress: 60 percent done.
RFC1
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: 2.881310e-02	ci left: 6.397543e-01	ci right 6.585588e-01	k: 6492	n:10000
KS ci ratio: 2.829633e-02	ci left: 6.480036e-01	ci right 6.667046e-01	k: 6574	n:10000
RFC1   10000 perm   2 sec   (5730 perm/sec)   p_kst 6.574000e-01   p_cons 6.492000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000145/RFC1.2_3544_10000_0.6574_0.6492_1.png
                gene_name: RFC1
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   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: 80 percent done.
RFC4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.002234e-02	ci left: 7.850257e-01	ci right 8.010033e-01	k: 7931	n:10000
Cons ci ratio: 2.539863e-02	ci left: 6.952470e-01	ci right 7.132339e-01	k: 7043	n:10000
KS ci ratio: 7.027581e-02	ci left: 2.288905e-01	ci right 2.456629e-01	k: 2372	n:10000
RFC4   10000 perm   1 sec   (7216 perm/sec)   p_kst 2.372000e-01   p_cons 7.043000e-01   p_joint 7.931000e-01

Outputting figure to mutsig2_images.part000000000145/RFC4.2_1132_10000_0.2372_0.7043_0.7931.png
                gene_name: RFC4
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.70 
      ci_cons_bounds_left: 0.70 
     ci_cons_bounds_right: 0.71 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.79 
    ci_joint_bounds_right: 0.80 

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.165.3896/
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/181708/iteration1/scatter.0000000145
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 145 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120210: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000146> was used as the working directory.
Started at Wed Oct 10 10:44:49 2012
Results reported at Wed Oct 10 10:46:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000146.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000146.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 146  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    109.98 sec.
    Max Memory :       831 MB
    Max Swap   :      3629 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.165.3896/
-whichjob
146
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 146: processing genes 13119 - 13209
Calculating significance of each gene.
Using projection method.
13119	RFPL2	1
13120	RFPL3	1
13121	RFPL4B	1
13122	RFT1	1
13123	RFTN1	1
13124	RFTN2	5.456727e-04
13125	RFWD2	1
13126	RFWD3	1.473212e-01
13127	RFX1	1
13128	RFX2	1
13129	RFX3	1
13130	RFX4	1
13131	RFX5	1
13132	RFX6	1
13133	RFX7	1
13134	RFXANK	1
13135	RFXAP	1
13136	RG9MTD1	1.676452e-01
13137	RG9MTD2	8.250208e-02
13138	RG9MTD3	1
13139	RGAG1	1
13140	RGAG4	1
13141	RGL1	1
13142	RGL2	2.592329e-01
13143	RGL3	1
13144	RGL4	1
13145	RGMA	1
13146	RGMB	1
13147	RGN	3.540997e-02
13148	RGNEF	1
13149	RGP1	1
13150	RGPD3	4.991926e-02
13151	RGPD4	1.142887e-02
13152	RGPD8	1
13153	RGR	1
13154	RGS1	1
13155	RGS10	1
13156	RGS11	1
13157	RGS12	3.180423e-01
13158	RGS13	1
13159	RGS14	1
13160	RGS16	1
13161	RGS17	1
13162	RGS18	7.068977e-02
13163	RGS19	1
13164	RGS2	1.057770e-01
13165	RGS20	1
13166	RGS21	1
13167	RGS22	2.362274e-01
13168	RGS3	1
13169	RGS4	1
13170	RGS5	1
13171	RGS6	8.566197e-02
13172	RGS7	5.423015e-02
13173	RGS7BP	1
13174	RGS8	1
13175	RGS9	1
13176	RHAG	1
13177	RHBDD1	1
13178	RHBDD2	1
13179	RHBDD3	1
13180	RHBDF1	1
13181	RHBDF2	1
13182	RHBDL1	1.120461e-01
13183	RHBDL2	1
13184	RHBDL3	1
13185	RHBG	1.101894e-01
13186	RHCE	1
13187	RHCG	1.147489e-01
13188	RHD	1
13189	RHEB	1
13190	RHEBL1	1
13191	RHO	1
13192	RHOA	1
13193	RHOB	7.337021e-02
13194	RHOBTB1	1
13195	RHOBTB2	1
13196	RHOBTB3	1
13197	RHOC	1
13198	RHOD	1
13199	RHOF	1
13200	RHOG	1
13201	RHOH	1
13202	RHOJ	1
13203	RHOQ	1
13204	RHOT1	1
13205	RHOT2	1
13206	RHOU	1
13207	RHOV	1
13208	RHOXF1	1
13209	RHPN1	1
Done

Running MutSig 2:
Scatter job 146: processing genes 13119 - 13209
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RFTN2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.242615e-02	ci left: 3.490931e-01	ci right 3.679893e-01	k: 3585	n:10000
Cons ci ratio: 4.031520e-02	ci left: 4.760594e-01	ci right 4.957488e-01	k: 4859	n:10000
KS ci ratio: 5.673863e-02	ci left: 3.138374e-01	ci right 3.322658e-01	k: 3230	n:10000
RFTN2   10000 perm   2 sec   (5928 perm/sec)   p_kst 3.230000e-01   p_cons 4.859000e-01   p_joint 3.585000e-01

Outputting figure to mutsig2_images.part000000000146/RFTN2.3_1542_10000_0.323_0.4859_0.3585.png
                gene_name: RFTN2
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 33 percent done.
RGPD4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.044241e-02	ci left: 7.780316e-01	ci right 7.942014e-01	k: 7862	n:10000
Cons ci ratio: 2.377877e-02	ci left: 7.221923e-01	ci right 7.396730e-01	k: 7310	n:10000
KS ci ratio: 3.361463e-02	ci left: 5.664436e-01	ci right 5.859120e-01	k: 5762	n:10000
RGPD4   10000 perm   3 sec   (3332 perm/sec)   p_kst 5.762000e-01   p_cons 7.310000e-01   p_joint 7.862000e-01

Outputting figure to mutsig2_images.part000000000146/RGPD4.3_5369_10000_0.5762_0.731_0.7862.png
                gene_name: RGPD4
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.58 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.59 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.74 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.79 

Current progress: 67 percent done.
RGPD3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.239686e-03	ci left: 9.634151e-01	ci right 9.705095e-01	k: 9671	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: 4.470359e-02	ci left: 4.248546e-01	ci right 4.443835e-01	k: 4346	n:10000
RGPD3   10000 perm   2 sec   (4081 perm/sec)   p_kst 4.346000e-01   p_cons 8.658000e-01   p_joint 9.671000e-01

Outputting figure to mutsig2_images.part000000000146/RGPD3.2_5369_10000_0.4346_0.8658_0.9671.png
                gene_name: RGPD3
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.87 
      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.165.3896/
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/181708/iteration1/scatter.0000000146
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 146 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120213: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000147> was used as the working directory.
Started at Wed Oct 10 10:44:49 2012
Results reported at Wed Oct 10 10:47:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000147.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000147.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 147  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    150.67 sec.
    Max Memory :      1509 MB
    Max Swap   :      3870 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.165.3896/
-whichjob
147
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 147: processing genes 13210 - 13299
Calculating significance of each gene.
Using projection method.
13210	RHPN2	1
13211	RIBC1	1
13212	RIBC2	1
13213	RIC3	1
13214	RIC8A	1
13215	RIC8B	2.070217e-01
13216	RICH2	2.758976e-01
13217	RICTOR	1
13218	RIF1	7.004847e-01
13219	RILP	1
13220	RILPL1	1
13221	RILPL2	1
13222	RIMBP2	2.989661e-01
13223	RIMKLA	1
13224	RIMKLB	3.764813e-03
13225	RIMS1	4.987500e-01
13226	RIMS2	5.565960e-01
13227	RIMS3	2.233782e-03
13228	RIMS4	1.310965e-01
13229	RIN1	1
13230	RIN2	2.965652e-01
13231	RIN3	3.312502e-01
13232	RING1	1
13233	RINL	7.650631e-02
13234	RINT1	1
13235	RIOK1	1
13236	RIOK2	1.411382e-02
13237	RIOK3	1
13238	RIPK1	1.576292e-01
13239	RIPK2	1
13240	RIPK3	1
13241	RIPK4	1
13242	RIPPLY1	4.271871e-02
13243	RIPPLY2	3.722451e-02
13244	RIT1	1.078064e-01
13245	RIT2	7.244461e-02
13246	RLBP1	1
13247	RLF	1.416262e-01
13248	RLIM	1
13249	RLN1	1
13250	RLN2	1
13251	RLN3	1
13252	RLTPR	1.013318e-01
13253	RMI1	1
13254	RMND1	1
13255	RMND5A	1
13256	RMND5B	1
13257	RNASE1	1
13258	RNASE10	5.950230e-02
13259	RNASE11	1
13260	RNASE12	1
13261	RNASE13	1
13262	RNASE2	1
13263	RNASE3	1
13264	RNASE4	1
13265	RNASE6	1
13266	RNASE7	1
13267	RNASE8	1
13268	RNASE9	1
13269	RNASEH1	1
13270	RNASEH2A	1
13271	RNASEH2B	1
13272	RNASEH2C	1
13273	RNASEK	1
13274	RNASEL	8.890707e-02
13275	RNASEN	1
13276	RNASET2	1
13277	RND1	9.196968e-02
13278	RND2	1
13279	RND3	3.386448e-02
13280	RNF10	1
13281	RNF103	1
13282	RNF11	1
13283	RNF111	3.963979e-01
13284	RNF112	7.888844e-02
13285	RNF113A	1
13286	RNF113B	1.129627e-02
13287	RNF114	1
13288	RNF115	1
13289	RNF121	1
13290	RNF122	1
13291	RNF123	8.814565e-02
13292	RNF125	1
13293	RNF126	1
13294	RNF128	1
13295	RNF13	1
13296	RNF130	1
13297	RNF133	2.754505e-02
13298	RNF135	9.177312e-02
13299	RNF138	1
Done

Running MutSig 2:
Scatter job 147: processing genes 13210 - 13299
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RIMKLB
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.305878e-03	ci left: 9.793064e-01	ci right 9.846075e-01	k: 9821	n:10000
Cons ci ratio: 4.054989e-02	ci left: 4.731620e-01	ci right 4.928479e-01	k: 4830	n:10000
KS ci ratio: 1.072702e-02	ci left: 9.252359e-01	ci right 9.353117e-01	k: 9304	n:10000
RIMKLB   10000 perm   2 sec   (6347 perm/sec)   p_kst 9.304000e-01   p_cons 4.830000e-01   p_joint 9.821000e-01

Outputting figure to mutsig2_images.part000000000147/RIMKLB.2_1181_10000_0.9304_0.483_0.9821.png
                gene_name: RIMKLB
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 12 percent done.
RIMS3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.759650e-02	ci left: 5.109538e-01	ci right 5.306341e-01	k: 5208	n:10000
Cons ci ratio: 3.099272e-02	ci left: 6.056818e-01	ci right 6.248510e-01	k: 6153	n:10000
KS ci ratio: 2.786829e-01	ci left: 1.669424e-02	ci right 2.219075e-02	k: 193	n:10000
RIMS3   10000 perm   1 sec   (6797 perm/sec)   p_kst 1.930000e-02   p_cons 6.153000e-01   p_joint 5.208000e-01

Joint ci ratio: 9.114699e-02	ci left: 8.077881e-02	ci right 8.854244e-02	k: 1692	n:20000
Cons ci ratio: 2.231869e-02	ci left: 5.998398e-01	ci right 6.134291e-01	k: 12133	n:20000
KS ci ratio: 1.968048e-01	ci left: 1.753359e-02	ci right 2.140790e-02	k: 388	n:20000
RIMS3   20000 perm   3 sec   (5950 perm/sec)   p_kst 1.940000e-02   p_cons 6.066500e-01   p_joint 8.460000e-02

Joint ci ratio: 7.406384e-02	ci left: 8.222831e-02	ci right 8.858559e-02	k: 2561	n:30000
Cons ci ratio: 1.810848e-02	ci left: 6.041194e-01	ci right 6.151927e-01	k: 18290	n:30000
KS ci ratio: 1.651492e-01	ci left: 1.690934e-02	ci right 1.998493e-02	k: 552	n:30000
RIMS3   30000 perm   5 sec   (5668 perm/sec)   p_kst 1.840000e-02   p_cons 6.096667e-01   p_joint 8.536667e-02

Joint ci ratio: 7.146786e-02	ci left: 6.744463e-02	ci right 7.246802e-02	k: 2797	n:40000
Cons ci ratio: 1.576228e-02	ci left: 6.024440e-01	ci right 6.120404e-01	k: 24290	n:40000
KS ci ratio: 1.433544e-01	ci left: 1.703317e-02	ci right 1.968741e-02	k: 733	n:40000
RIMS3   40000 perm   7 sec   (5440 perm/sec)   p_kst 1.832500e-02   p_cons 6.072500e-01   p_joint 6.992500e-02

Joint ci ratio: 6.390819e-02	ci left: 6.773918e-02	ci right 7.223090e-02	k: 3498	n:50000
Cons ci ratio: 1.407436e-02	ci left: 6.037648e-01	ci right 6.123427e-01	k: 30403	n:50000
KS ci ratio: 1.270614e-01	ci left: 1.749189e-02	ci right 1.988446e-02	k: 933	n:50000
RIMS3   50000 perm   10 sec   (5120 perm/sec)   p_kst 1.866000e-02   p_cons 6.080600e-01   p_joint 6.996000e-02

Joint ci ratio: 5.844335e-02	ci left: 6.770788e-02	ci right 7.180052e-02	k: 4184	n:60000
Cons ci ratio: 1.285108e-02	ci left: 6.040301e-01	ci right 6.118594e-01	k: 36477	n:60000
KS ci ratio: 1.154567e-01	ci left: 1.776062e-02	ci right 1.995293e-02	k: 1130	n:60000
RIMS3   60000 perm   12 sec   (5030 perm/sec)   p_kst 1.883333e-02   p_cons 6.079500e-01   p_joint 6.973333e-02

Joint ci ratio: 5.034659e-02	ci left: 7.768990e-02	ci right 8.171645e-02	k: 5578	n:70000
Cons ci ratio: 1.189087e-02	ci left: 6.046008e-01	ci right 6.118473e-01	k: 42576	n:70000
KS ci ratio: 1.072032e-01	ci left: 1.773716e-02	ci right 1.976016e-02	k: 1311	n:70000
RIMS3   70000 perm   14 sec   (4943 perm/sec)   p_kst 1.872857e-02   p_cons 6.082286e-01   p_joint 7.968571e-02

Joint ci ratio: 4.814909e-02	ci left: 7.466729e-02	ci right 7.836349e-02	k: 6120	n:80000
Cons ci ratio: 1.113788e-02	ci left: 6.041938e-01	ci right 6.109734e-01	k: 48607	n:80000
KS ci ratio: 1.000562e-01	ci left: 1.788227e-02	ci right 1.977785e-02	k: 1505	n:80000
RIMS3   80000 perm   16 sec   (4850 perm/sec)   p_kst 1.881250e-02   p_cons 6.075875e-01   p_joint 7.650000e-02

Joint ci ratio: 4.525016e-02	ci left: 7.522242e-02	ci right 7.871602e-02	k: 6926	n:90000
Cons ci ratio: 1.049574e-02	ci left: 6.046235e-01	ci right 6.110140e-01	k: 54704	n:90000
KS ci ratio: 9.386221e-02	ci left: 1.811803e-02	ci right 1.991316e-02	k: 1710	n:90000
RIMS3   90000 perm   19 sec   (4757 perm/sec)   p_kst 1.900000e-02   p_cons 6.078222e-01   p_joint 7.695556e-02

Outputting figure to mutsig2_images.part000000000147/RIMS3.2_951_90000_0.019_0.60782_0.076956.png
                gene_name: RIMS3
               theta_stop: 0.094 
                    nperm: 90000 
                     p_ks: 0.019 
        ci_ks_bounds_left: 0.018 
       ci_ks_bounds_right: 0.020 
                   p_cons: 0.61 
      ci_cons_bounds_left: 0.60 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.077 
     ci_joint_bounds_left: 0.075 
    ci_joint_bounds_right: 0.079 

Current progress: 25 percent done.
RINL
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.928828e-02	ci left: 4.889518e-01	ci right 5.086489e-01	k: 4988	n:10000
Cons ci ratio: 4.630365e-02	ci left: 4.077101e-01	ci right 4.271381e-01	k: 4174	n:10000
KS ci ratio: 6.791337e-02	ci left: 2.413392e-01	ci right 2.584067e-01	k: 2498	n:10000
RINL   10000 perm   2 sec   (6465 perm/sec)   p_kst 2.498000e-01   p_cons 4.174000e-01   p_joint 4.988000e-01

Outputting figure to mutsig2_images.part000000000147/RINL.2_1391_10000_0.2498_0.4174_0.4988.png
                gene_name: RINL
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.42 
      ci_cons_bounds_left: 0.41 
     ci_cons_bounds_right: 0.43 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    ci_joint_bounds_right: 0.51 

Current progress: 38 percent done.
RIOK2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.273958e-02	ci left: 4.470006e-01	ci right 4.666246e-01	k: 4568	n:10000
Cons ci ratio: 6.268811e-02	ci left: 2.722050e-01	ci right 2.899227e-01	k: 2810	n:10000
KS ci ratio: 3.485564e-02	ci left: 5.486014e-01	ci right 5.681645e-01	k: 5584	n:10000
RIOK2   10000 perm   2 sec   (6406 perm/sec)   p_kst 5.584000e-01   p_cons 2.810000e-01   p_joint 4.568000e-01

Outputting figure to mutsig2_images.part000000000147/RIOK2.2_1727_10000_0.5584_0.281_0.4568.png
                gene_name: RIOK2
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.28 
      ci_cons_bounds_left: 0.27 
     ci_cons_bounds_right: 0.29 
                  p_joint: 0.46 
     ci_joint_bounds_left: 0.45 
    ci_joint_bounds_right: 0.47 

Current progress: 50 percent done.
RLF
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.234863e-02	ci left: 2.743835e-01	ci right 2.921429e-01	k: 2832	n:10000
Cons ci ratio: 1.627940e-01	ci left: 5.032338e-02	ci right 5.933816e-02	k: 547	n:10000
KS ci ratio: 9.719346e-02	ci left: 1.330589e-01	ci right 1.467516e-01	k: 1398	n:10000
RLF   10000 perm   2 sec   (4635 perm/sec)   p_kst 1.398000e-01   p_cons 5.470000e-02   p_joint 2.832000e-01

Joint ci ratio: 4.825408e-02	ci left: 2.420765e-01	ci right 2.540968e-01	k: 4961	n:20000
Cons ci ratio: 1.136954e-01	ci left: 5.290189e-02	ci right 5.932793e-02	k: 1121	n:20000
KS ci ratio: 6.918798e-02	ci left: 1.334942e-01	ci right 1.431112e-01	k: 2765	n:20000
RLF   20000 perm   5 sec   (4045 perm/sec)   p_kst 1.382500e-01   p_cons 5.605000e-02   p_joint 2.480500e-01

Joint ci ratio: 3.732417e-02	ci left: 2.637892e-01	ci right 2.738556e-01	k: 8064	n:30000
Cons ci ratio: 9.274508e-02	ci left: 5.358768e-02	ci right 5.883202e-02	k: 1685	n:30000
KS ci ratio: 5.608486e-02	ci left: 1.360919e-01	ci right 1.439780e-01	k: 4200	n:30000
RLF   30000 perm   8 sec   (3888 perm/sec)   p_kst 1.400000e-01   p_cons 5.616667e-02   p_joint 2.688000e-01

Outputting figure to mutsig2_images.part000000000147/RLF.2_5777_30000_0.14_0.056167_0.2688.png
                gene_name: RLF
               theta_stop: 0.093 
                    nperm: 30000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.056 
      ci_cons_bounds_left: 0.054 
     ci_cons_bounds_right: 0.059 
                  p_joint: 0.27 
     ci_joint_bounds_left: 0.26 
    ci_joint_bounds_right: 0.27 

Current progress: 62 percent done.
RLTPR
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.098941e-02	ci left: 9.219324e-01	ci right 9.322172e-01	k: 9272	n:10000
Cons ci ratio: 1.931253e-02	ci left: 7.967918e-01	ci right 8.124303e-01	k: 8047	n:10000
KS ci ratio: 3.119598e-02	ci left: 6.025685e-01	ci right 6.217661e-01	k: 6122	n:10000
RLTPR   10000 perm   2 sec   (5300 perm/sec)   p_kst 6.122000e-01   p_cons 8.047000e-01   p_joint 9.272000e-01

Outputting figure to mutsig2_images.part000000000147/RLTPR.2_4460_10000_0.6122_0.8047_0.9272.png
                gene_name: RLTPR
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.80 
     ci_cons_bounds_right: 0.81 
                  p_joint: 0.93 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

Current progress: 75 percent done.
RNF113B
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: 1.140784e-01	ci left: 9.954457e-02	ci right 1.116863e-01	k: 1055	n:10000
KS ci ratio: 6.592598e-02	ci left: 2.525117e-01	ci right 2.698276e-01	k: 2611	n:10000
RNF113B   10000 perm   1 sec   (6733 perm/sec)   p_kst 2.611000e-01   p_cons 1.055000e-01   p_joint 1

Joint ci ratio: 2.546063e-02	ci left: 5.354146e-01	ci right 5.492730e-01	k: 10847	n:20000
Cons ci ratio: 8.060316e-02	ci left: 1.014715e-01	ci right 1.100435e-01	k: 2114	n:20000
KS ci ratio: 4.632892e-02	ci left: 2.574540e-01	ci right 2.697148e-01	k: 5271	n:20000
RNF113B   20000 perm   3 sec   (5948 perm/sec)   p_kst 2.635500e-01   p_cons 1.057000e-01   p_joint 5.423500e-01

Outputting figure to mutsig2_images.part000000000147/RNF113B.2_977_20000_0.26355_0.1057_0.54235.png
                gene_name: RNF113B
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.10 
     ci_cons_bounds_right: 0.11 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.54 
    ci_joint_bounds_right: 0.55 

Current progress: 88 percent done.
RNF123
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: 9.418105e-03	ci left: 9.408695e-01	ci right 9.498689e-01	k: 9455	n:10000
KS ci ratio: 1.092424e-02	ci left: 9.227580e-01	ci right 9.329911e-01	k: 9280	n:10000
RNF123   10000 perm   2 sec   (5376 perm/sec)   p_kst 9.280000e-01   p_cons 9.455000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000147/RNF123.2_4097_10000_0.928_0.9455_1.png
                gene_name: RNF123
               theta_stop: 0.011 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.92 
       ci_ks_bounds_right: 0.93 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000147
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 147 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120216: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000148> was used as the working directory.
Started at Wed Oct 10 10:44:49 2012
Results reported at Wed Oct 10 10:46:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000148.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000148.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 148  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    136.14 sec.
    Max Memory :      1237 MB
    Max Swap   :      3872 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.165.3896/
-whichjob
148
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 148: processing genes 13300 - 13390
Calculating significance of each gene.
Using projection method.
13300	RNF139	1
13301	RNF14	1
13302	RNF141	6.370010e-02
13303	RNF144A	1
13304	RNF144B	1
13305	RNF145	1
13306	RNF146	1
13307	RNF148	1
13308	RNF149	1
13309	RNF150	1
13310	RNF151	1
13311	RNF152	1
13312	RNF157	2.494008e-01
13313	RNF160	1
13314	RNF165	1
13315	RNF166	1
13316	RNF167	1
13317	RNF168	1
13318	RNF169	1.557325e-01
13319	RNF17	1
13320	RNF170	1
13321	RNF175	1
13322	RNF180	1
13323	RNF181	1
13324	RNF182	1
13325	RNF183	1
13326	RNF185	1
13327	RNF186	3.372449e-02
13328	RNF19A	1
13329	RNF19B	1
13330	RNF2	1
13331	RNF20	1
13332	RNF207	1
13333	RNF208	1
13334	RNF212	1
13335	RNF213	1
13336	RNF214	1
13337	RNF215	1
13338	RNF216	3.264830e-02
13339	RNF217	3.847345e-02
13340	RNF219	1
13341	RNF220	1.222236e-01
13342	RNF24	1
13343	RNF25	1.636164e-01
13344	RNF26	1
13345	RNF31	1
13346	RNF32	1
13347	RNF34	1
13348	RNF38	1
13349	RNF39	5.851758e-02
13350	RNF4	1
13351	RNF40	1
13352	RNF41	9.168776e-02
13353	RNF43	1
13354	RNF44	1
13355	RNF5	7.700450e-02
13356	RNF6	1
13357	RNF7	1
13358	RNF8	1.136979e-01
13359	RNFT1	1
13360	RNFT2	3.437571e-02
13361	RNGTT	1
13362	RNH1	1
13363	RNLS	1
13364	RNMT	1
13365	RNMTL1	1
13366	RNPC3	1
13367	RNPEP	1.908874e-01
13368	RNPEPL1	1
13369	RNPS1	4.445695e-02
13370	ROBLD3	1
13371	ROBO1	2.326093e-01
13372	ROBO2	1
13373	ROBO3	1
13374	ROBO4	7.401083e-03
13375	ROCK1	5.178953e-01
13376	ROCK2	1.330580e-01
13377	ROD1	1
13378	ROGDI	1
13379	ROM1	1
13380	ROMO1	1
13381	ROPN1	1
13382	ROPN1B	1
13383	ROPN1L	1
13384	ROR1	1
13385	ROR2	1
13386	RORA	1
13387	RORB	1.327062e-01
13388	RORC	8.544057e-02
13389	ROS1	2.807600e-01
13390	RP1	1.549498e-01
Done

Running MutSig 2:
Scatter job 148: processing genes 13300 - 13390
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RNF216
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.426517e-02	ci left: 1.703508e-01	ci right 1.854373e-01	k: 1778	n:10000
Cons ci ratio: 2.591170e-02	ci left: 6.867776e-01	ci right 7.049082e-01	k: 6959	n:10000
KS ci ratio: 1.065542e-01	ci left: 1.128131e-01	ci right 1.256096e-01	k: 1191	n:10000
RNF216   10000 perm   2 sec   (5128 perm/sec)   p_kst 1.191000e-01   p_cons 6.959000e-01   p_joint 1.778000e-01

Joint ci ratio: 5.068060e-02	ci left: 2.243804e-01	ci right 2.360981e-01	k: 4604	n:20000
Cons ci ratio: 1.855911e-02	ci left: 6.839905e-01	ci right 6.968541e-01	k: 13809	n:20000
KS ci ratio: 7.502540e-02	ci left: 1.155760e-01	ci right 1.246348e-01	k: 2401	n:20000
RNF216   20000 perm   7 sec   (3009 perm/sec)   p_kst 1.200500e-01   p_cons 6.904500e-01   p_joint 2.302000e-01

Outputting figure to mutsig2_images.part000000000148/RNF216.4_2836_20000_0.12005_0.69045_0.2302.png
                gene_name: RNF216
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.69 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.70 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.24 

Current progress: 20 percent done.
ROBO4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.234648e-02	ci left: 3.497889e-01	ci right 3.686932e-01	k: 3592	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: 7.415534e-02	ci left: 2.102365e-01	ci right 2.265279e-01	k: 2183	n:10000
ROBO4   10000 perm   2 sec   (5277 perm/sec)   p_kst 2.183000e-01   p_cons 9.132000e-01   p_joint 3.592000e-01

Outputting figure to mutsig2_images.part000000000148/ROBO4.3_3096_10000_0.2183_0.9132_0.3592.png
                gene_name: ROBO4
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.91 
      ci_cons_bounds_left: 0.91 
     ci_cons_bounds_right: 0.92 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 40 percent done.
ROCK2
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: 1.107050e-02	ci left: 9.209006e-01	ci right 9.312496e-01	k: 9262	n:10000
KS ci ratio: 5.992136e-02	ci left: 2.906312e-01	ci right 3.086857e-01	k: 2996	n:10000
ROCK2   10000 perm   2 sec   (4680 perm/sec)   p_kst 2.996000e-01   p_cons 9.262000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000148/ROCK2.2_4299_10000_0.2996_0.9262_1.png
                gene_name: ROCK2
               theta_stop: 0.060 
                    nperm: 10000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.29 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.93 
      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: 60 percent done.
ROS1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.259546e-01	ci left: 8.271234e-02	ci right 9.392883e-02	k: 882	n:10000
Cons ci ratio: 1.395808e-01	ci left: 6.797633e-02	ci right 7.827401e-02	k: 730	n:10000
KS ci ratio: 6.141010e-02	ci left: 2.805242e-01	ci right 2.983986e-01	k: 2894	n:10000
ROS1   10000 perm   2 sec   (4248 perm/sec)   p_kst 2.894000e-01   p_cons 7.300000e-02   p_joint 8.820000e-02

Joint ci ratio: 5.504969e-02	ci left: 1.966522e-01	ci right 2.078345e-01	k: 4044	n:20000
Cons ci ratio: 9.317593e-02	ci left: 7.749952e-02	ci right 8.512273e-02	k: 1625	n:20000
KS ci ratio: 4.354540e-02	ci left: 2.820284e-01	ci right 2.946332e-01	k: 5766	n:20000
ROS1   20000 perm   5 sec   (3726 perm/sec)   p_kst 2.883000e-01   p_cons 8.125000e-02   p_joint 2.022000e-01

Outputting figure to mutsig2_images.part000000000148/ROS1.2_7216_20000_0.2883_0.08125_0.2022.png
                gene_name: ROS1
               theta_stop: 0.093 
                    nperm: 20000 
                     p_ks: 0.29 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.081 
      ci_cons_bounds_left: 0.077 
     ci_cons_bounds_right: 0.085 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.21 

Current progress: 80 percent done.
RP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.289489e-02	ci left: 4.452043e-01	ci right 4.648220e-01	k: 4550	n:10000
Cons ci ratio: 9.888455e-02	ci left: 1.290445e-01	ci right 1.425684e-01	k: 1357	n:10000
KS ci ratio: 1.465614e-02	ci left: 8.708117e-01	ci right 8.837677e-01	k: 8774	n:10000
RP1   10000 perm   2 sec   (4410 perm/sec)   p_kst 8.774000e-01   p_cons 1.357000e-01   p_joint 4.550000e-01

Outputting figure to mutsig2_images.part000000000148/RP1.2_6483_10000_0.8774_0.1357_0.455.png
                gene_name: RP1
               theta_stop: 0.099 
                    nperm: 10000 
                     p_ks: 0.88 
        ci_ks_bounds_left: 0.87 
       ci_ks_bounds_right: 0.88 
                   p_cons: 0.14 
      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: 0.46 

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.165.3896/
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/181708/iteration1/scatter.0000000148
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 148 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120219: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000149> was used as the working directory.
Started at Wed Oct 10 10:44:49 2012
Results reported at Wed Oct 10 10:49:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000149.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000149.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 149  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    286.57 sec.
    Max Memory :      1422 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.165.3896/
-whichjob
149
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 149: processing genes 13391 - 13480
Calculating significance of each gene.
Using projection method.
13391	RP1L1	1.933028e-01
13392	RP2	1
13393	RP9	3.487674e-02
13394	RPA1	1
13395	RPA2	1
13396	RPA3	1
13397	RPA4	1
13398	RPAIN	1
13399	RPAP1	4.788126e-02
13400	RPAP2	1
13401	RPAP3	1
13402	RPE	1
13403	RPE65	1
13404	RPF1	1
13405	RPF2	1
13406	RPGR	1
13407	RPGRIP1	1.251401e-01
13408	RPGRIP1L	2.024439e-01
13409	RPH3A	1.331856e-01
13410	RPH3AL	1
13411	RPIA	1
13412	RPL10	1.030047e-01
13413	RPL10A	1
13414	RPL10L	1
13415	RPL11	1
13416	RPL12	1
13417	RPL13	1
13418	RPL13A	1
13419	RPL14	1
13420	RPL15	1
13421	RPL17	1
13422	RPL18	1
13423	RPL18A	1
13424	RPL19	1
13425	RPL21	1
13426	RPL22	1
13427	RPL22L1	1
13428	RPL23	1
13429	RPL23A	1
13430	RPL24	1
13431	RPL26	4.977870e-02
13432	RPL26L1	1
13433	RPL27	1
13434	RPL27A	1
13435	RPL28	1
13436	RPL29	1
13437	RPL3	1
13438	RPL30	1
13439	RPL31	7.107675e-02
13440	RPL32	1
13441	RPL34	1
13442	RPL35	1
13443	RPL35A	2.319180e-02
13444	RPL36	1
13445	RPL36A	1
13446	RPL36AL	1
13447	RPL37	1
13448	RPL37A	1
13449	RPL38	1
13450	RPL39	1
13451	RPL39L	1
13452	RPL3L	1
13453	RPL4	1.791271e-01
13454	RPL41	1
13455	RPL5	1
13456	RPL6	1
13457	RPL7	1
13458	RPL7A	1
13459	RPL7L1	1
13460	RPL8	1
13461	RPL9	1
13462	RPLP0	1
13463	RPLP1	1
13464	RPLP2	1
13465	RPN1	1
13466	RPN2	1
13467	RPP14	1
13468	RPP21	1
13469	RPP25	1
13470	RPP30	1
13471	RPP38	1
13472	RPP40	1.383444e-01
13473	RPRD1A	1
13474	RPRD1B	1
13475	RPRD2	4.844208e-02
13476	RPRM	1
13477	RPRML	1
13478	RPS10	1
13479	RPS11	1
13480	RPS12	1
Done

Running MutSig 2:
Scatter job 149: processing genes 13391 - 13480
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RPAP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.884244e-02	ci left: 1.291424e-01	ci right 1.426705e-01	k: 1358	n:10000
Cons ci ratio: 2.897138e-02	ci left: 6.372398e-01	ci right 6.560747e-01	k: 6467	n:10000
KS ci ratio: 2.019685e-01	ci left: 3.262466e-02	ci right 4.004861e-02	k: 362	n:10000
RPAP1   10000 perm   2 sec   (4806 perm/sec)   p_kst 3.620000e-02   p_cons 6.467000e-01   p_joint 1.358000e-01

Joint ci ratio: 8.827251e-02	ci left: 8.577461e-02	ci right 9.374513e-02	k: 1794	n:20000
Cons ci ratio: 2.160270e-02	ci left: 6.153379e-01	ci right 6.288266e-01	k: 12442	n:20000
KS ci ratio: 1.430211e-01	ci left: 3.360565e-02	ci right 3.883031e-02	k: 723	n:20000
RPAP1   20000 perm   6 sec   (3165 perm/sec)   p_kst 3.615000e-02   p_cons 6.221000e-01   p_joint 8.970000e-02

Joint ci ratio: 8.529901e-02	ci left: 6.295458e-02	ci right 6.859654e-02	k: 1972	n:30000
Cons ci ratio: 1.757636e-02	ci left: 6.182564e-01	ci right 6.292530e-01	k: 18713	n:30000
KS ci ratio: 1.185439e-01	ci left: 3.307835e-02	ci right 3.727896e-02	k: 1054	n:30000
RPAP1   30000 perm   9 sec   (3394 perm/sec)   p_kst 3.513333e-02   p_cons 6.237667e-01   p_joint 6.573333e-02

Joint ci ratio: 5.988669e-02	ci left: 9.384519e-02	ci right 9.966350e-02	k: 3869	n:40000
Cons ci ratio: 1.496792e-02	ci left: 6.268760e-01	ci right 6.363549e-01	k: 25265	n:40000
KS ci ratio: 1.036465e-01	ci left: 3.273280e-02	ci right 3.633519e-02	k: 1380	n:40000
RPAP1   40000 perm   11 sec   (3507 perm/sec)   p_kst 3.450000e-02   p_cons 6.316250e-01   p_joint 9.672500e-02

Joint ci ratio: 5.668321e-02	ci left: 8.482007e-02	ci right 8.978797e-02	k: 4364	n:50000
Cons ci ratio: 1.340634e-02	ci left: 6.267329e-01	ci right 6.352119e-01	k: 31549	n:50000
KS ci ratio: 9.196895e-02	ci left: 3.344528e-02	ci right 3.668899e-02	k: 1752	n:50000
RPAP1   50000 perm   15 sec   (3350 perm/sec)   p_kst 3.504000e-02   p_cons 6.309800e-01   p_joint 8.728000e-02

Outputting figure to mutsig2_images.part000000000149/RPAP1.5_4278_50000_0.03504_0.63098_0.08728.png
                gene_name: RPAP1
               theta_stop: 0.092 
                    nperm: 50000 
                     p_ks: 0.035 
        ci_ks_bounds_left: 0.033 
       ci_ks_bounds_right: 0.037 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.64 
                  p_joint: 0.087 
     ci_joint_bounds_left: 0.085 
    ci_joint_bounds_right: 0.090 

Current progress: 20 percent done.
RP1L1
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: 2.466887e-02	ci left: 7.073525e-01	ci right 7.251214e-01	k: 7163	n:10000
KS ci ratio: 5.111871e-02	ci left: 3.607251e-01	ci right 3.797506e-01	k: 3702	n:10000
RP1L1   10000 perm   2 sec   (4029 perm/sec)   p_kst 3.702000e-01   p_cons 7.163000e-01   p_joint 5.921000e-01

Outputting figure to mutsig2_images.part000000000149/RP1L1.3_7215_10000_0.3702_0.7163_0.5921.png
                gene_name: RP1L1
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.36 
       ci_ks_bounds_right: 0.38 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.73 
                  p_joint: 0.59 
     ci_joint_bounds_left: 0.58 
    ci_joint_bounds_right: 0.60 

Current progress: 40 percent done.
RPGRIP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.574205e-02	ci left: 3.215787e-01	ci right 3.401199e-01	k: 3308	n:10000
Cons ci ratio: 2.026603e-02	ci left: 7.809707e-01	ci right 7.970605e-01	k: 7891	n:10000
KS ci ratio: 9.480348e-02	ci left: 1.390351e-01	ci right 1.529718e-01	k: 1459	n:10000
RPGRIP1   10000 perm   2 sec   (5407 perm/sec)   p_kst 1.459000e-01   p_cons 7.891000e-01   p_joint 3.308000e-01

Outputting figure to mutsig2_images.part000000000149/RPGRIP1.3_3957_10000_0.1459_0.7891_0.3308.png
                gene_name: RPGRIP1
               theta_stop: 0.095 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.79 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.80 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 60 percent done.
RPL31
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.258860e-01	ci left: 6.616170e-03	ci right 1.027885e-02	k: 83	n:10000
Cons ci ratio: 9.323853e-02	ci left: 1.431522e-01	ci right 1.572522e-01	k: 1501	n:10000
KS ci ratio: 6.614075e-01	ci left: 2.355713e-03	ci right 4.747948e-03	k: 34	n:10000
RPL31   10000 perm   1 sec   (7044 perm/sec)   p_kst 3.400000e-03   p_cons 1.501000e-01   p_joint 8.300000e-03

Joint ci ratio: 2.976019e-01	ci left: 7.320842e-03	ci right 9.925044e-03	k: 171	n:20000
Cons ci ratio: 6.642579e-02	ci left: 1.433516e-01	ci right 1.532509e-01	k: 2965	n:20000
KS ci ratio: 4.242687e-01	ci left: 3.351426e-03	ci right 5.197284e-03	k: 84	n:20000
RPL31   20000 perm   3 sec   (6207 perm/sec)   p_kst 4.200000e-03   p_cons 1.482500e-01   p_joint 8.550000e-03

Joint ci ratio: 2.397339e-01	ci left: 7.774275e-03	ci right 9.922465e-03	k: 264	n:30000
Cons ci ratio: 5.436592e-02	ci left: 1.436697e-01	ci right 1.517320e-01	k: 4430	n:30000
KS ci ratio: 3.601489e-01	ci left: 3.226442e-03	ci right 4.672237e-03	k: 117	n:30000
RPL31   30000 perm   5 sec   (5855 perm/sec)   p_kst 3.900000e-03   p_cons 1.476667e-01   p_joint 8.800000e-03

Joint ci ratio: 2.068304e-01	ci left: 7.979184e-03	ci right 9.843160e-03	k: 355	n:40000
Cons ci ratio: 4.715734e-02	ci left: 1.438153e-01	ci right 1.507860e-01	k: 5891	n:40000
KS ci ratio: 3.092789e-01	ci left: 3.382116e-03	ci right 4.641571e-03	k: 159	n:40000
RPL31   40000 perm   7 sec   (5639 perm/sec)   p_kst 3.975000e-03   p_cons 1.472750e-01   p_joint 8.875000e-03

Joint ci ratio: 2.100080e-01	ci left: 6.193167e-03	ci right 7.664955e-03	k: 345	n:50000
Cons ci ratio: 4.204173e-02	ci left: 1.449971e-01	ci right 1.512438e-01	k: 7405	n:50000
KS ci ratio: 2.766282e-01	ci left: 3.447092e-03	ci right 4.571698e-03	k: 199	n:50000
RPL31   50000 perm   9 sec   (5473 perm/sec)   p_kst 3.980000e-03   p_cons 1.481000e-01   p_joint 6.900000e-03

Joint ci ratio: 1.946106e-01	ci left: 6.062863e-03	ci right 7.385528e-03	k: 402	n:60000
Cons ci ratio: 3.831093e-02	ci left: 1.457130e-01	ci right 1.514210e-01	k: 8913	n:60000
KS ci ratio: 2.563065e-01	ci left: 3.385869e-03	ci right 4.396384e-03	k: 232	n:60000
RPL31   60000 perm   11 sec   (5326 perm/sec)   p_kst 3.866667e-03   p_cons 1.485500e-01   p_joint 6.700000e-03

Joint ci ratio: 1.817708e-01	ci left: 5.999905e-03	ci right 7.212966e-03	k: 461	n:70000
Cons ci ratio: 3.554872e-02	ci left: 1.453627e-01	ci right 1.506379e-01	k: 10359	n:70000
KS ci ratio: 2.421874e-01	ci left: 3.277181e-03	ci right 4.193285e-03	k: 260	n:70000
RPL31   70000 perm   13 sec   (5195 perm/sec)   p_kst 3.714286e-03   p_cons 1.479857e-01   p_joint 6.585714e-03

Joint ci ratio: 1.720099e-01	ci left: 5.895018e-03	ci right 7.016225e-03	k: 515	n:80000
Cons ci ratio: 3.330399e-02	ci left: 1.451486e-01	ci right 1.500769e-01	k: 11808	n:80000
KS ci ratio: 2.285877e-01	ci left: 3.243954e-03	ci right 4.092667e-03	k: 292	n:80000
RPL31   80000 perm   16 sec   (5076 perm/sec)   p_kst 3.650000e-03   p_cons 1.476000e-01   p_joint 6.437500e-03

Joint ci ratio: 1.621023e-01	ci left: 5.932071e-03	ci right 6.989007e-03	k: 580	n:90000
Cons ci ratio: 3.141614e-02	ci left: 1.451560e-01	ci right 1.498001e-01	k: 13272	n:90000
KS ci ratio: 2.173842e-01	ci left: 3.208723e-03	ci right 4.001580e-03	k: 323	n:90000
RPL31   90000 perm   18 sec   (4964 perm/sec)   p_kst 3.588889e-03   p_cons 1.474667e-01   p_joint 6.444444e-03

Joint ci ratio: 1.549423e-01	ci left: 5.867037e-03	ci right 6.861921e-03	k: 635	n:100000
Cons ci ratio: 3.290233e-02	ci left: 1.222511e-01	ci right 1.263507e-01	k: 12429	n:100000
KS ci ratio: 2.079755e-01	ci left: 3.171871e-03	ci right 3.917382e-03	k: 353	n:100000
RPL31   100000 perm   21 sec   (4861 perm/sec)   p_kst 3.530000e-03   p_cons 1.242900e-01   p_joint 6.350000e-03

Joint ci ratio: 1.472664e-01	ci left: 5.928502e-03	ci right 6.879622e-03	k: 703	n:110000
Cons ci ratio: 3.138950e-02	ci left: 1.222202e-01	ci right 1.261269e-01	k: 13658	n:110000
KS ci ratio: 1.976359e-01	ci left: 3.211446e-03	ci right 3.924214e-03	k: 391	n:110000
RPL31   110000 perm   23 sec   (4726 perm/sec)   p_kst 3.554545e-03   p_cons 1.241636e-01   p_joint 6.390909e-03

Joint ci ratio: 1.399010e-01	ci left: 6.045077e-03	ci right 6.962351e-03	k: 779	n:120000
Cons ci ratio: 3.008052e-02	ci left: 1.221071e-01	ci right 1.258445e-01	k: 14876	n:120000
KS ci ratio: 1.878247e-01	ci left: 3.276956e-03	ci right 3.964043e-03	k: 433	n:120000
RPL31   120000 perm   26 sec   (4558 perm/sec)   p_kst 3.608333e-03   p_cons 1.239667e-01   p_joint 6.491667e-03

Joint ci ratio: 1.349765e-01	ci left: 6.010878e-03	ci right 6.888278e-03	k: 837	n:130000
Cons ci ratio: 2.891042e-02	ci left: 1.221059e-01	ci right 1.256955e-01	k: 16106	n:130000
KS ci ratio: 1.814595e-01	ci left: 3.252320e-03	ci right 3.908592e-03	k: 464	n:130000
RPL31   130000 perm   29 sec   (4484 perm/sec)   p_kst 3.569231e-03   p_cons 1.238923e-01   p_joint 6.438462e-03

Joint ci ratio: 1.302455e-01	ci left: 6.009697e-03	ci right 6.853798e-03	k: 899	n:140000
Cons ci ratio: 2.783315e-02	ci left: 1.223701e-01	ci right 1.258312e-01	k: 17373	n:140000
KS ci ratio: 1.749938e-01	ci left: 3.258862e-03	ci right 3.890545e-03	k: 499	n:140000
RPL31   140000 perm   32 sec   (4411 perm/sec)   p_kst 3.564286e-03   p_cons 1.240929e-01   p_joint 6.421429e-03

Joint ci ratio: 1.250024e-01	ci left: 6.106017e-03	ci right 6.926566e-03	k: 976	n:150000
Cons ci ratio: 2.688855e-02	ci left: 1.224355e-01	ci right 1.257791e-01	k: 18615	n:150000
KS ci ratio: 1.682292e-01	ci left: 3.303207e-03	ci right 3.916227e-03	k: 540	n:150000
RPL31   150000 perm   35 sec   (4342 perm/sec)   p_kst 3.600000e-03   p_cons 1.241000e-01   p_joint 6.506667e-03

Joint ci ratio: 1.216297e-01	ci left: 6.057529e-03	ci right 6.848016e-03	k: 1031	n:160000
Cons ci ratio: 2.603104e-02	ci left: 1.225193e-01	ci right 1.257568e-01	k: 19861	n:160000
KS ci ratio: 1.637534e-01	ci left: 3.276464e-03	ci right 3.866750e-03	k: 570	n:160000
RPL31   160000 perm   37 sec   (4275 perm/sec)   p_kst 3.562500e-03   p_cons 1.241312e-01   p_joint 6.443750e-03

Joint ci ratio: 1.176477e-01	ci left: 6.106362e-03	ci right 6.875320e-03	k: 1102	n:170000
Cons ci ratio: 2.523020e-02	ci left: 1.227702e-01	ci right 1.259132e-01	k: 21137	n:170000
KS ci ratio: 1.580411e-01	ci left: 3.320850e-03	ci right 3.896283e-03	k: 612	n:170000
RPL31   170000 perm   40 sec   (4206 perm/sec)   p_kst 3.600000e-03   p_cons 1.243353e-01   p_joint 6.482353e-03

Joint ci ratio: 1.136437e-01	ci left: 6.193330e-03	ci right 6.944916e-03	k: 1181	n:180000
Cons ci ratio: 2.450710e-02	ci left: 1.229228e-01	ci right 1.259782e-01	k: 22400	n:180000
KS ci ratio: 1.526540e-01	ci left: 3.371309e-03	ci right 3.933752e-03	k: 656	n:180000
RPL31   180000 perm   43 sec   (4142 perm/sec)   p_kst 3.644444e-03   p_cons 1.244444e-01   p_joint 6.561111e-03

Joint ci ratio: 1.106871e-01	ci left: 6.194758e-03	ci right 6.925683e-03	k: 1245	n:190000
Cons ci ratio: 2.385952e-02	ci left: 1.229086e-01	ci right 1.258818e-01	k: 23634	n:190000
KS ci ratio: 1.485288e-01	ci left: 3.381272e-03	ci right 3.928780e-03	k: 693	n:190000
RPL31   190000 perm   47 sec   (4080 perm/sec)   p_kst 3.647368e-03   p_cons 1.243895e-01   p_joint 6.552632e-03

Joint ci ratio: 1.084931e-01	ci left: 6.133019e-03	ci right 6.841399e-03	k: 1296	n:200000
Cons ci ratio: 2.326176e-02	ci left: 1.228869e-01	ci right 1.257840e-01	k: 24866	n:200000
KS ci ratio: 1.454214e-01	ci left: 3.356689e-03	ci right 3.887858e-03	k: 723	n:200000
RPL31   200000 perm   50 sec   (4015 perm/sec)   p_kst 3.615000e-03   p_cons 1.243300e-01   p_joint 6.480000e-03

Joint ci ratio: 1.052521e-01	ci left: 6.216390e-03	ci right 6.911622e-03	k: 1377	n:210000
Cons ci ratio: 2.269389e-02	ci left: 1.229912e-01	ci right 1.258191e-01	k: 26124	n:210000
KS ci ratio: 1.410994e-01	ci left: 3.403459e-03	ci right 3.924675e-03	k: 768	n:210000
RPL31   210000 perm   53 sec   (3952 perm/sec)   p_kst 3.657143e-03   p_cons 1.244000e-01   p_joint 6.557143e-03

Joint ci ratio: 1.022499e-01	ci left: 6.296896e-03	ci right 6.979837e-03	k: 1459	n:220000
Cons ci ratio: 2.216197e-02	ci left: 1.231231e-01	ci right 1.258868e-01	k: 27390	n:220000
KS ci ratio: 1.371412e-01	ci left: 3.446188e-03	ci right 3.957934e-03	k: 813	n:220000
RPL31   220000 perm   57 sec   (3893 perm/sec)   p_kst 3.695455e-03   p_cons 1.245000e-01   p_joint 6.631818e-03

Joint ci ratio: 1.001466e-01	ci left: 6.285858e-03	ci right 6.952754e-03	k: 1521	n:230000
Cons ci ratio: 2.165068e-02	ci left: 1.233956e-01	ci right 1.261008e-01	k: 28691	n:230000
KS ci ratio: 1.342852e-01	ci left: 3.443361e-03	ci right 3.943188e-03	k: 848	n:230000
RPL31   230000 perm   60 sec   (3840 perm/sec)   p_kst 3.686957e-03   p_cons 1.247435e-01   p_joint 6.613043e-03

Joint ci ratio: 9.813676e-02	ci left: 6.279938e-03	ci right 6.932064e-03	k: 1584	n:240000
Cons ci ratio: 2.118007e-02	ci left: 1.235756e-01	ci right 1.262251e-01	k: 29975	n:240000
KS ci ratio: 1.317502e-01	ci left: 3.432810e-03	ci right 3.920963e-03	k: 881	n:240000
RPL31   240000 perm   63 sec   (3788 perm/sec)   p_kst 3.670833e-03   p_cons 1.248958e-01   p_joint 6.600000e-03

Joint ci ratio: 9.595067e-02	ci left: 6.313658e-03	ci right 6.953860e-03	k: 1657	n:250000
Cons ci ratio: 2.076317e-02	ci left: 1.234869e-01	ci right 1.260818e-01	k: 31195	n:250000
KS ci ratio: 1.285105e-01	ci left: 3.469643e-03	ci right 3.949976e-03	k: 926	n:250000
RPL31   250000 perm   67 sec   (3734 perm/sec)   p_kst 3.704000e-03   p_cons 1.247800e-01   p_joint 6.628000e-03

Joint ci ratio: 9.442757e-02	ci left: 6.273567e-03	ci right 6.899047e-03	k: 1711	n:260000
Cons ci ratio: 2.035668e-02	ci left: 1.235472e-01	ci right 1.260919e-01	k: 32452	n:260000
KS ci ratio: 1.262834e-01	ci left: 3.459072e-03	ci right 3.929021e-03	k: 959	n:260000
RPL31   260000 perm   71 sec   (3680 perm/sec)   p_kst 3.688462e-03   p_cons 1.248154e-01   p_joint 6.580769e-03

Joint ci ratio: 9.203516e-02	ci left: 6.366788e-03	ci right 6.984613e-03	k: 1801	n:270000
Cons ci ratio: 1.997791e-02	ci left: 1.235519e-01	ci right 1.260488e-01	k: 33695	n:270000
KS ci ratio: 1.229928e-01	ci left: 3.517553e-03	ci right 3.982088e-03	k: 1011	n:270000
RPL31   270000 perm   74 sec   (3628 perm/sec)   p_kst 3.744444e-03   p_cons 1.247963e-01   p_joint 6.670370e-03

Joint ci ratio: 9.049236e-02	ci left: 6.355776e-03	ci right 6.961646e-03	k: 1863	n:280000
Cons ci ratio: 1.963043e-02	ci left: 1.234357e-01	ci right 1.258864e-01	k: 34904	n:280000
KS ci ratio: 1.210944e-01	ci left: 3.502721e-03	ci right 3.957646e-03	k: 1043	n:280000
RPL31   280000 perm   78 sec   (3577 perm/sec)   p_kst 3.725000e-03   p_cons 1.246571e-01   p_joint 6.653571e-03

Joint ci ratio: 8.907121e-02	ci left: 6.338860e-03	ci right 6.933133e-03	k: 1923	n:290000
Cons ci ratio: 1.928584e-02	ci left: 1.234927e-01	ci right 1.259010e-01	k: 36161	n:290000
KS ci ratio: 1.191701e-01	ci left: 3.495655e-03	ci right 3.941939e-03	k: 1077	n:290000
RPL31   290000 perm   82 sec   (3528 perm/sec)   p_kst 3.713793e-03   p_cons 1.246931e-01   p_joint 6.631034e-03

Joint ci ratio: 8.760391e-02	ci left: 6.339444e-03	ci right 6.923481e-03	k: 1988	n:300000
Cons ci ratio: 1.895502e-02	ci left: 1.235895e-01	ci right 1.259578e-01	k: 37431	n:300000
KS ci ratio: 1.172290e-01	ci left: 3.495585e-03	ci right 3.934088e-03	k: 1113	n:300000
RPL31   300000 perm   87 sec   (3432 perm/sec)   p_kst 3.710000e-03   p_cons 1.247700e-01   p_joint 6.626667e-03

Joint ci ratio: 8.610138e-02	ci left: 6.355850e-03	ci right 6.930850e-03	k: 2058	n:310000
Cons ci ratio: 1.862472e-02	ci left: 1.238666e-01	ci right 1.261985e-01	k: 38759	n:310000
KS ci ratio: 1.150788e-01	ci left: 3.514374e-03	ci right 3.946598e-03	k: 1155	n:310000
RPL31   310000 perm   92 sec   (3382 perm/sec)   p_kst 3.725806e-03   p_cons 1.250290e-01   p_joint 6.638710e-03

Joint ci ratio: 8.485434e-02	ci left: 6.343778e-03	ci right 6.908962e-03	k: 2119	n:320000
Cons ci ratio: 1.832442e-02	ci left: 1.239680e-01	ci right 1.262638e-01	k: 40036	n:320000
KS ci ratio: 1.134713e-01	ci left: 3.504726e-03	ci right 3.929339e-03	k: 1188	n:320000
RPL31   320000 perm   96 sec   (3328 perm/sec)   p_kst 3.712500e-03   p_cons 1.251125e-01   p_joint 6.621875e-03

Joint ci ratio: 8.356360e-02	ci left: 6.347331e-03	ci right 6.903810e-03	k: 2185	n:330000
Cons ci ratio: 1.803968e-02	ci left: 1.240455e-01	ci right 1.263066e-01	k: 41307	n:330000
KS ci ratio: 1.122062e-01	ci left: 3.478028e-03	ci right 3.894398e-03	k: 1215	n:330000
RPL31   330000 perm   100 sec   (3288 perm/sec)   p_kst 3.681818e-03   p_cons 1.251727e-01   p_joint 6.621212e-03

Joint ci ratio: 8.223816e-02	ci left: 6.365142e-03	ci right 6.913906e-03	k: 2256	n:340000
Cons ci ratio: 1.778215e-02	ci left: 1.239428e-01	ci right 1.261695e-01	k: 42518	n:340000
KS ci ratio: 1.106258e-01	ci left: 3.475806e-03	ci right 3.885666e-03	k: 1250	n:340000
RPL31   340000 perm   105 sec   (3245 perm/sec)   p_kst 3.676471e-03   p_cons 1.250529e-01   p_joint 6.635294e-03

Joint ci ratio: 8.120241e-02	ci left: 6.345605e-03	ci right 6.885469e-03	k: 2314	n:350000
Cons ci ratio: 1.752137e-02	ci left: 1.240199e-01	ci right 1.262149e-01	k: 43790	n:350000
KS ci ratio: 1.093238e-01	ci left: 3.459852e-03	ci right 3.862720e-03	k: 1280	n:350000
RPL31   350000 perm   109 sec   (3203 perm/sec)   p_kst 3.657143e-03   p_cons 1.251143e-01   p_joint 6.611429e-03

Joint ci ratio: 7.991717e-02	ci left: 6.373478e-03	ci right 6.906732e-03	k: 2389	n:360000
Cons ci ratio: 1.727109e-02	ci left: 1.241012e-01	ci right 1.262660e-01	k: 45065	n:360000
KS ci ratio: 1.077783e-01	ci left: 3.463732e-03	ci right 3.860989e-03	k: 1317	n:360000
RPL31   360000 perm   114 sec   (3164 perm/sec)   p_kst 3.658333e-03   p_cons 1.251806e-01   p_joint 6.636111e-03

Joint ci ratio: 7.888461e-02	ci left: 6.368111e-03	ci right 6.893715e-03	k: 2452	n:370000
Cons ci ratio: 1.703501e-02	ci left: 1.241298e-01	ci right 1.262652e-01	k: 46322	n:370000
KS ci ratio: 1.063359e-01	ci left: 3.464810e-03	ci right 3.856540e-03	k: 1353	n:370000
RPL31   370000 perm   118 sec   (3126 perm/sec)   p_kst 3.656757e-03   p_cons 1.251946e-01   p_joint 6.627027e-03

Joint ci ratio: 7.764293e-02	ci left: 6.404360e-03	ci right 6.924259e-03	k: 2531	n:380000
Cons ci ratio: 1.679444e-02	ci left: 1.243381e-01	ci right 1.264466e-01	k: 47648	n:380000
KS ci ratio: 1.044982e-01	ci left: 3.496619e-03	ci right 3.884694e-03	k: 1401	n:380000
RPL31   380000 perm   123 sec   (3091 perm/sec)   p_kst 3.686842e-03   p_cons 1.253895e-01   p_joint 6.660526e-03

Joint ci ratio: 7.665043e-02	ci left: 6.406111e-03	ci right 6.919208e-03	k: 2597	n:390000
Cons ci ratio: 1.657500e-02	ci left: 1.243877e-01	ci right 1.264692e-01	k: 48916	n:390000
KS ci ratio: 1.033625e-01	ci left: 3.484382e-03	ci right 3.866640e-03	k: 1432	n:390000
RPL31   390000 perm   128 sec   (3055 perm/sec)   p_kst 3.671795e-03   p_cons 1.254256e-01   p_joint 6.658974e-03

Joint ci ratio: 7.555241e-02	ci left: 6.432346e-03	ci right 6.939840e-03	k: 2673	n:400000
Cons ci ratio: 1.635798e-02	ci left: 1.245147e-01	ci right 1.265707e-01	k: 50216	n:400000
KS ci ratio: 1.021930e-01	ci left: 3.477651e-03	ci right 3.854595e-03	k: 1465	n:400000
RPL31   400000 perm   132 sec   (3020 perm/sec)   p_kst 3.662500e-03   p_cons 1.255400e-01   p_joint 6.682500e-03

Joint ci ratio: 7.465072e-02	ci left: 6.431018e-03	ci right 6.932089e-03	k: 2738	n:410000
Cons ci ratio: 1.615967e-02	ci left: 1.244947e-01	ci right 1.265253e-01	k: 51458	n:410000
KS ci ratio: 1.011301e-01	ci left: 3.466517e-03	ci right 3.838113e-03	k: 1496	n:410000
RPL31   410000 perm   137 sec   (2985 perm/sec)   p_kst 3.648780e-03   p_cons 1.255073e-01   p_joint 6.678049e-03

Joint ci ratio: 7.388675e-02	ci left: 6.411090e-03	ci right 6.905277e-03	k: 2795	n:420000
Cons ci ratio: 1.596321e-02	ci left: 1.245469e-01	ci right 1.265535e-01	k: 52730	n:420000
KS ci ratio: 1.000011e-01	ci left: 3.462897e-03	ci right 3.829718e-03	k: 1530	n:420000
RPL31   420000 perm   142 sec   (2950 perm/sec)   p_kst 3.642857e-03   p_cons 1.255476e-01   p_joint 6.654762e-03

Joint ci ratio: 7.304273e-02	ci left: 6.410381e-03	ci right 6.898628e-03	k: 2860	n:430000
Cons ci ratio: 1.578009e-02	ci left: 1.245089e-01	ci right 1.264915e-01	k: 53964	n:430000
KS ci ratio: 9.884582e-02	ci left: 3.464003e-03	ci right 3.826457e-03	k: 1566	n:430000
RPL31   430000 perm   147 sec   (2916 perm/sec)   p_kst 3.641860e-03   p_cons 1.254977e-01   p_joint 6.651163e-03

Outputting figure to mutsig2_images.part000000000149/RPL31.3_459_430000_0.0036419_0.1255_0.0066512.png
                gene_name: RPL31
               theta_stop: 0.099 
                    nperm: 430000 
                     p_ks: 0.0036 
        ci_ks_bounds_left: 0.0035 
       ci_ks_bounds_right: 0.0038 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.0067 
     ci_joint_bounds_left: 0.0064 
    ci_joint_bounds_right: 0.0069 

Current progress: 80 percent done.
RPRD2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.492393e-02	ci left: 2.067847e-01	ci right 2.229817e-01	k: 2148	n:10000
Cons ci ratio: 6.540060e-02	ci left: 2.555781e-01	ci right 2.729595e-01	k: 2642	n:10000
KS ci ratio: 1.656929e-01	ci left: 4.859368e-02	ci right 5.746898e-02	k: 529	n:10000
RPRD2   10000 perm   2 sec   (5185 perm/sec)   p_kst 5.290000e-02   p_cons 2.642000e-01   p_joint 2.148000e-01

Joint ci ratio: 4.684764e-02	ci left: 2.531870e-01	ci right 2.653831e-01	k: 5185	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: 1.186500e-01	ci left: 4.867167e-02	ci right 5.485947e-02	k: 1034	n:20000
RPRD2   20000 perm   4 sec   (4669 perm/sec)   p_kst 5.170000e-02   p_cons 2.626500e-01   p_joint 2.592500e-01

Joint ci ratio: 3.337709e-02	ci left: 3.096787e-01	ci right 3.202238e-01	k: 9448	n:30000
Cons ci ratio: 3.799384e-02	ci left: 2.568982e-01	ci right 2.668813e-01	k: 7856	n:30000
KS ci ratio: 9.715883e-02	ci left: 4.896076e-02	ci right 5.399322e-02	k: 1543	n:30000
RPRD2   30000 perm   7 sec   (4455 perm/sec)   p_kst 5.143333e-02   p_cons 2.618667e-01   p_joint 3.149333e-01

Outputting figure to mutsig2_images.part000000000149/RPRD2.2_4430_30000_0.051433_0.26187_0.31493.png
                gene_name: RPRD2
               theta_stop: 0.097 
                    nperm: 30000 
                     p_ks: 0.051 
        ci_ks_bounds_left: 0.049 
       ci_ks_bounds_right: 0.054 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.31 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.32 

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.165.3896/
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/181708/iteration1/scatter.0000000149
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 149 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1546>
Subject: Job 1120222: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1546>, 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/181708/iteration1/scatter.0000000150> was used as the working directory.
Started at Wed Oct 10 10:44:49 2012
Results reported at Wed Oct 10 10:46:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000150.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000150.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 150  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    115.37 sec.
    Max Memory :       936 MB
    Max Swap   :      3728 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.165.3896/
-whichjob
150
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 150: processing genes 13481 - 13571
Calculating significance of each gene.
Using projection method.
13481	RPS13	1
13482	RPS14	1
13483	RPS15	1
13484	RPS15A	1
13485	RPS16	1
13486	RPS18	7.713117e-02
13487	RPS19	1
13488	RPS19BP1	1
13489	RPS2	3.179243e-02
13490	RPS20	1
13491	RPS21	1
13492	RPS23	1
13493	RPS24	1
13494	RPS25	1
13495	RPS26	1
13496	RPS27	1
13497	RPS27A	6.584913e-02
13498	RPS27L	1
13499	RPS28	1
13500	RPS29	1
13501	RPS3	1
13502	RPS3A	1
13503	RPS4X	1
13504	RPS4Y1	1
13505	RPS4Y2	1
13506	RPS5	1
13507	RPS6	1.136827e-01
13508	RPS6KA1	1
13509	RPS6KA2	1
13510	RPS6KA3	1
13511	RPS6KA4	1
13512	RPS6KA5	3.084608e-01
13513	RPS6KA6	1
13514	RPS6KB1	1
13515	RPS6KB2	1
13516	RPS6KC1	1.061308e-02
13517	RPS6KL1	1
13518	RPS7	1
13519	RPS8	1
13520	RPS9	7.281228e-02
13521	RPSA	1
13522	RPTN	1
13523	RPTOR	1
13524	RPUSD1	1
13525	RPUSD2	1
13526	RPUSD3	1
13527	RPUSD4	1
13528	RQCD1	1
13529	RRAD	1.099657e-01
13530	RRAGA	1
13531	RRAGB	1
13532	RRAGC	1
13533	RRAGD	1
13534	RRAS	1
13535	RRAS2	1
13536	RRBP1	1
13537	RREB1	1
13538	RRH	1
13539	RRM1	1
13540	RRM2	1
13541	RRM2B	1
13542	RRN3	1
13543	RRP1	1
13544	RRP12	1
13545	RRP15	1
13546	RRP1B	1
13547	RRP7A	1
13548	RRP8	1
13549	RRP9	1
13550	RRS1	1
13551	RS1	1
13552	RSAD1	1
13553	RSAD2	1
13554	RSBN1	2.715082e-01
13555	RSBN1L	2.633426e-01
13556	RSC1A1	1
13557	RSF1	1
13558	RSL1D1	2.423072e-01
13559	RSL24D1	1
13560	RSPH1	1
13561	RSPH10B	1
13562	RSPH10B2	1
13563	RSPH3	1
13564	RSPH4A	1
13565	RSPH6A	8.487825e-02
13566	RSPH9	1.096436e-01
13567	RSPO1	1
13568	RSPO2	1
13569	RSPO3	1
13570	RSPO4	1
13571	RSPRY1	2.707225e-02
Done

Running MutSig 2:
Scatter job 150: processing genes 13481 - 13571
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
RPS6KC1
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: 1.605409e-02	ci left: 8.493730e-01	ci right 8.632188e-01	k: 8564	n:10000
KS ci ratio: 3.827998e-02	ci left: 5.019507e-01	ci right 5.216425e-01	k: 5118	n:10000
RPS6KC1   10000 perm   2 sec   (4385 perm/sec)   p_kst 5.118000e-01   p_cons 8.564000e-01   p_joint 8.083000e-01

Outputting figure to mutsig2_images.part000000000150/RPS6KC1.3_3261_10000_0.5118_0.8564_0.8083.png
                gene_name: RPS6KC1
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.52 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.81 
     ci_joint_bounds_left: 0.80 
    ci_joint_bounds_right: 0.82 

Current progress: 50 percent done.
RSPRY1
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: 2.796419e-02	ci left: 6.533372e-01	ci right 6.719680e-01	k: 6627	n:10000
KS ci ratio: 4.944042e-02	ci left: 3.763431e-01	ci right 3.955234e-01	k: 3859	n:10000
RSPRY1   10000 perm   2 sec   (5307 perm/sec)   p_kst 3.859000e-01   p_cons 6.627000e-01   p_joint 4.006000e-01

Outputting figure to mutsig2_images.part000000000150/RSPRY1.3_1787_10000_0.3859_0.6627_0.4006.png
                gene_name: RSPRY1
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.66 
      ci_cons_bounds_left: 0.65 
     ci_cons_bounds_right: 0.67 
                  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.165.3896/
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/181708/iteration1/scatter.0000000150
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 150 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120225: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000151> was used as the working directory.
Started at Wed Oct 10 10:44:49 2012
Results reported at Wed Oct 10 10:47:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000151.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000151.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 151  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    194.54 sec.
    Max Memory :      1446 MB
    Max Swap   :      3855 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.165.3896/
-whichjob
151
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 151: processing genes 13572 - 13661
Calculating significance of each gene.
Using projection method.
13572	RSRC1	1
13573	RSRC2	6.574060e-02
13574	RSU1	1
13575	RTBDN	1
13576	RTCD1	1
13577	RTDR1	1
13578	RTEL1	1
13579	RTF1	1
13580	RTKN	1
13581	RTKN2	2.691216e-01
13582	RTN1	1.272279e-01
13583	RTN2	2.082918e-01
13584	RTN3	3.982179e-01
13585	RTN4	1
13586	RTN4IP1	1
13587	RTN4R	1
13588	RTN4RL1	1
13589	RTN4RL2	1
13590	RTP1	1
13591	RTP2	1
13592	RTP3	7.713051e-02
13593	RTP4	1
13594	RTTN	6.751745e-01
13595	RUFY1	2.330056e-01
13596	RUFY2	1
13597	RUFY3	1
13598	RUFY4	1
13599	RUNDC1	1
13600	RUNDC2A	1
13601	RUNDC3A	1
13602	RUNDC3B	1
13603	RUNX1	1
13604	RUNX1T1	1
13605	RUNX2	3.626060e-02
13606	RUNX3	1
13607	RUSC1	3.925417e-02
13608	RUSC2	3.960512e-01
13609	RUVBL1	1
13610	RUVBL2	2.162369e-01
13611	RWDD1	1
13612	RWDD2A	1
13613	RWDD2B	1
13614	RWDD3	1
13615	RWDD4A	1
13616	RXFP1	1
13617	RXFP2	1
13618	RXFP3	1
13619	RXFP4	1
13620	RXRA	1
13621	RXRB	1
13622	RXRG	1.009901e-02
13623	RYBP	1
13624	RYK	1
13625	RYR1	7.233931e-01
13626	RYR2	6.579424e-02
13627	RYR3	5.923209e-01
13628	S100A1	1
13629	S100A10	1
13630	S100A11	1
13631	S100A12	1
13632	S100A13	1
13633	S100A14	1
13634	S100A16	1
13635	S100A2	1
13636	S100A3	1
13637	S100A4	1
13638	S100A5	1
13639	S100A6	1
13640	S100A7	1
13641	S100A7A	1
13642	S100A7L2	1
13643	S100A8	1
13644	S100A9	1
13645	S100B	1
13646	S100G	1.211826e-02
13647	S100P	1
13648	S100PBP	1
13649	S100Z	1
13650	S1PR1	2.330523e-02
13651	S1PR2	1
13652	S1PR3	1
13653	S1PR4	1
13654	S1PR5	1
13655	SAA1	1
13656	SAA2	1
13657	SAA4	1
13658	SAAL1	1
13659	SAC3D1	1
13660	SACM1L	1
13661	SACS	4.680441e-01
Done

Running MutSig 2:
Scatter job 151: processing genes 13572 - 13661
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SACS
Processing conservation and coverage...
72% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.043521e-02	ci left: 3.669909e-01	ci right 3.860810e-01	k: 3765	n:10000
Cons ci ratio: 3.347034e-02	ci left: 5.685494e-01	ci right 5.880049e-01	k: 5783	n:10000
KS ci ratio: 6.312521e-02	ci left: 2.694328e-01	ci right 2.870966e-01	k: 2782	n:10000
SACS   10000 perm   5 sec   (2209 perm/sec)   p_kst 2.782000e-01   p_cons 5.783000e-01   p_joint 3.765000e-01

Outputting figure to mutsig2_images.part000000000151/SACS.6_13776_10000_0.2782_0.5783_0.3765.png
                gene_name: SACS
               theta_stop: 0.063 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.58 
      ci_cons_bounds_left: 0.57 
     ci_cons_bounds_right: 0.59 
                  p_joint: 0.38 
     ci_joint_bounds_left: 0.37 
    ci_joint_bounds_right: 0.39 

Current progress: 17 percent done.
RYR2
Processing conservation and coverage...
65% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.397384e-02	ci left: 8.809390e-01	ci right 8.934345e-01	k: 8873	n:10000
Cons ci ratio: 3.289058e-02	ci left: 5.770748e-01	ci right 5.964746e-01	k: 5868	n:10000
KS ci ratio: 3.500427e-02	ci left: 5.464973e-01	ci right 5.660699e-01	k: 5563	n:10000
RYR2   10000 perm   5 sec   (2213 perm/sec)   p_kst 5.563000e-01   p_cons 5.868000e-01   p_joint 8.873000e-01

Outputting figure to mutsig2_images.part000000000151/RYR2.5_15324_10000_0.5563_0.5868_0.8873.png
                gene_name: RYR2
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.60 
                  p_joint: 0.89 
     ci_joint_bounds_left: 0.88 
    ci_joint_bounds_right: 0.89 

Current progress: 33 percent done.
RYR1
Processing conservation and coverage...
64% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.913932e-02	ci left: 3.792292e-01	ci right 3.984357e-01	k: 3888	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: 5.781514e-03	ci left: 9.757832e-01	ci right 9.815332e-01	k: 9788	n:10000
RYR1   10000 perm   4 sec   (2285 perm/sec)   p_kst 9.788000e-01   p_cons 1.217000e-01   p_joint 3.888000e-01

Joint ci ratio: 2.924693e-02	ci left: 4.662098e-01	ci right 4.800980e-01	k: 9463	n:20000
Cons ci ratio: 7.425455e-02	ci left: 1.177403e-01	ci right 1.268698e-01	k: 2445	n:20000
KS ci ratio: 4.083757e-03	ci left: 9.767076e-01	ci right 9.807516e-01	k: 19576	n:20000
RYR1   20000 perm   9 sec   (2123 perm/sec)   p_kst 9.788000e-01   p_cons 1.222500e-01   p_joint 4.731500e-01

Outputting figure to mutsig2_images.part000000000151/RYR1.4_15541_20000_0.9788_0.12225_0.47315.png
                gene_name: RYR1
               theta_stop: 0.074 
                    nperm: 20000 
                     p_ks: 0.98 
        ci_ks_bounds_left: 0.98 
       ci_ks_bounds_right: 0.98 
                   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: 50 percent done.
RUSC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.974550e-03	ci left: 9.658346e-01	ci right 9.726884e-01	k: 9694	n:10000
Cons ci ratio: 3.266055e-02	ci left: 5.804858e-01	ci right 5.998616e-01	k: 5902	n:10000
KS ci ratio: 4.081055e-02	ci left: 4.699653e-01	ci right 4.896465e-01	k: 4798	n:10000
RUSC1   10000 perm   2 sec   (5310 perm/sec)   p_kst 4.798000e-01   p_cons 5.902000e-01   p_joint 9.694000e-01

Outputting figure to mutsig2_images.part000000000151/RUSC1.2_2876_10000_0.4798_0.5902_0.9694.png
                gene_name: RUSC1
               theta_stop: 0.041 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.60 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.97 

Current progress: 67 percent done.
RXRG
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.437178e-02	ci left: 7.122978e-01	ci right 7.299732e-01	k: 7212	n:10000
Cons ci ratio: 1.221968e-01	ci left: 8.757121e-02	ci right 9.906697e-02	k: 932	n:10000
KS ci ratio: 5.023176e-02	ci left: 3.688810e-01	ci right 3.879899e-01	k: 3784	n:10000
RXRG   10000 perm   2 sec   (6366 perm/sec)   p_kst 3.784000e-01   p_cons 9.320000e-02   p_joint 7.212000e-01

Joint ci ratio: 1.087617e-02	ci left: 8.618095e-01	ci right 8.712836e-01	k: 17332	n:20000
Cons ci ratio: 8.734023e-02	ci left: 8.748975e-02	ci right 9.552946e-02	k: 1829	n:20000
KS ci ratio: 3.534228e-02	ci left: 3.740630e-01	ci right 3.875717e-01	k: 7616	n:20000
RXRG   20000 perm   4 sec   (5544 perm/sec)   p_kst 3.808000e-01   p_cons 9.145000e-02   p_joint 8.666000e-01

Outputting figure to mutsig2_images.part000000000151/RXRG.2_1489_20000_0.3808_0.09145_0.8666.png
                gene_name: RXRG
               theta_stop: 0.087 
                    nperm: 20000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.091 
      ci_cons_bounds_left: 0.087 
     ci_cons_bounds_right: 0.096 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

Current progress: 83 percent done.
RYR3
Processing conservation and coverage...
66% 
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: 1.196764e-02	ci left: 9.091566e-01	ci right 9.202004e-01	k: 9148	n:10000
KS ci ratio: 2.320499e-02	ci left: 7.317890e-01	ci right 7.490707e-01	k: 7405	n:10000
RYR3   10000 perm   4 sec   (2413 perm/sec)   p_kst 7.405000e-01   p_cons 9.148000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000151/RYR3.2_15029_10000_0.7405_0.9148_1.png
                gene_name: RYR3
               theta_stop: 0.023 
                    nperm: 10000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.75 
                   p_cons: 0.91 
      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: 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.165.3896/
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/181708/iteration1/scatter.0000000151
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 151 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120229: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000152> was used as the working directory.
Started at Wed Oct 10 10:44:49 2012
Results reported at Wed Oct 10 10:45:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000152.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000152.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 152  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     68.75 sec.
    Max Memory :      1239 MB
    Max Swap   :      3884 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.165.3896/
-whichjob
152
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 152: processing genes 13662 - 13751
Calculating significance of each gene.
Using projection method.
13662	SAE1	1
13663	SAFB	1
13664	SAFB2	2.469728e-01
13665	SAG	1
13666	SAGE1	8.396640e-02
13667	SALL1	1
13668	SALL2	6.301576e-02
13669	SALL3	1
13670	SALL4	4.443360e-01
13671	SAMD1	1
13672	SAMD10	1
13673	SAMD11	3.835705e-02
13674	SAMD12	1
13675	SAMD13	1
13676	SAMD14	1.371730e-01
13677	SAMD3	1
13678	SAMD4A	1
13679	SAMD4B	1.655014e-01
13680	SAMD5	1
13681	SAMD7	1.784004e-01
13682	SAMD8	1
13683	SAMD9	4.314587e-01
13684	SAMD9L	1
13685	SAMHD1	1
13686	SAMM50	1
13687	SAMSN1	5.508455e-02
13688	SAP130	9.606650e-02
13689	SAP18	1
13690	SAP30	1
13691	SAP30BP	1
13692	SAP30L	1
13693	SAPS1	1.470198e-01
13694	SAPS2	1
13695	SAPS3	2.114889e-02
13696	SAR1A	1
13697	SAR1B	1
13698	SARDH	1
13699	SARM1	1
13700	SARNP	1
13701	SARS	1
13702	SARS2	1
13703	SART1	1.493685e-01
13704	SART3	1
13705	SASH1	1
13706	SASH3	1
13707	SASS6	1
13708	SAT1	1
13709	SAT2	1
13710	SATB1	1
13711	SATB2	8.796362e-02
13712	SATL1	1
13713	SAV1	1
13714	SBDS	1
13715	SBF1	1
13716	SBF2	6.079773e-01
13717	SBK1	1
13718	SBK2	1
13719	SBNO1	1
13720	SBNO2	1
13721	SBSN	1
13722	SC4MOL	1
13723	SC5DL	1
13724	SC65	1
13725	SCAF1	1
13726	SCAI	2.905140e-01
13727	SCAMP1	1
13728	SCAMP2	1
13729	SCAMP3	1
13730	SCAMP4	1
13731	SCAMP5	1
13732	SCAND3	1
13733	SCAP	1.625061e-01
13734	SCAPER	2.634758e-01
13735	SCARA3	1.621643e-01
13736	SCARA5	1
13737	SCARB1	1
13738	SCARB2	1
13739	SCARF1	1
13740	SCARF2	1
13741	SCCPDH	1
13742	SCD	1
13743	SCD5	1
13744	SCEL	1.447029e-01
13745	SCFD1	1
13746	SCFD2	1
13747	SCG2	1
13748	SCG3	1.885054e-01
13749	SCG5	1
13750	SCGB1A1	1
13751	SCGB1C1	1
Done

Running MutSig 2:
Scatter job 152: processing genes 13662 - 13751
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SALL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.746868e-02	ci left: 5.126548e-01	ci right 5.323321e-01	k: 5225	n:10000
Cons ci ratio: 6.728524e-02	ci left: 2.447989e-01	ci right 2.619450e-01	k: 2533	n:10000
KS ci ratio: 4.054177e-02	ci left: 4.732619e-01	ci right 4.929479e-01	k: 4831	n:10000
SALL2   10000 perm   2 sec   (5586 perm/sec)   p_kst 4.831000e-01   p_cons 2.533000e-01   p_joint 5.225000e-01

Outputting figure to mutsig2_images.part000000000152/SALL2.2_3032_10000_0.4831_0.2533_0.5225.png
                gene_name: SALL2
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.52 
     ci_joint_bounds_left: 0.51 
    ci_joint_bounds_right: 0.53 

Current progress: 33 percent done.
SAP130
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.106031e-03	ci left: 9.732324e-01	ci right 9.792858e-01	k: 9764	n:10000
Cons ci ratio: 3.817613e-03	ci left: 9.886188e-01	ci right 9.924873e-01	k: 9907	n:10000
KS ci ratio: 3.439163e-02	ci left: 5.552156e-01	ci right 5.747465e-01	k: 5650	n:10000
SAP130   10000 perm   2 sec   (5754 perm/sec)   p_kst 5.650000e-01   p_cons 9.907000e-01   p_joint 9.764000e-01

Outputting figure to mutsig2_images.part000000000152/SAP130.2_3336_10000_0.565_0.9907_0.9764.png
                gene_name: SAP130
               theta_stop: 0.034 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.99 
      ci_cons_bounds_left: 0.99 
     ci_cons_bounds_right: 0.99 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.98 

Current progress: 67 percent done.
SAPS3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.317272e-03	ci left: 9.528388e-01	ci right 9.608923e-01	k: 9570	n:10000
Cons ci ratio: 2.760228e-02	ci left: 6.591754e-01	ci right 6.777264e-01	k: 6685	n:10000
KS ci ratio: 2.243869e-02	ci left: 7.446266e-01	ci right 7.616257e-01	k: 7532	n:10000
SAPS3   10000 perm   2 sec   (5966 perm/sec)   p_kst 7.532000e-01   p_cons 6.685000e-01   p_joint 9.570000e-01

Outputting figure to mutsig2_images.part000000000152/SAPS3.2_2782_10000_0.7532_0.6685_0.957.png
                gene_name: SAPS3
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  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.165.3896/
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/181708/iteration1/scatter.0000000152
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 152 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120232: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000153> was used as the working directory.
Started at Wed Oct 10 10:44:59 2012
Results reported at Wed Oct 10 10:47:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000153.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000153.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 153  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    175.06 sec.
    Max Memory :      1622 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.165.3896/
-whichjob
153
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 153: processing genes 13752 - 13842
Calculating significance of each gene.
Using projection method.
13752	SCGB1D1	1
13753	SCGB1D2	1
13754	SCGB1D4	1
13755	SCGB2A1	1
13756	SCGB2A2	1
13757	SCGB3A1	1
13758	SCGB3A2	1
13759	SCGBL	1
13760	SCGN	1
13761	SCHIP1	1
13762	SCIN	1
13763	SCLT1	1
13764	SCLY	1.144876e-01
13765	SCMH1	1
13766	SCML1	1
13767	SCML2	1
13768	SCML4	1
13769	SCN10A	4.847743e-01
13770	SCN11A	1.472124e-01
13771	SCN1A	5.613798e-01
13772	SCN1B	1
13773	SCN2A	2.909715e-01
13774	SCN2B	1
13775	SCN3A	6.695113e-02
13776	SCN3B	1
13777	SCN4A	1
13778	SCN4B	1
13779	SCN5A	1
13780	SCN7A	3.072777e-01
13781	SCN8A	3.930161e-01
13782	SCN9A	3.435205e-01
13783	SCNM1	7.370484e-03
13784	SCNN1A	9.689571e-02
13785	SCNN1B	1.572848e-01
13786	SCNN1D	1
13787	SCNN1G	1
13788	SCO1	1
13789	SCO2	1
13790	SCOC	1
13791	SCP2	1.594743e-01
13792	SCPEP1	1
13793	SCRG1	1
13794	SCRIB	1
13795	SCRN1	1
13796	SCRN2	1
13797	SCRN3	1
13798	SCRT1	1
13799	SCRT2	1
13800	SCTR	1
13801	SCUBE1	3.637225e-01
13802	SCUBE2	1
13803	SCUBE3	3.226129e-01
13804	SCYL1	1
13805	SCYL2	1
13806	SCYL3	3.940763e-02
13807	SDAD1	1
13808	SDC1	1
13809	SDC2	1
13810	SDC3	1.543445e-01
13811	SDC4	1
13812	SDCBP	1
13813	SDCBP2	1
13814	SDCCAG1	3.384734e-01
13815	SDCCAG3	1
13816	SDCCAG8	1.802013e-01
13817	SDF2	1
13818	SDF2L1	1
13819	SDF4	1
13820	SDHA	1
13821	SDHAF2	1
13822	SDHB	1
13823	SDHC	6.374238e-02
13824	SDHD	1
13825	SDK1	1.642685e-01
13826	SDK2	6.351033e-02
13827	SDPR	1.329391e-01
13828	SDR16C5	1
13829	SDR39U1	1
13830	SDR42E1	1
13831	SDR9C7	1
13832	SDS	1.190017e-01
13833	SDSL	1
13834	SEBOX	1
13835	SEC11A	1
13836	SEC11C	1
13837	SEC13	1
13838	SEC14L1	1
13839	SEC14L2	1
13840	SEC14L3	9.229858e-02
13841	SEC14L4	1
13842	SEC14L5	1
Done

Running MutSig 2:
Scatter job 153: processing genes 13752 - 13842
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SDPR
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: 8.490444e-02	ci left: 1.681880e-01	ci right 1.832014e-01	k: 1756	n:10000
KS ci ratio: 1.039952e-01	ci left: 1.178937e-01	ci right 1.309260e-01	k: 1243	n:10000
SDPR   10000 perm   2 sec   (5741 perm/sec)   p_kst 1.243000e-01   p_cons 1.756000e-01   p_joint 2.278000e-01

Joint ci ratio: 7.268865e-02	ci left: 1.223163e-01	ci right 1.315924e-01	k: 2538	n:20000
Cons ci ratio: 5.912097e-02	ci left: 1.748456e-01	ci right 1.855476e-01	k: 3603	n:20000
KS ci ratio: 7.357079e-02	ci left: 1.197082e-01	ci right 1.289013e-01	k: 2485	n:20000
SDPR   20000 perm   8 sec   (2598 perm/sec)   p_kst 1.242500e-01   p_cons 1.801500e-01   p_joint 1.269000e-01

Outputting figure to mutsig2_images.part000000000153/SDPR.4_1286_20000_0.12425_0.18015_0.1269.png
                gene_name: SDPR
               theta_stop: 0.074 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.18 
      ci_cons_bounds_left: 0.17 
     ci_cons_bounds_right: 0.19 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 12 percent done.
SCN3A
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: 7.764659e-02	ci left: 1.951537e-01	ci right 2.110196e-01	k: 2030	n:10000
KS ci ratio: 1.920191e-02	ci left: 7.986185e-01	ci right 8.142026e-01	k: 8065	n:10000
SCN3A   10000 perm   3 sec   (3793 perm/sec)   p_kst 8.065000e-01   p_cons 2.030000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000153/SCN3A.3_6203_10000_0.8065_0.203_1.png
                gene_name: SCN3A
               theta_stop: 0.078 
                    nperm: 10000 
                     p_ks: 0.81 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 25 percent done.
SCN11A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.648024e-02	ci left: 3.158221e-01	ci right 3.342799e-01	k: 3250	n:10000
Cons ci ratio: 6.108332e-02	ci left: 2.827037e-01	ci right 3.006178e-01	k: 2916	n:10000
KS ci ratio: 3.315575e-02	ci left: 5.731628e-01	ci right 5.925889e-01	k: 5829	n:10000
SCN11A   10000 perm   3 sec   (3843 perm/sec)   p_kst 5.829000e-01   p_cons 2.916000e-01   p_joint 3.250000e-01

Outputting figure to mutsig2_images.part000000000153/SCN11A.2_5480_10000_0.5829_0.2916_0.325.png
                gene_name: SCN11A
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.58 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.59 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.28 
     ci_cons_bounds_right: 0.30 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.33 

Current progress: 38 percent done.
SCN2A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.840317e-02	ci left: 6.462931e-01	ci right 6.650161e-01	k: 6557	n:10000
Cons ci ratio: 3.780034e-02	ci left: 5.082525e-01	ci right 5.279369e-01	k: 5181	n:10000
KS ci ratio: 7.213041e-02	ci left: 2.197085e-01	ci right 2.362502e-01	k: 2279	n:10000
SCN2A   10000 perm   2 sec   (4057 perm/sec)   p_kst 2.279000e-01   p_cons 5.181000e-01   p_joint 6.557000e-01

Outputting figure to mutsig2_images.part000000000153/SCN2A.2_6218_10000_0.2279_0.5181_0.6557.png
                gene_name: SCN2A
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.52 
      ci_cons_bounds_left: 0.51 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.66 
     ci_joint_bounds_left: 0.65 
    ci_joint_bounds_right: 0.67 

Current progress: 50 percent done.
SCNM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.051038e-02	ci left: 6.131152e-01	ci right 6.322133e-01	k: 6227	n:10000
Cons ci ratio: 3.532443e-02	ci left: 5.419890e-01	ci right 5.615808e-01	k: 5518	n:10000
KS ci ratio: 3.942995e-02	ci left: 4.871524e-01	ci right 5.068493e-01	k: 4970	n:10000
SCNM1   10000 perm   1 sec   (7330 perm/sec)   p_kst 4.970000e-01   p_cons 5.518000e-01   p_joint 6.227000e-01

Outputting figure to mutsig2_images.part000000000153/SCNM1.2_721_10000_0.497_0.5518_0.6227.png
                gene_name: SCNM1
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.50 
        ci_ks_bounds_left: 0.49 
       ci_ks_bounds_right: 0.51 
                   p_cons: 0.55 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.62 
     ci_joint_bounds_left: 0.61 
    ci_joint_bounds_right: 0.63 

Current progress: 62 percent done.
SCYL3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.166009e-02	ci left: 3.558529e-01	ci right 3.748256e-01	k: 3653	n:10000
Cons ci ratio: 8.106743e-02	ci left: 1.817616e-01	ci right 1.972197e-01	k: 1894	n:10000
KS ci ratio: 6.658135e-02	ci left: 2.487538e-01	ci right 2.659878e-01	k: 2573	n:10000
SCYL3   10000 perm   2 sec   (5708 perm/sec)   p_kst 2.573000e-01   p_cons 1.894000e-01   p_joint 3.653000e-01

Outputting figure to mutsig2_images.part000000000153/SCYL3.2_2281_10000_0.2573_0.1894_0.3653.png
                gene_name: SCYL3
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.37 

Current progress: 75 percent done.
SDK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.525856e-02	ci left: 2.053056e-01	ci right 2.214617e-01	k: 2133	n:10000
Cons ci ratio: 9.367929e-02	ci left: 1.419757e-01	ci right 1.560294e-01	k: 1489	n:10000
KS ci ratio: 2.248696e-02	ci left: 7.438177e-01	ci right 7.608351e-01	k: 7524	n:10000
SDK1   10000 perm   3 sec   (3613 perm/sec)   p_kst 7.524000e-01   p_cons 1.489000e-01   p_joint 2.133000e-01

Outputting figure to mutsig2_images.part000000000153/SDK1.2_6822_10000_0.7524_0.1489_0.2133.png
                gene_name: SDK1
               theta_stop: 0.094 
                    nperm: 10000 
                     p_ks: 0.75 
        ci_ks_bounds_left: 0.74 
       ci_ks_bounds_right: 0.76 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.16 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 88 percent done.
SDK2
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: 6.707253e-02	ci left: 2.459853e-01	ci right 2.631579e-01	k: 2545	n:10000
KS ci ratio: 2.909827e-02	ci left: 6.352285e-01	ci right 6.540872e-01	k: 6447	n:10000
SDK2   10000 perm   3 sec   (3743 perm/sec)   p_kst 6.447000e-01   p_cons 2.545000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000153/SDK2.2_6699_10000_0.6447_0.2545_1.png
                gene_name: SDK2
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.65 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000153
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 153 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120237: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000154> was used as the working directory.
Started at Wed Oct 10 10:44:59 2012
Results reported at Wed Oct 10 10:46:20 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000154.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000154.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 154  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     95.09 sec.
    Max Memory :       898 MB
    Max Swap   :      3683 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.165.3896/
-whichjob
154
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 154: processing genes 13843 - 13932
Calculating significance of each gene.
Using projection method.
13843	SEC16A	4.455859e-01
13844	SEC16B	1
13845	SEC22A	1
13846	SEC22B	1
13847	SEC22C	1
13848	SEC23A	1
13849	SEC23B	1
13850	SEC23IP	1.796782e-01
13851	SEC24A	1.191871e-01
13852	SEC24B	1
13853	SEC24C	1
13854	SEC24D	1
13855	SEC31A	1
13856	SEC31B	3.866193e-01
13857	SEC61A1	1
13858	SEC61A2	1
13859	SEC61B	1
13860	SEC61G	1
13861	SEC62	1
13862	SEC63	1
13863	SECISBP2	1
13864	SECISBP2L	2.996825e-01
13865	SECTM1	1
13866	SEH1L	1
13867	SEL1L	4.407675e-02
13868	SEL1L2	2.952033e-01
13869	SEL1L3	3.733410e-01
13870	SELE	1
13871	SELENBP1	1
13872	SELK	1
13873	SELL	1
13874	SELM	1
13875	SELO	1.188494e-01
13876	SELP	1
13877	SELPLG	1
13878	SELS	1
13879	SELT	1
13880	SELV	1
13881	SEMA3A	1.064407e-01
13882	SEMA3B	1
13883	SEMA3C	2.441002e-01
13884	SEMA3D	1
13885	SEMA3E	1
13886	SEMA3F	1
13887	SEMA3G	1
13888	SEMA4A	3.219853e-01
13889	SEMA4B	1
13890	SEMA4C	1
13891	SEMA4D	1
13892	SEMA4F	1
13893	SEMA4G	1
13894	SEMA5A	2.457642e-01
13895	SEMA5B	1
13896	SEMA6A	1
13897	SEMA6B	1.171796e-01
13898	SEMA6C	1
13899	SEMA6D	1
13900	SEMA7A	1
13901	SEMG1	4.748867e-02
13902	SEMG2	2.675346e-01
13903	SENP1	1
13904	SENP2	1
13905	SENP3	1
13906	SENP5	1
13907	SENP6	1
13908	SENP7	2.339189e-01
13909	SENP8	1
13910	SEP15	1
13911	SEPHS1	1
13912	SEPHS2	1
13913	SEPN1	1
13914	SEPP1	1
13915	SEPSECS	1
13916	SEPT1	1.276704e-01
13917	SEPT10	1
13918	SEPT11	1
13919	SEPT12	1
13920	SEPT14	1
13921	SEPT2	1
13922	SEPT3	1
13923	SEPT4	1
13924	SEPT5	1
13925	SEPT6	1
13926	SEPT7	1
13927	SEPT8	9.173243e-02
13928	SEPT9	1
13929	SEPW1	1
13930	SEPX1	1
13931	SERAC1	1
13932	SERBP1	1
Done

Running MutSig 2:
Scatter job 154: processing genes 13843 - 13932
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SEL1L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.285505e-02	ci left: 2.162545e-01	ci right 2.327063e-01	k: 2244	n:10000
Cons ci ratio: 1.598823e-01	ci left: 5.215064e-02	ci right 6.130972e-02	k: 566	n:10000
KS ci ratio: 1.510425e-01	ci left: 5.831582e-02	ci right 6.794061e-02	k: 630	n:10000
SEL1L   10000 perm   2 sec   (5720 perm/sec)   p_kst 6.300000e-02   p_cons 5.660000e-02   p_joint 2.244000e-01

Joint ci ratio: 2.063489e-02	ci left: 6.367161e-01	ci right 6.500422e-01	k: 12868	n:20000
Cons ci ratio: 1.136418e-01	ci left: 5.295054e-02	ci right 5.937926e-02	k: 1122	n:20000
KS ci ratio: 1.074889e-01	ci left: 5.898909e-02	ci right 6.573884e-02	k: 1246	n:20000
SEL1L   20000 perm   6 sec   (3449 perm/sec)   p_kst 6.230000e-02   p_cons 5.610000e-02   p_joint 6.434000e-01

Joint ci ratio: 1.706209e-02	ci left: 6.321308e-01	ci right 6.430426e-01	k: 19128	n:30000
Cons ci ratio: 9.248383e-02	ci left: 5.388111e-02	ci right 5.913852e-02	k: 1694	n:30000
KS ci ratio: 8.750336e-02	ci left: 5.994991e-02	ci right 6.546848e-02	k: 1880	n:30000
SEL1L   30000 perm   8 sec   (3761 perm/sec)   p_kst 6.266667e-02   p_cons 5.646667e-02   p_joint 6.376000e-01

Outputting figure to mutsig2_images.part000000000154/SEL1L.2_2469_30000_0.062667_0.056467_0.6376.png
                gene_name: SEL1L
               theta_stop: 0.092 
                    nperm: 30000 
                     p_ks: 0.063 
        ci_ks_bounds_left: 0.060 
       ci_ks_bounds_right: 0.065 
                   p_cons: 0.056 
      ci_cons_bounds_left: 0.054 
     ci_cons_bounds_right: 0.059 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.64 

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.165.3896/
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/181708/iteration1/scatter.0000000154
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 154 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120239: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000155> was used as the working directory.
Started at Wed Oct 10 10:45:00 2012
Results reported at Wed Oct 10 10:46:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000155.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000155.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 155  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    111.17 sec.
    Max Memory :      1351 MB
    Max Swap   :      3815 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.165.3896/
-whichjob
155
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 155: processing genes 13933 - 14023
Calculating significance of each gene.
Using projection method.
13933	SERF2	1
13934	SERGEF	1
13935	SERHL2	1
13936	SERINC1	1
13937	SERINC2	1
13938	SERINC3	2.057443e-01
13939	SERINC4	1
13940	SERINC5	1
13941	SERP1	1
13942	SERP2	1
13943	SERPINA1	1
13944	SERPINA10	1
13945	SERPINA11	1
13946	SERPINA12	1.806985e-01
13947	SERPINA3	1
13948	SERPINA4	1
13949	SERPINA5	1
13950	SERPINA6	1
13951	SERPINA7	1
13952	SERPINA9	1
13953	SERPINB1	1
13954	SERPINB10	1
13955	SERPINB11	1
13956	SERPINB12	1
13957	SERPINB13	6.740585e-02
13958	SERPINB2	1
13959	SERPINB3	1
13960	SERPINB4	1
13961	SERPINB5	1
13962	SERPINB6	1
13963	SERPINB7	1
13964	SERPINB8	1
13965	SERPINB9	1
13966	SERPINC1	1
13967	SERPIND1	1.082716e-01
13968	SERPINE1	1
13969	SERPINE2	1
13970	SERPINE3	1
13971	SERPINF1	1
13972	SERPINF2	1
13973	SERPING1	1
13974	SERPINH1	1
13975	SERPINI1	1
13976	SERPINI2	1
13977	SERTAD1	1
13978	SERTAD2	1
13979	SERTAD3	1
13980	SERTAD4	1.743671e-01
13981	SESN1	1.527341e-01
13982	SESN2	1
13983	SESN3	1
13984	SESTD1	1
13985	SET	1
13986	SETBP1	7.501547e-02
13987	SETD1A	5.318781e-01
13988	SETD2	3.625589e-03
13989	SETD3	1
13990	SETD4	1
13991	SETD5	1.881679e-01
13992	SETD6	1
13993	SETD7	1
13994	SETD8	1.622015e-01
13995	SETDB1	1
13996	SETDB2	1
13997	SETMAR	1
13998	SETX	1.444562e-01
13999	SEZ6	1
14000/18094 14000	SEZ6L	1
14001	SEZ6L2	3.792486e-01
14002	SF1	1
14003	SF3A1	1
14004	SF3A2	1
14005	SF3A3	1
14006	SF3B1	3.138293e-01
14007	SF3B14	1
14008	SF3B2	3.872174e-01
14009	SF3B3	5.954441e-02
14010	SF3B4	1
14011	SF3B5	1
14012	SF4	2.885292e-01
14013	SFI1	1
14014	SFMBT1	1
14015	SFMBT2	2.774264e-01
14016	SFN	1
14017	SFPQ	2.314834e-01
14018	SFRP1	1
14019	SFRP2	1
14020	SFRP4	8.320381e-02
14021	SFRP5	1
14022	SFRS1	1.445631e-01
14023	SFRS11	1
Done

Running MutSig 2:
Scatter job 155: processing genes 13933 - 14023
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SETD2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.534169e-02	ci left: 3.247555e-01	ci right 3.433413e-01	k: 3340	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: 6.626932e-02	ci left: 2.505337e-01	ci right 2.678068e-01	k: 2591	n:10000
SETD2   10000 perm   3 sec   (3880 perm/sec)   p_kst 2.591000e-01   p_cons 3.350000e-01   p_joint 3.340000e-01

Outputting figure to mutsig2_images.part000000000155/SETD2.5_7779_10000_0.2591_0.335_0.334.png
                gene_name: SETD2
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.34 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 25 percent done.
SETBP1
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: 3.347720e-02	ci left: 5.684492e-01	ci right 5.879053e-01	k: 5782	n:10000
KS ci ratio: 9.896889e-02	ci left: 1.288487e-01	ci right 1.423643e-01	k: 1355	n:10000
SETBP1   10000 perm   2 sec   (5155 perm/sec)   p_kst 1.355000e-01   p_cons 5.782000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000155/SETBP1.2_5004_10000_0.1355_0.5782_1.png
                gene_name: SETBP1
               theta_stop: 0.099 
                    nperm: 10000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.13 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.58 
      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.
SETX
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.749955e-02	ci left: 3.080829e-01	ci right 3.264237e-01	k: 3172	n:10000
Cons ci ratio: 5.702521e-02	ci left: 3.116545e-01	ci right 3.300500e-01	k: 3208	n:10000
KS ci ratio: 7.004364e-02	ci left: 2.300756e-01	ci right 2.468770e-01	k: 2384	n:10000
SETX   10000 perm   2 sec   (4272 perm/sec)   p_kst 2.384000e-01   p_cons 3.208000e-01   p_joint 3.172000e-01

Outputting figure to mutsig2_images.part000000000155/SETX.2_8130_10000_0.2384_0.3208_0.3172.png
                gene_name: SETX
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.31 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.32 
     ci_joint_bounds_left: 0.31 
    ci_joint_bounds_right: 0.33 

Current progress: 75 percent done.
SF3B3
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: 3.423102e-02	ci left: 5.575209e-01	ci right 5.770399e-01	k: 5673	n:10000
KS ci ratio: 5.321015e-02	ci left: 3.423355e-01	ci right 3.611510e-01	k: 3517	n:10000
SF3B3   10000 perm   2 sec   (5389 perm/sec)   p_kst 3.517000e-01   p_cons 5.673000e-01   p_joint 5.357000e-01

Outputting figure to mutsig2_images.part000000000155/SF3B3.2_3754_10000_0.3517_0.5673_0.5357.png
                gene_name: SF3B3
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.35 
        ci_ks_bounds_left: 0.34 
       ci_ks_bounds_right: 0.36 
                   p_cons: 0.57 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.58 
                  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.165.3896/
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/181708/iteration1/scatter.0000000155
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 155 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120242: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000156> was used as the working directory.
Started at Wed Oct 10 10:45:08 2012
Results reported at Wed Oct 10 10:47:09 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000156.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000156.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 156  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    137.18 sec.
    Max Memory :      1090 MB
    Max Swap   :      3809 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.165.3896/
-whichjob
156
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 156: processing genes 14024 - 14113
Calculating significance of each gene.
Using projection method.
14024	SFRS12	1
14025	SFRS12IP1	1
14026	SFRS13B	1
14027	SFRS14	4.390724e-01
14028	SFRS15	4.610667e-02
14029	SFRS16	1
14030	SFRS17A	1
14031	SFRS18	1
14032	SFRS2	1
14033	SFRS2B	1
14034	SFRS2IP	5.698502e-02
14035	SFRS3	1
14036	SFRS4	1
14037	SFRS5	1
14038	SFRS6	1
14039	SFRS7	1
14040	SFRS8	1
14041	SFRS9	1
14042	SFT2D1	1
14043	SFT2D2	1
14044	SFTA2	1
14045	SFTA3	1
14046	SFTPA1	1
14047	SFTPA2	1
14048	SFTPB	1
14049	SFTPC	1
14050	SFTPD	1
14051	SFXN1	1
14052	SFXN2	1
14053	SFXN3	1
14054	SFXN4	1
14055	SFXN5	1
14056	SGCA	1
14057	SGCB	1
14058	SGCD	1
14059	SGCE	1
14060	SGCG	1
14061	SGCZ	1
14062	SGEF	1.674868e-01
14063	SGIP1	1
14064	SGK1	1.241983e-01
14065	SGK196	1
14066	SGK2	1.861672e-01
14067	SGK223	1
14068	SGK269	3.198123e-01
14069	SGK3	1
14070	SGK494	1
14071	SGMS1	1
14072	SGMS2	1
14073	SGOL1	1.605192e-02
14074	SGOL2	1.183425e-01
14075	SGPL1	1
14076	SGPP1	1
14077	SGPP2	1
14078	SGSH	1
14079	SGSM1	1
14080	SGSM2	1
14081	SGSM3	1
14082	SGTA	1
14083	SGTB	1
14084	SH2B1	2.241746e-01
14085	SH2B2	1
14086	SH2B3	1
14087	SH2D1A	3.795846e-02
14088	SH2D1B	1
14089	SH2D2A	1
14090	SH2D3A	1
14091	SH2D3C	3.193003e-01
14092	SH2D4A	1
14093	SH2D4B	1
14094	SH2D5	1
14095	SH2D6	1
14096	SH2D7	1
14097	SH3BGR	1
14098	SH3BGRL	1
14099	SH3BGRL2	1
14100	SH3BGRL3	1
14101	SH3BP1	1
14102	SH3BP2	1
14103	SH3BP4	3.086090e-01
14104	SH3BP5	1
14105	SH3BP5L	1
14106	SH3D19	1.930884e-01
14107	SH3GL1	1
14108	SH3GL2	1
14109	SH3GL3	1.884598e-02
14110	SH3GLB1	1
14111	SH3GLB2	1
14112	SH3KBP1	1
14113	SH3PXD2A	1
Done

Running MutSig 2:
Scatter job 156: processing genes 14024 - 14113
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SFRS2IP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.872080e-01	ci left: 3.805695e-02	ci right 4.601263e-02	k: 419	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: 1.933710e-02	ci left: 7.963859e-01	ci right 8.120365e-01	k: 8043	n:10000
SFRS2IP   10000 perm   2 sec   (5054 perm/sec)   p_kst 8.043000e-01   p_cons 1.590000e-02   p_joint 4.190000e-02

Joint ci ratio: 1.181691e-01	ci left: 4.906042e-02	ci right 5.527060e-02	k: 1042	n:20000
Cons ci ratio: 2.281111e-01	ci left: 1.288916e-02	ci right 1.625414e-02	k: 290	n:20000
KS ci ratio: 1.364269e-02	ci left: 7.994399e-01	ci right 8.104713e-01	k: 16100	n:20000
SFRS2IP   20000 perm   6 sec   (3203 perm/sec)   p_kst 8.050000e-01   p_cons 1.450000e-02   p_joint 5.210000e-02

Joint ci ratio: 7.900680e-02	ci left: 7.282946e-02	ci right 7.885299e-02	k: 2274	n:30000
Cons ci ratio: 1.885683e-01	ci left: 1.285992e-02	ci right 1.556869e-02	k: 425	n:30000
KS ci ratio: 1.112848e-02	ci left: 8.007731e-01	ci right 8.097677e-01	k: 24159	n:30000
SFRS2IP   30000 perm   9 sec   (3465 perm/sec)   p_kst 8.053000e-01   p_cons 1.416667e-02   p_joint 7.580000e-02

Joint ci ratio: 6.795460e-02	ci left: 7.418424e-02	ci right 7.942739e-02	k: 3071	n:40000
Cons ci ratio: 1.649332e-01	ci left: 1.277557e-02	ci right 1.509579e-02	k: 556	n:40000
KS ci ratio: 9.202605e-03	ci left: 8.155693e-01	ci right 8.231343e-01	k: 32775	n:40000
SFRS2IP   40000 perm   11 sec   (3593 perm/sec)   p_kst 8.193750e-01   p_cons 1.390000e-02   p_joint 7.677500e-02

Joint ci ratio: 7.491216e-02	ci left: 4.997171e-02	ci right 5.388052e-02	k: 2595	n:50000
Cons ci ratio: 1.476556e-01	ci left: 1.287283e-02	ci right 1.494417e-02	k: 694	n:50000
KS ci ratio: 8.252019e-03	ci left: 8.152140e-01	ci right 8.219890e-01	k: 40931	n:50000
SFRS2IP   50000 perm   14 sec   (3655 perm/sec)   p_kst 8.186200e-01   p_cons 1.388000e-02   p_joint 5.190000e-02

Joint ci ratio: 7.241270e-02	ci left: 4.487793e-02	ci right 4.826610e-02	k: 2793	n:60000
Cons ci ratio: 1.354510e-01	ci left: 1.283345e-02	ci right 1.471401e-02	k: 825	n:60000
KS ci ratio: 7.546198e-03	ci left: 8.149896e-01	ci right 8.211796e-01	k: 49086	n:60000
SFRS2IP   60000 perm   16 sec   (3681 perm/sec)   p_kst 8.181000e-01   p_cons 1.375000e-02   p_joint 4.655000e-02

Joint ci ratio: 6.955920e-02	ci left: 4.188835e-02	ci right 4.492108e-02	k: 3037	n:70000
Cons ci ratio: 1.192577e-01	ci left: 1.429278e-02	ci right 1.611916e-02	k: 1063	n:70000
KS ci ratio: 7.004512e-03	ci left: 8.144459e-01	ci right 8.201849e-01	k: 57213	n:70000
SFRS2IP   70000 perm   19 sec   (3686 perm/sec)   p_kst 8.173286e-01   p_cons 1.518571e-02   p_joint 4.338571e-02

Joint ci ratio: 6.731739e-02	ci left: 3.929200e-02	ci right 4.204144e-02	k: 3252	n:80000
Cons ci ratio: 1.128824e-01	ci left: 1.401108e-02	ci right 1.569937e-02	k: 1187	n:80000
KS ci ratio: 6.543689e-03	ci left: 8.150194e-01	ci right 8.203826e-01	k: 65417	n:80000
SFRS2IP   80000 perm   22 sec   (3677 perm/sec)   p_kst 8.177125e-01   p_cons 1.483750e-02   p_joint 4.065000e-02

Joint ci ratio: 6.619837e-02	ci left: 3.625723e-02	ci right 3.875047e-02	k: 3374	n:90000
Cons ci ratio: 1.066090e-01	ci left: 1.401040e-02	ci right 1.559888e-02	k: 1331	n:90000
KS ci ratio: 6.160273e-03	ci left: 8.156198e-01	ci right 8.206708e-01	k: 73634	n:90000
SFRS2IP   90000 perm   25 sec   (3660 perm/sec)   p_kst 8.181556e-01   p_cons 1.478889e-02   p_joint 3.748889e-02

Joint ci ratio: 6.050784e-02	ci left: 3.905988e-02	ci right 4.150687e-02	k: 4027	n:100000
Cons ci ratio: 1.014518e-01	ci left: 1.396318e-02	ci right 1.546516e-02	k: 1470	n:100000
KS ci ratio: 5.860155e-03	ci left: 8.149310e-01	ci right 8.197306e-01	k: 81734	n:100000
SFRS2IP   100000 perm   28 sec   (3567 perm/sec)   p_kst 8.173400e-01   p_cons 1.470000e-02   p_joint 4.027000e-02

Joint ci ratio: 4.880419e-02	ci left: 5.404635e-02	ci right 5.675897e-02	k: 6093	n:110000
Cons ci ratio: 9.649173e-02	ci left: 1.406806e-02	ci right 1.550314e-02	k: 1625	n:110000
KS ci ratio: 5.596518e-03	ci left: 8.145559e-01	ci right 8.191364e-01	k: 89854	n:110000
SFRS2IP   110000 perm   31 sec   (3546 perm/sec)   p_kst 8.168545e-01   p_cons 1.477273e-02   p_joint 5.539091e-02

Outputting figure to mutsig2_images.part000000000156/SFRS2IP.3_4448_110000_0.81685_0.014773_0.055391.png
                gene_name: SFRS2IP
               theta_stop: 0.096 
                    nperm: 110000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.015 
      ci_cons_bounds_left: 0.014 
     ci_cons_bounds_right: 0.016 
                  p_joint: 0.055 
     ci_joint_bounds_left: 0.054 
    ci_joint_bounds_right: 0.057 

Current progress: 25 percent done.
SFRS15
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.962823e-03	ci left: 9.659399e-01	ci right 9.727830e-01	k: 9695	n:10000
Cons ci ratio: 3.986605e-02	ci left: 4.816553e-01	ci right 5.013497e-01	k: 4915	n:10000
KS ci ratio: 1.287374e-02	ci left: 8.967235e-01	ci right 9.084408e-01	k: 9027	n:10000
SFRS15   10000 perm   2 sec   (5536 perm/sec)   p_kst 9.027000e-01   p_cons 4.915000e-01   p_joint 9.695000e-01

Outputting figure to mutsig2_images.part000000000156/SFRS15.2_3524_10000_0.9027_0.4915_0.9695.png
                gene_name: SFRS15
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.90 
        ci_ks_bounds_left: 0.90 
       ci_ks_bounds_right: 0.91 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.97 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.97 

Current progress: 50 percent done.
SGOL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.829633e-02	ci left: 6.480036e-01	ci right 6.667046e-01	k: 6574	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: 6.868280e-02	ci left: 2.371885e-01	ci right 2.541599e-01	k: 2456	n:10000
SGOL1   10000 perm   1 sec   (6702 perm/sec)   p_kst 2.456000e-01   p_cons 4.286000e-01   p_joint 6.574000e-01

Outputting figure to mutsig2_images.part000000000156/SGOL1.2_1738_10000_0.2456_0.4286_0.6574.png
                gene_name: SGOL1
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.66 
     ci_joint_bounds_left: 0.65 
    ci_joint_bounds_right: 0.67 

Current progress: 75 percent done.
SGOL2
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: 2.859839e-02	ci left: 6.431744e-01	ci right 6.619367e-01	k: 6526	n:10000
KS ci ratio: 3.345662e-02	ci left: 5.687500e-01	ci right 5.882042e-01	k: 5785	n:10000
SGOL2   10000 perm   2 sec   (5695 perm/sec)   p_kst 5.785000e-01   p_cons 6.526000e-01   p_joint 9.119000e-01

Outputting figure to mutsig2_images.part000000000156/SGOL2.2_3838_10000_0.5785_0.6526_0.9119.png
                gene_name: SGOL2
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.58 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.59 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  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.165.3896/
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/181708/iteration1/scatter.0000000156
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 156 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120246: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000157> was used as the working directory.
Started at Wed Oct 10 10:45:08 2012
Results reported at Wed Oct 10 10:46:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000157.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000157.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 157  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     88.95 sec.
    Max Memory :       855 MB
    Max Swap   :      3650 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.165.3896/
-whichjob
157
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 157: processing genes 14114 - 14204
Calculating significance of each gene.
Using projection method.
14114	SH3PXD2B	1.574349e-01
14115	SH3RF1	1
14116	SH3RF2	1
14117	SH3RF3	1
14118	SH3TC1	1
14119	SH3TC2	1
14120	SH3YL1	1
14121	SHANK1	1
14122	SHANK2	4.292758e-01
14123	SHANK3	1
14124	SHARPIN	1
14125	SHB	1
14126	SHBG	1
14127	SHC1	1
14128	SHC2	1
14129	SHC3	1
14130	SHC4	1
14131	SHCBP1	1
14132	SHD	1
14133	SHE	1
14134	SHF	1
14135	SHFM1	1
14136	SHH	1
14137	SHISA2	1
14138	SHISA3	1
14139	SHISA4	1
14140	SHISA5	1
14141	SHKBP1	1.937947e-01
14142	SHMT1	1
14143	SHMT2	1
14144	SHOC2	1
14145	SHOX	1
14146	SHOX2	1
14147	SHPK	1
14148	SHPRH	2.852668e-01
14149	SHQ1	1
14150	SHROOM1	2.915772e-01
14151	SHROOM2	1
14152	SHROOM3	1
14153	SHROOM4	1
14154	SI	3.376261e-01
14155	SIAE	1
14156	SIAH1	1
14157	SIAH2	1
14158	SIAH3	1
14159	SIDT1	2.606685e-01
14160	SIDT2	1
14161	SIGIRR	8.453580e-02
14162	SIGLEC1	1
14163	SIGLEC10	1.911239e-01
14164	SIGLEC11	1
14165	SIGLEC12	1
14166	SIGLEC14	1
14167	SIGLEC15	1
14168	SIGLEC5	1
14169	SIGLEC6	1
14170	SIGLEC7	1
14171	SIGLEC8	2.010622e-01
14172	SIGLEC9	1
14173	SIGMAR1	1
14174	SIK1	8.589693e-02
14175	SIK2	1
14176	SIK3	1
14177	SIKE1	1
14178	SIL1	1
14179	SILV	1
14180	SIM1	2.173816e-02
14181	SIM2	1
14182	SIN3A	1
14183	SIN3B	1
14184	SIP1	1
14185	SIPA1	7.079626e-02
14186	SIPA1L1	1
14187	SIPA1L2	1
14188	SIPA1L3	1
14189	SIRPA	1
14190	SIRPB1	1
14191	SIRPB2	2.593123e-02
14192	SIRPD	1
14193	SIRPG	1
14194	SIRT1	1
14195	SIRT2	1
14196	SIRT3	1
14197	SIRT4	1
14198	SIRT5	1
14199	SIRT6	1
14200	SIRT7	1
14201	SIT1	1
14202	SIVA1	1
14203	SIX1	1
14204	SIX2	1
Done

Running MutSig 2:
Scatter job 157: processing genes 14114 - 14204
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SIM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.727431e-02	ci left: 1.328630e-01	ci right 1.465476e-01	k: 1396	n:10000
Cons ci ratio: 1.846669e-02	ci left: 8.107017e-01	ci right 8.259124e-01	k: 8184	n:10000
KS ci ratio: 1.373633e-01	ci left: 7.010558e-02	ci right 8.054343e-02	k: 752	n:10000
SIM1   10000 perm   2 sec   (5807 perm/sec)   p_kst 7.520000e-02   p_cons 8.184000e-01   p_joint 1.396000e-01

Joint ci ratio: 6.692997e-02	ci left: 1.414781e-01	ci right 1.513250e-01	k: 2927	n:20000
Cons ci ratio: 1.269815e-02	ci left: 8.212301e-01	ci right 8.317748e-01	k: 16531	n:20000
KS ci ratio: 9.556323e-02	ci left: 7.387984e-02	ci right 8.134352e-02	k: 1551	n:20000
SIM1   20000 perm   6 sec   (3547 perm/sec)   p_kst 7.755000e-02   p_cons 8.265500e-01   p_joint 1.463500e-01

Outputting figure to mutsig2_images.part000000000157/SIM1.2_2345_20000_0.07755_0.82655_0.14635.png
                gene_name: SIM1
               theta_stop: 0.096 
                    nperm: 20000 
                     p_ks: 0.078 
        ci_ks_bounds_left: 0.074 
       ci_ks_bounds_right: 0.081 
                   p_cons: 0.83 
      ci_cons_bounds_left: 0.82 
     ci_cons_bounds_right: 0.83 
                  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.165.3896/
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/181708/iteration1/scatter.0000000157
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 157 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120250: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000158> was used as the working directory.
Started at Wed Oct 10 10:45:08 2012
Results reported at Wed Oct 10 10:46:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000158.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000158.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 158  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     99.85 sec.
    Max Memory :       623 MB
    Max Swap   :      3450 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.165.3896/
-whichjob
158
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 158: processing genes 14205 - 14294
Calculating significance of each gene.
Using projection method.
14205	SIX3	1
14206	SIX4	2.519991e-01
14207	SIX5	1
14208	SIX6	1
14209	SKA1	1
14210	SKA2	1
14211	SKA3	1
14212	SKAP1	1
14213	SKAP2	1
14214	SKI	1
14215	SKIL	4.689711e-02
14216	SKIV2L	1
14217	SKIV2L2	1
14218	SKP1	1
14219	SKP2	1
14220	SLA	1
14221	SLA2	1
14222	SLAIN1	1
14223	SLAIN2	1
14224	SLAMF1	1
14225	SLAMF6	1
14226	SLAMF7	1
14227	SLAMF8	1
14228	SLAMF9	1
14229	SLBP	1
14230	SLC10A1	1
14231	SLC10A2	9.441868e-02
14232	SLC10A3	1
14233	SLC10A4	4.309216e-02
14234	SLC10A5	1
14235	SLC10A6	1
14236	SLC10A7	1
14237	SLC11A1	1
14238	SLC11A2	1
14239	SLC12A1	1
14240	SLC12A2	3.065895e-01
14241	SLC12A3	3.519128e-01
14242	SLC12A4	1.710712e-02
14243	SLC12A5	1
14244	SLC12A6	1
14245	SLC12A7	1
14246	SLC12A8	1
14247	SLC12A9	2.728425e-01
14248	SLC13A1	1
14249	SLC13A2	1
14250	SLC13A3	1
14251	SLC13A4	1
14252	SLC13A5	2.005093e-01
14253	SLC14A1	1
14254	SLC14A2	1
14255	SLC15A1	1
14256	SLC15A2	1
14257	SLC15A3	1
14258	SLC15A4	1
14259	SLC16A1	1.343840e-01
14260	SLC16A10	1
14261	SLC16A11	1
14262	SLC16A12	1
14263	SLC16A13	1
14264	SLC16A14	1.603722e-01
14265	SLC16A2	1
14266	SLC16A3	1
14267	SLC16A4	1
14268	SLC16A5	1
14269	SLC16A6	1.008047e-01
14270	SLC16A7	1
14271	SLC16A8	1
14272	SLC16A9	1
14273	SLC17A1	1
14274	SLC17A2	1
14275	SLC17A3	1
14276	SLC17A4	1.916717e-01
14277	SLC17A5	9.238166e-02
14278	SLC17A6	1
14279	SLC17A7	1
14280	SLC17A8	1
14281	SLC17A9	1
14282	SLC18A1	1
14283	SLC18A2	1
14284	SLC18A3	1
14285	SLC19A1	1
14286	SLC19A2	1
14287	SLC19A3	1
14288	SLC1A1	1
14289	SLC1A2	4.316914e-02
14290	SLC1A3	1
14291	SLC1A4	1
14292	SLC1A5	1
14293	SLC1A6	1
14294	SLC1A7	1
Done

Running MutSig 2:
Scatter job 158: processing genes 14205 - 14294
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SLC12A4
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.013812e-02	ci left: 4.782576e-01	ci right 4.979493e-01	k: 4881	n:10000
Cons ci ratio: 4.962867e-02	ci left: 3.745520e-01	ci right 3.937155e-01	k: 3841	n:10000
KS ci ratio: 4.368164e-02	ci left: 4.362244e-01	ci right 4.558070e-01	k: 4460	n:10000
SLC12A4   10000 perm   2 sec   (4940 perm/sec)   p_kst 4.460000e-01   p_cons 3.841000e-01   p_joint 4.881000e-01

Outputting figure to mutsig2_images.part000000000158/SLC12A4.3_3582_10000_0.446_0.3841_0.4881.png
                gene_name: SLC12A4
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 50 percent done.
SKIL
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.138285e-02	ci left: 9.168793e-01	ci right 9.274733e-01	k: 9223	n:10000
Cons ci ratio: 3.293807e-02	ci left: 5.763726e-01	ci right 5.957772e-01	k: 5861	n:10000
KS ci ratio: 1.409920e-02	ci left: 8.790966e-01	ci right 8.916780e-01	k: 8855	n:10000
SKIL   10000 perm   2 sec   (6124 perm/sec)   p_kst 8.855000e-01   p_cons 5.861000e-01   p_joint 9.223000e-01

Outputting figure to mutsig2_images.part000000000158/SKIL.2_2079_10000_0.8855_0.5861_0.9223.png
                gene_name: SKIL
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   p_cons: 0.59 
      ci_cons_bounds_left: 0.58 
     ci_cons_bounds_right: 0.60 
                  p_joint: 0.92 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

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.165.3896/
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/181708/iteration1/scatter.0000000158
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 158 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1529>
Subject: Job 1120252: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1529>, 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/181708/iteration1/scatter.0000000159> was used as the working directory.
Started at Wed Oct 10 10:45:08 2012
Results reported at Wed Oct 10 10:47:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000159.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000159.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 159  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    127.75 sec.
    Max Memory :       895 MB
    Max Swap   :      3735 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.165.3896/
-whichjob
159
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 159: processing genes 14295 - 14385
Calculating significance of each gene.
Using projection method.
14295	SLC20A1	2.568439e-02
14296	SLC20A2	1
14297	SLC22A1	1
14298	SLC22A10	1.953374e-01
14299	SLC22A11	1
14300	SLC22A12	1
14301	SLC22A13	1
14302	SLC22A14	1
14303	SLC22A15	8.035252e-02
14304	SLC22A16	1
14305	SLC22A17	1
14306	SLC22A18	1
14307	SLC22A2	1
14308	SLC22A20	1
14309	SLC22A23	1
14310	SLC22A25	1
14311	SLC22A3	1
14312	SLC22A4	1.875410e-01
14313	SLC22A5	1
14314	SLC22A6	1
14315	SLC22A7	1
14316	SLC22A8	1
14317	SLC22A9	1
14318	SLC23A1	1
14319	SLC23A2	1
14320	SLC23A3	1.156530e-01
14321	SLC24A1	1
14322	SLC24A2	1
14323	SLC24A3	1
14324	SLC24A4	1
14325	SLC24A5	1
14326	SLC24A6	1
14327	SLC25A1	1
14328	SLC25A10	9.533993e-02
14329	SLC25A11	1
14330	SLC25A12	1
14331	SLC25A13	1
14332	SLC25A14	1
14333	SLC25A15	1.641496e-02
14334	SLC25A16	1
14335	SLC25A17	1
14336	SLC25A18	1
14337	SLC25A19	1
14338	SLC25A2	5.518199e-02
14339	SLC25A20	1
14340	SLC25A21	1
14341	SLC25A22	1
14342	SLC25A23	1
14343	SLC25A24	1
14344	SLC25A25	1
14345	SLC25A26	6.676183e-02
14346	SLC25A27	1.129183e-01
14347	SLC25A28	1
14348	SLC25A3	1
14349	SLC25A30	1
14350	SLC25A31	1
14351	SLC25A32	1
14352	SLC25A33	1
14353	SLC25A34	1
14354	SLC25A35	1
14355	SLC25A36	1
14356	SLC25A37	1
14357	SLC25A38	1
14358	SLC25A39	1
14359	SLC25A4	1
14360	SLC25A40	1
14361	SLC25A41	1
14362	SLC25A42	1
14363	SLC25A43	1
14364	SLC25A44	1
14365	SLC25A45	1
14366	SLC25A46	1
14367	SLC25A5	1
14368	SLC25A6	1
14369	SLC26A1	1
14370	SLC26A10	1
14371	SLC26A11	1
14372	SLC26A2	1
14373	SLC26A3	2.442854e-01
14374	SLC26A4	1
14375	SLC26A5	1
14376	SLC26A6	1
14377	SLC26A7	1
14378	SLC26A8	1
14379	SLC26A9	3.982344e-02
14380	SLC27A1	1
14381	SLC27A2	1.444814e-01
14382	SLC27A3	1
14383	SLC27A4	1
14384	SLC27A5	2.354786e-01
14385	SLC27A6	1
Done

Running MutSig 2:
Scatter job 159: processing genes 14295 - 14385
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SLC20A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.476486e-02	ci left: 8.691762e-01	ci right 8.822040e-01	k: 8758	n:10000
Cons ci ratio: 2.304807e-02	ci left: 7.344164e-01	ci right 7.516418e-01	k: 7431	n:10000
KS ci ratio: 3.469341e-02	ci left: 5.509062e-01	ci right 5.704585e-01	k: 5607	n:10000
SLC20A1   10000 perm   2 sec   (5703 perm/sec)   p_kst 5.607000e-01   p_cons 7.431000e-01   p_joint 8.758000e-01

Outputting figure to mutsig2_images.part000000000159/SLC20A1.2_2080_10000_0.5607_0.7431_0.8758.png
                gene_name: SLC20A1
               theta_stop: 0.035 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.74 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.75 
                  p_joint: 0.88 
     ci_joint_bounds_left: 0.87 
    ci_joint_bounds_right: 0.88 

Current progress: 50 percent done.
SLC26A9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.086757e-02	ci left: 3.630124e-01	ci right 3.820619e-01	k: 3725	n:10000
Cons ci ratio: 3.389760e-02	ci left: 5.623328e-01	ci right 5.818252e-01	k: 5721	n:10000
KS ci ratio: 1.235896e-01	ci left: 8.572423e-02	ci right 9.711508e-02	k: 913	n:10000
SLC26A9   10000 perm   2 sec   (5538 perm/sec)   p_kst 9.130000e-02   p_cons 5.721000e-01   p_joint 3.725000e-01

Joint ci ratio: 4.004706e-02	ci left: 3.173657e-01	ci right 3.303855e-01	k: 6477	n:20000
Cons ci ratio: 2.410064e-02	ci left: 5.625530e-01	ci right 5.763268e-01	k: 11389	n:20000
KS ci ratio: 8.681902e-02	ci left: 8.847004e-02	ci right 9.654888e-02	k: 1849	n:20000
SLC26A9   20000 perm   4 sec   (4984 perm/sec)   p_kst 9.245000e-02   p_cons 5.694500e-01   p_joint 3.238500e-01

Outputting figure to mutsig2_images.part000000000159/SLC26A9.2_2752_20000_0.09245_0.56945_0.32385.png
                gene_name: SLC26A9
               theta_stop: 0.087 
                    nperm: 20000 
                     p_ks: 0.092 
        ci_ks_bounds_left: 0.088 
       ci_ks_bounds_right: 0.097 
                   p_cons: 0.57 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.58 
                  p_joint: 0.32 
     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.165.3896/
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/181708/iteration1/scatter.0000000159
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 159 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120254: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000160> was used as the working directory.
Started at Wed Oct 10 10:45:08 2012
Results reported at Wed Oct 10 10:47:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000160.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000160.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 160  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    142.43 sec.
    Max Memory :      1182 MB
    Max Swap   :      3827 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.165.3896/
-whichjob
160
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 160: processing genes 14386 - 14475
Calculating significance of each gene.
Using projection method.
14386	SLC28A1	1
14387	SLC28A2	1
14388	SLC28A3	1
14389	SLC29A1	1
14390	SLC29A2	1
14391	SLC29A3	1
14392	SLC29A4	1
14393	SLC2A1	1
14394	SLC2A10	1
14395	SLC2A11	1
14396	SLC2A12	1
14397	SLC2A13	5.586227e-02
14398	SLC2A14	1
14399	SLC2A2	1
14400	SLC2A3	1
14401	SLC2A4	1
14402	SLC2A4RG	1
14403	SLC2A5	1.354970e-01
14404	SLC2A6	1
14405	SLC2A7	1
14406	SLC2A8	1
14407	SLC2A9	1
14408	SLC30A1	1
14409	SLC30A10	1
14410	SLC30A2	1
14411	SLC30A3	1
14412	SLC30A4	1
14413	SLC30A5	1
14414	SLC30A6	1.946898e-01
14415	SLC30A7	1
14416	SLC30A8	1
14417	SLC30A9	1
14418	SLC31A1	1
14419	SLC31A2	1
14420	SLC32A1	1.762922e-01
14421	SLC33A1	1
14422	SLC34A1	3.548367e-02
14423	SLC34A2	1
14424	SLC34A3	1
14425	SLC35A1	1
14426	SLC35A2	1
14427	SLC35A3	1
14428	SLC35A4	1
14429	SLC35A5	1
14430	SLC35B1	1.329094e-01
14431	SLC35B2	6.503414e-02
14432	SLC35B3	1
14433	SLC35B4	1
14434	SLC35C1	1
14435	SLC35C2	1
14436	SLC35D1	1
14437	SLC35D2	1
14438	SLC35D3	1
14439	SLC35E1	1
14440	SLC35E2	2.285792e-02
14441	SLC35E3	1
14442	SLC35E4	1
14443	SLC35F1	1
14444	SLC35F2	5.819653e-02
14445	SLC35F3	1.038418e-01
14446	SLC35F4	1.222358e-01
14447	SLC35F5	1
14448	SLC36A1	6.670669e-02
14449	SLC36A2	1
14450	SLC36A3	1
14451	SLC36A4	1
14452	SLC37A1	1
14453	SLC37A2	1
14454	SLC37A3	1
14455	SLC37A4	1
14456	SLC38A1	1
14457	SLC38A10	1.582009e-01
14458	SLC38A11	1
14459	SLC38A2	8.223875e-02
14460	SLC38A3	1
14461	SLC38A4	1
14462	SLC38A5	1
14463	SLC38A6	5.405737e-02
14464	SLC38A7	1
14465	SLC38A8	1
14466	SLC38A9	1
14467	SLC39A1	7.447938e-02
14468	SLC39A10	1
14469	SLC39A11	1
14470	SLC39A12	2.839372e-01
14471	SLC39A13	1
14472	SLC39A14	1
14473	SLC39A2	1
14474	SLC39A3	1.103973e-02
14475	SLC39A4	1
Done

Running MutSig 2:
Scatter job 160: processing genes 14386 - 14475
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SLC34A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.098745e-02	ci left: 3.619185e-01	ci right 3.809565e-01	k: 3714	n:10000
Cons ci ratio: 3.640872e-02	ci left: 5.269672e-01	ci right 5.466113e-01	k: 5368	n:10000
KS ci ratio: 7.876742e-02	ci left: 1.906225e-01	ci right 2.063536e-01	k: 1984	n:10000
SLC34A1   10000 perm   2 sec   (5707 perm/sec)   p_kst 1.984000e-01   p_cons 5.368000e-01   p_joint 3.714000e-01

Outputting figure to mutsig2_images.part000000000160/SLC34A1.2_2059_10000_0.1984_0.5368_0.3714.png
                gene_name: SLC34A1
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.55 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.38 

Current progress: 50 percent done.
SLC39A3
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: 3.045847e-02	ci left: 6.139190e-01	ci right 6.330091e-01	k: 6235	n:10000
KS ci ratio: 3.920006e-01	ci left: 7.963073e-03	ci right 1.193024e-02	k: 98	n:10000
SLC39A3   10000 perm   2 sec   (6582 perm/sec)   p_kst 9.800000e-03   p_cons 6.235000e-01   p_joint 3.950000e-02

Joint ci ratio: 1.038922e-01	ci left: 6.298759e-02	ci right 6.993910e-02	k: 1328	n:20000
Cons ci ratio: 2.153156e-02	ci left: 6.168931e-01	ci right 6.303709e-01	k: 12473	n:20000
KS ci ratio: 2.677895e-01	ci left: 9.180527e-03	ci right 1.206441e-02	k: 211	n:20000
SLC39A3   20000 perm   4 sec   (4921 perm/sec)   p_kst 1.055000e-02   p_cons 6.236500e-01   p_joint 6.640000e-02

Joint ci ratio: 8.423012e-02	ci left: 6.449025e-02	ci right 7.019389e-02	k: 2019	n:30000
Cons ci ratio: 1.747416e-02	ci left: 6.209974e-01	ci right 6.319781e-01	k: 18795	n:30000
KS ci ratio: 2.136156e-01	ci left: 9.913730e-03	ci right 1.231569e-02	k: 332	n:30000
SLC39A3   30000 perm   6 sec   (4664 perm/sec)   p_kst 1.106667e-02   p_cons 6.265000e-01   p_joint 6.730000e-02

Joint ci ratio: 7.266165e-02	ci left: 6.535524e-02	ci right 7.030772e-02	k: 2712	n:40000
Cons ci ratio: 1.510087e-02	ci left: 6.227405e-01	ci right 6.322410e-01	k: 25100	n:40000
KS ci ratio: 1.860596e-01	ci left: 9.953278e-03	ci right 1.201864e-02	k: 438	n:40000
SLC39A3   40000 perm   8 sec   (4732 perm/sec)   p_kst 1.095000e-02   p_cons 6.275000e-01   p_joint 6.780000e-02

Joint ci ratio: 6.475798e-02	ci left: 6.606460e-02	ci right 7.050569e-02	k: 3413	n:50000
Cons ci ratio: 1.348070e-02	ci left: 6.241470e-01	ci right 6.326381e-01	k: 31420	n:50000
KS ci ratio: 1.629616e-01	ci left: 1.050712e-02	ci right 1.239024e-02	k: 571	n:50000
SLC39A3   50000 perm   11 sec   (4698 perm/sec)   p_kst 1.142000e-02   p_cons 6.284000e-01   p_joint 6.826000e-02

Joint ci ratio: 1.857774e-02	ci left: 4.219887e-01	ci right 4.299185e-01	k: 25557	n:60000
Cons ci ratio: 1.232463e-02	ci left: 6.238175e-01	ci right 6.315702e-01	k: 37662	n:60000
KS ci ratio: 1.494697e-01	ci left: 1.048566e-02	ci right 1.219543e-02	k: 679	n:60000
SLC39A3   60000 perm   13 sec   (4588 perm/sec)   p_kst 1.131667e-02   p_cons 6.277000e-01   p_joint 4.259500e-01

Joint ci ratio: 1.723066e-02	ci left: 4.214053e-01	ci right 4.287438e-01	k: 29755	n:70000
Cons ci ratio: 1.139125e-02	ci left: 6.248937e-01	ci right 6.320671e-01	k: 43994	n:70000
KS ci ratio: 1.391231e-01	ci left: 1.043359e-02	ci right 1.200732e-02	k: 784	n:70000
SLC39A3   70000 perm   15 sec   (4581 perm/sec)   p_kst 1.120000e-02   p_cons 6.284857e-01   p_joint 4.250714e-01

Joint ci ratio: 5.163035e-02	ci left: 6.547454e-02	ci right 6.895693e-02	k: 5376	n:80000
Cons ci ratio: 1.063955e-02	ci left: 6.258295e-01	ci right 6.325361e-01	k: 50335	n:80000
KS ci ratio: 1.300019e-01	ci left: 1.050648e-02	ci right 1.197929e-02	k: 898	n:80000
SLC39A3   80000 perm   18 sec   (4532 perm/sec)   p_kst 1.122500e-02   p_cons 6.291875e-01   p_joint 6.720000e-02

Joint ci ratio: 4.875161e-02	ci left: 6.538596e-02	ci right 6.866424e-02	k: 6031	n:90000
Cons ci ratio: 1.004156e-02	ci left: 6.255338e-01	ci right 6.318579e-01	k: 56583	n:90000
KS ci ratio: 1.230214e-01	ci left: 1.046884e-02	ci right 1.185183e-02	k: 1003	n:90000
SLC39A3   90000 perm   20 sec   (4467 perm/sec)   p_kst 1.114444e-02   p_cons 6.287000e-01   p_joint 6.701111e-02

Joint ci ratio: 4.626178e-02	ci left: 6.543817e-02	ci right 6.854701e-02	k: 6698	n:100000
Cons ci ratio: 9.525858e-03	ci left: 6.257168e-01	ci right 6.317158e-01	k: 62872	n:100000
KS ci ratio: 1.167908e-01	ci left: 1.048898e-02	ci right 1.179960e-02	k: 1113	n:100000
SLC39A3   100000 perm   23 sec   (4414 perm/sec)   p_kst 1.113000e-02   p_cons 6.287200e-01   p_joint 6.698000e-02

Joint ci ratio: 4.407653e-02	ci left: 6.560136e-02	ci right 6.856697e-02	k: 7378	n:110000
Cons ci ratio: 9.083476e-03	ci left: 6.258096e-01	ci right 6.315291e-01	k: 69154	n:110000
KS ci ratio: 1.119765e-01	ci left: 1.040084e-02	ci right 1.164333e-02	k: 1211	n:110000
SLC39A3   110000 perm   25 sec   (4362 perm/sec)   p_kst 1.100909e-02   p_cons 6.286727e-01   p_joint 6.707273e-02

Joint ci ratio: 4.222487e-02	ci left: 6.559170e-02	ci right 6.842927e-02	k: 8040	n:120000
Cons ci ratio: 8.696265e-03	ci left: 6.259591e-01	ci right 6.314347e-01	k: 75444	n:120000
KS ci ratio: 1.069310e-01	ci left: 1.048244e-02	ci right 1.167470e-02	k: 1328	n:120000
SLC39A3   120000 perm   28 sec   (4312 perm/sec)   p_kst 1.106667e-02   p_cons 6.287000e-01   p_joint 6.700000e-02

Joint ci ratio: 4.059105e-02	ci left: 6.557814e-02	ci right 6.830276e-02	k: 8701	n:130000
Cons ci ratio: 8.361577e-03	ci left: 6.257049e-01	ci right 6.309663e-01	k: 81684	n:130000
KS ci ratio: 1.030895e-01	ci left: 1.043260e-02	ci right 1.157398e-02	k: 1429	n:130000
SLC39A3   130000 perm   31 sec   (4261 perm/sec)   p_kst 1.099231e-02   p_cons 6.283385e-01   p_joint 6.693077e-02

Joint ci ratio: 3.902619e-02	ci left: 6.590807e-02	ci right 6.853846e-02	k: 9410	n:140000
Cons ci ratio: 8.064617e-03	ci left: 6.253833e-01	ci right 6.304543e-01	k: 87909	n:140000
KS ci ratio: 9.891829e-02	ci left: 1.054383e-02	ci right 1.164799e-02	k: 1552	n:140000
SLC39A3   140000 perm   33 sec   (4210 perm/sec)   p_kst 1.108571e-02   p_cons 6.279214e-01   p_joint 6.721429e-02

Outputting figure to mutsig2_images.part000000000160/SLC39A3.2_1061_140000_0.011086_0.62792_0.067214.png
                gene_name: SLC39A3
               theta_stop: 0.099 
                    nperm: 140000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.011 
       ci_ks_bounds_right: 0.012 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.63 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.067 
     ci_joint_bounds_left: 0.066 
    ci_joint_bounds_right: 0.069 

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.165.3896/
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/181708/iteration1/scatter.0000000160
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 160 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120258: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000161> was used as the working directory.
Started at Wed Oct 10 10:45:08 2012
Results reported at Wed Oct 10 10:46:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000161.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000161.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 161  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     99.09 sec.
    Max Memory :       631 MB
    Max Swap   :      3418 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.165.3896/
-whichjob
161
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 161: processing genes 14476 - 14566
Calculating significance of each gene.
Using projection method.
14476	SLC39A5	5.595118e-02
14477	SLC39A6	1
14478	SLC39A7	1
14479	SLC39A8	2.348611e-02
14480	SLC39A9	1
14481	SLC3A1	1
14482	SLC3A2	1
14483	SLC40A1	1
14484	SLC41A1	1
14485	SLC41A2	1
14486	SLC41A3	6.684409e-02
14487	SLC43A1	1
14488	SLC43A2	1
14489	SLC43A3	1
14490	SLC44A1	1
14491	SLC44A2	1
14492	SLC44A3	1
14493	SLC44A4	1.808501e-01
14494	SLC44A5	3.100819e-01
14495	SLC45A1	1
14496	SLC45A2	1
14497	SLC45A3	1
14498	SLC45A4	1
14499	SLC46A1	1
14500	SLC46A2	1
14501	SLC46A3	1
14502	SLC47A1	1
14503	SLC47A2	1
14504	SLC48A1	1
14505	SLC4A1	2.167253e-01
14506	SLC4A10	4.357229e-01
14507	SLC4A11	1.060966e-01
14508	SLC4A1AP	1
14509	SLC4A2	1
14510	SLC4A3	1
14511	SLC4A4	2.158120e-01
14512	SLC4A5	3.328598e-01
14513	SLC4A7	1
14514	SLC4A8	4.196042e-03
14515	SLC4A9	1
14516	SLC5A1	1
14517	SLC5A10	1
14518	SLC5A11	1
14519	SLC5A12	1
14520	SLC5A2	1
14521	SLC5A3	1
14522	SLC5A4	1
14523	SLC5A5	1
14524	SLC5A6	1
14525	SLC5A7	1.015246e-02
14526	SLC5A8	1.055854e-01
14527	SLC5A9	1.904029e-01
14528	SLC6A1	1
14529	SLC6A11	1
14530	SLC6A12	1
14531	SLC6A13	1.710975e-01
14532	SLC6A14	1
14533	SLC6A15	1
14534	SLC6A16	3.372632e-01
14535	SLC6A17	1
14536	SLC6A18	1
14537	SLC6A19	1
14538	SLC6A2	1
14539	SLC6A20	1.424454e-01
14540	SLC6A3	1
14541	SLC6A4	1
14542	SLC6A5	1
14543	SLC6A6	1
14544	SLC6A7	1
14545	SLC6A8	1
14546	SLC6A9	1.523218e-01
14547	SLC7A1	1.837171e-01
14548	SLC7A10	1
14549	SLC7A11	1
14550	SLC7A13	1
14551	SLC7A14	1
14552	SLC7A2	1
14553	SLC7A3	7.913653e-02
14554	SLC7A4	1
14555	SLC7A5	1
14556	SLC7A6	1
14557	SLC7A6OS	1
14558	SLC7A7	1
14559	SLC7A8	1
14560	SLC7A9	9.522453e-02
14561	SLC8A1	1
14562	SLC8A2	1
14563	SLC8A3	1
14564	SLC9A1	1
14565	SLC9A10	3.416154e-01
14566	SLC9A11	1
Done

Running MutSig 2:
Scatter job 161: processing genes 14476 - 14566
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SLC4A8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.735752e-02	ci left: 8.286969e-01	ci right 8.433068e-01	k: 8361	n:10000
Cons ci ratio: 5.078065e-02	ci left: 3.638081e-01	ci right 3.828658e-01	k: 3733	n:10000
KS ci ratio: 3.992989e-02	ci left: 4.808558e-01	ci right 5.005496e-01	k: 4907	n:10000
SLC4A8   10000 perm   2 sec   (4985 perm/sec)   p_kst 4.907000e-01   p_cons 3.733000e-01   p_joint 8.361000e-01

Outputting figure to mutsig2_images.part000000000161/SLC4A8.3_3436_10000_0.4907_0.3733_0.8361.png
                gene_name: SLC4A8
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.84 
     ci_joint_bounds_left: 0.83 
    ci_joint_bounds_right: 0.84 

Current progress: 50 percent done.
SLC5A7
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: 8.254871e-02	ci left: 1.763499e-01	ci right 1.916346e-01	k: 1839	n:10000
KS ci ratio: 1.615181e-02	ci left: 8.478437e-01	ci right 8.617489e-01	k: 8549	n:10000
SLC5A7   10000 perm   2 sec   (6235 perm/sec)   p_kst 8.549000e-01   p_cons 1.839000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000161/SLC5A7.2_1775_10000_0.8549_0.1839_1.png
                gene_name: SLC5A7
               theta_stop: 0.083 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.85 
       ci_ks_bounds_right: 0.86 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000161
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 161 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1699>
Subject: Job 1120260: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1699>, 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/181708/iteration1/scatter.0000000162> was used as the working directory.
Started at Wed Oct 10 10:45:08 2012
Results reported at Wed Oct 10 10:47:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000162.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000162.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 162  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    135.02 sec.
    Max Memory :      1224 MB
    Max Swap   :      3868 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.165.3896/
-whichjob
162
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 162: processing genes 14567 - 14656
Calculating significance of each gene.
Using projection method.
14567	SLC9A2	2.722955e-01
14568	SLC9A3	7.166561e-02
14569	SLC9A3R1	1
14570	SLC9A3R2	1
14571	SLC9A4	1
14572	SLC9A5	1
14573	SLC9A6	1
14574	SLC9A7	1
14575	SLC9A8	2.721516e-01
14576	SLC9A9	1
14577	SLCO1A2	1
14578	SLCO1B1	1
14579	SLCO1B3	3.615976e-02
14580	SLCO1C1	1
14581	SLCO2A1	1
14582	SLCO2B1	1
14583	SLCO3A1	1
14584	SLCO4A1	1
14585	SLCO4C1	3.198555e-02
14586	SLCO5A1	3.652993e-01
14587	SLCO6A1	2.260486e-01
14588	SLFN11	1
14589	SLFN12	1
14590	SLFN12L	1
14591	SLFN13	1
14592	SLFN5	1
14593	SLFNL1	1
14594	SLIT1	1
14595	SLIT2	1
14596	SLIT3	3.925640e-01
14597	SLITRK1	1
14598	SLITRK2	1
14599	SLITRK3	1
14600	SLITRK4	1
14601	SLITRK5	1
14602	SLITRK6	2.180667e-01
14603	SLK	1
14604	SLMAP	1.061323e-03
14605	SLMO1	1
14606	SLMO2	1
14607	SLN	1
14608	SLPI	1
14609	SLTM	1.782560e-01
14610	SLU7	1
14611	SLURP1	1
14612	SMAD1	1
14613	SMAD2	2.248401e-01
14614	SMAD3	1
14615	SMAD4	2.520579e-01
14616	SMAD5	1
14617	SMAD6	1
14618	SMAD7	1
14619	SMAD9	1
14620	SMAGP	1
14621	SMAP1	1.473506e-02
14622	SMAP2	1
14623	SMARCA1	1
14624	SMARCA2	1.577569e-01
14625	SMARCA4	3.857031e-01
14626	SMARCA5	3.154464e-01
14627	SMARCAD1	3.734433e-01
14628	SMARCAL1	1
14629	SMARCB1	1
14630	SMARCC1	8.126517e-02
14631	SMARCC2	1
14632	SMARCD1	1
14633	SMARCD2	1
14634	SMARCD3	1
14635	SMARCE1	1
14636	SMC1A	1
14637	SMC1B	1
14638	SMC2	1
14639	SMC3	1.352430e-01
14640	SMC4	2.364387e-01
14641	SMC5	1
14642	SMC6	1
14643	SMCHD1	1
14644	SMCP	1
14645	SMCR7	1
14646	SMCR7L	1
14647	SMCR8	1
14648	SMEK1	1
14649	SMEK2	1
14650	SMG1	6.743075e-01
14651	SMG5	1
14652	SMG6	1.676265e-01
14653	SMG7	4.349996e-01
14654	SMNDC1	1
14655	SMO	1.912161e-01
14656	SMOC1	1.305779e-01
Done

Running MutSig 2:
Scatter job 162: processing genes 14567 - 14656
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SLMAP
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: 8.673992e-03	ci left: 9.490847e-01	ci right 9.574486e-01	k: 9534	n:10000
KS ci ratio: 3.751375e-02	ci left: 5.120544e-01	ci right 5.317328e-01	k: 5219	n:10000
SLMAP   10000 perm   2 sec   (4939 perm/sec)   p_kst 5.219000e-01   p_cons 9.534000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000162/SLMAP.3_2520_10000_0.5219_0.9534_1.png
                gene_name: SLMAP
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.51 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.95 
      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: 17 percent done.
SLCO1B3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.023114e-01	ci left: 1.214132e-01	ci right 1.346043e-01	k: 1279	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: 9.755860e-02	ci left: 1.321775e-01	ci right 1.458335e-01	k: 1389	n:10000
SLCO1B3   10000 perm   2 sec   (6002 perm/sec)   p_kst 1.389000e-01   p_cons 1.256000e-01   p_joint 1.279000e-01

Joint ci ratio: 8.948263e-02	ci left: 8.361907e-02	ci right 9.150132e-02	k: 1750	n:20000
Cons ci ratio: 7.315137e-02	ci left: 1.209384e-01	ci right 1.301708e-01	k: 2510	n:20000
KS ci ratio: 6.830217e-02	ci left: 1.365491e-01	ci right 1.462554e-01	k: 2827	n:20000
SLCO1B3   20000 perm   4 sec   (5323 perm/sec)   p_kst 1.413500e-01   p_cons 1.255000e-01   p_joint 8.750000e-02

Outputting figure to mutsig2_images.part000000000162/SLCO1B3.2_2165_20000_0.14135_0.1255_0.0875.png
                gene_name: SLCO1B3
               theta_stop: 0.089 
                    nperm: 20000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.15 
                   p_cons: 0.13 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.087 
     ci_joint_bounds_left: 0.084 
    ci_joint_bounds_right: 0.092 

Current progress: 33 percent done.
SLCO4C1
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: 4.337364e-02	ci left: 4.397162e-01	ci right 4.593132e-01	k: 4495	n:10000
KS ci ratio: 6.211914e-02	ci left: 2.758690e-01	ci right 2.936566e-01	k: 2847	n:10000
SLCO4C1   10000 perm   2 sec   (5989 perm/sec)   p_kst 2.847000e-01   p_cons 4.495000e-01   p_joint 3.411000e-01

Outputting figure to mutsig2_images.part000000000162/SLCO4C1.2_2227_10000_0.2847_0.4495_0.3411.png
                gene_name: SLCO4C1
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.45 
      ci_cons_bounds_left: 0.44 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.34 
     ci_joint_bounds_left: 0.33 
    ci_joint_bounds_right: 0.35 

Current progress: 50 percent done.
SMAP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.141594e-02	ci left: 3.580403e-01	ci right 3.770370e-01	k: 3675	n:10000
Cons ci ratio: 5.444600e-02	ci left: 3.320042e-01	ci right 3.506883e-01	k: 3413	n:10000
KS ci ratio: 4.642761e-02	ci left: 4.064147e-01	ci right 4.258341e-01	k: 4161	n:10000
SMAP1   10000 perm   2 sec   (6422 perm/sec)   p_kst 4.161000e-01   p_cons 3.413000e-01   p_joint 3.675000e-01

Outputting figure to mutsig2_images.part000000000162/SMAP1.2_1448_10000_0.4161_0.3413_0.3675.png
                gene_name: SMAP1
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.42 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.43 
                   p_cons: 0.34 
      ci_cons_bounds_left: 0.33 
     ci_cons_bounds_right: 0.35 
                  p_joint: 0.37 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.38 

Current progress: 67 percent done.
SMARCA2
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: 7.859457e-02	ci left: 1.913119e-01	ci right 2.070637e-01	k: 1991	n:10000
KS ci ratio: 6.207343e-02	ci left: 2.761661e-01	ci right 2.939593e-01	k: 2850	n:10000
SMARCA2   10000 perm   2 sec   (5094 perm/sec)   p_kst 2.850000e-01   p_cons 1.991000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000162/SMARCA2.2_4905_10000_0.285_0.1991_1.png
                gene_name: SMARCA2
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.29 
                   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: 83 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: 7.441696e-02	ci left: 2.090529e-01	ci right 2.253122e-01	k: 2171	n:10000
KS ci ratio: 1.609381e-01	ci left: 5.147727e-02	ci right 6.058353e-02	k: 559	n:10000
SMARCC1   10000 perm   2 sec   (5760 perm/sec)   p_kst 5.590000e-02   p_cons 2.171000e-01   p_joint 1

Joint ci ratio: 1.227752e-02	ci left: 8.307946e-01	ci right 8.411076e-01	k: 16720	n:20000
Cons ci ratio: 5.331969e-02	ci left: 2.070457e-01	ci right 2.184379e-01	k: 4254	n:20000
KS ci ratio: 1.152823e-01	ci left: 5.149119e-02	ci right 5.783907e-02	k: 1092	n:20000
SMARCC1   20000 perm   4 sec   (5131 perm/sec)   p_kst 5.460000e-02   p_cons 2.127000e-01   p_joint 8.360000e-01

Joint ci ratio: 9.982936e-03	ci left: 8.329058e-01	ci right 8.412955e-01	k: 25114	n:30000
Cons ci ratio: 4.353768e-02	ci left: 2.080807e-01	ci right 2.173750e-01	k: 6381	n:30000
KS ci ratio: 9.447933e-02	ci left: 5.169714e-02	ci right 5.685627e-02	k: 1627	n:30000
SMARCC1   30000 perm   6 sec   (4847 perm/sec)   p_kst 5.423333e-02   p_cons 2.127000e-01   p_joint 8.371333e-01

Outputting figure to mutsig2_images.part000000000162/SMARCC1.2_3430_30000_0.054233_0.2127_0.83713.png
                gene_name: SMARCC1
               theta_stop: 0.094 
                    nperm: 30000 
                     p_ks: 0.054 
        ci_ks_bounds_left: 0.052 
       ci_ks_bounds_right: 0.057 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.22 
                  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.165.3896/
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/181708/iteration1/scatter.0000000162
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 162 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120263: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000163> was used as the working directory.
Started at Wed Oct 10 10:45:08 2012
Results reported at Wed Oct 10 10:46:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000163.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000163.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 163  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    133.59 sec.
    Max Memory :      1120 MB
    Max Swap   :      3851 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.165.3896/
-whichjob
163
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 163: processing genes 14657 - 14747
Calculating significance of each gene.
Using projection method.
14657	SMOC2	1.405280e-02
14658	SMOX	1.332204e-01
14659	SMPD1	2.565515e-03
14660	SMPD2	1
14661	SMPD3	1
14662	SMPD4	1
14663	SMPDL3A	1.894251e-01
14664	SMPDL3B	1
14665	SMPX	1
14666	SMR3A	1
14667	SMR3B	1
14668	SMS	1
14669	SMTN	1
14670	SMTNL1	1
14671	SMTNL2	3.207772e-02
14672	SMU1	1
14673	SMUG1	1
14674	SMURF1	1
14675	SMURF2	1
14676	SMYD1	6.203630e-03
14677	SMYD2	1
14678	SMYD3	1
14679	SMYD4	1
14680	SMYD5	1
14681	SNAI1	1
14682	SNAI2	1
14683	SNAI3	1
14684	SNAP23	1
14685	SNAP25	1
14686	SNAP29	1
14687	SNAP47	1
14688	SNAP91	1.309993e-01
14689	SNAPC1	1
14690	SNAPC2	1
14691	SNAPC3	1
14692	SNAPC4	1
14693	SNAPC5	1
14694	SNAPIN	1
14695	SNCA	1
14696	SNCAIP	1
14697	SNCB	1
14698	SNCG	1
14699	SND1	7.016276e-02
14700	SNED1	1
14701	SNF8	1
14702	SNHG3-RCC1	1
14703	SNIP1	1
14704	SNN	1
14705	SNPH	1
14706	SNRK	1
14707	SNRNP200	1
14708	SNRNP25	1
14709	SNRNP27	1
14710	SNRNP35	1
14711	SNRNP40	1
14712	SNRNP48	1
14713	SNRNP70	1
14714	SNRPA	1
14715	SNRPA1	1
14716	SNRPB	1.710305e-02
14717	SNRPB2	3.114278e-02
14718	SNRPC	1
14719	SNRPD1	1
14720	SNRPD2	1
14721	SNRPD3	1
14722	SNRPE	1
14723	SNRPF	1
14724	SNRPG	1
14725	SNRPN	1
14726	SNTA1	1
14727	SNTB1	1
14728	SNTB2	1
14729	SNTG1	1
14730	SNTG2	1
14731	SNTN	1
14732	SNUPN	1
14733	SNURF	1
14734	SNW1	1.737321e-01
14735	SNX1	1
14736	SNX10	1
14737	SNX11	1
14738	SNX12	1
14739	SNX13	1
14740	SNX14	1
14741	SNX15	1
14742	SNX16	1
14743	SNX17	1
14744	SNX18	1
14745	SNX19	1
14746	SNX2	1
14747	SNX20	1
Done

Running MutSig 2:
Scatter job 163: processing genes 14657 - 14747
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SMPD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.006293e-02	ci left: 2.299769e-01	ci right 2.467758e-01	k: 2383	n:10000
Cons ci ratio: 1.582613e-01	ci left: 5.320919e-02	ci right 6.245049e-02	k: 577	n:10000
KS ci ratio: 3.243155e-02	ci left: 5.838973e-01	ci right 6.032481e-01	k: 5936	n:10000
SMPD1   10000 perm   2 sec   (5734 perm/sec)   p_kst 5.936000e-01   p_cons 5.770000e-02   p_joint 2.383000e-01

Joint ci ratio: 3.061670e-02	ci left: 4.434873e-01	ci right 4.573271e-01	k: 9008	n:20000
Cons ci ratio: 1.098083e-01	ci left: 5.660168e-02	ci right 6.322698e-02	k: 1197	n:20000
KS ci ratio: 2.310296e-02	ci left: 5.831961e-01	ci right 5.968777e-01	k: 11801	n:20000
SMPD1   20000 perm   6 sec   (3426 perm/sec)   p_kst 5.900500e-01   p_cons 5.985000e-02   p_joint 4.504000e-01

Joint ci ratio: 3.431488e-02	ci left: 2.979019e-01	ci right 3.083363e-01	k: 9093	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: 1.882942e-02	ci left: 5.853445e-01	ci right 5.965045e-01	k: 17728	n:30000
SMPD1   30000 perm   8 sec   (3746 perm/sec)   p_kst 5.909333e-01   p_cons 6.346667e-02   p_joint 3.031000e-01

Outputting figure to mutsig2_images.part000000000163/SMPD1.3_1960_30000_0.59093_0.063467_0.3031.png
                gene_name: SMPD1
               theta_stop: 0.087 
                    nperm: 30000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.59 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.063 
      ci_cons_bounds_left: 0.061 
     ci_cons_bounds_right: 0.066 
                  p_joint: 0.30 
     ci_joint_bounds_left: 0.30 
    ci_joint_bounds_right: 0.31 

Current progress: 25 percent done.
SMOC2
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: 2.499077e-02	ci left: 7.020050e-01	ci right 7.198720e-01	k: 7110	n:10000
KS ci ratio: 4.193901e-02	ci left: 4.563836e-01	ci right 4.760361e-01	k: 4662	n:10000
SMOC2   10000 perm   2 sec   (6388 perm/sec)   p_kst 4.662000e-01   p_cons 7.110000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000163/SMOC2.2_1426_10000_0.4662_0.711_1.png
                gene_name: SMOC2
               theta_stop: 0.042 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.71 
      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: 50 percent done.
SMYD1
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: 9.258663e-02	ci left: 1.449173e-01	ci right 1.590860e-01	k: 1519	n:10000
KS ci ratio: 1.437565e-02	ci left: 8.750041e-01	ci right 8.877728e-01	k: 8815	n:10000
SMYD1   10000 perm   2 sec   (5880 perm/sec)   p_kst 8.815000e-01   p_cons 1.519000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000163/SMYD1.2_1513_10000_0.8815_0.1519_1.png
                gene_name: SMYD1
               theta_stop: 0.093 
                    nperm: 10000 
                     p_ks: 0.88 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.16 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
SND1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.261923e-02	ci left: 4.483979e-01	ci right 4.680265e-01	k: 4582	n:10000
Cons ci ratio: 1.699685e-01	ci left: 4.619368e-02	ci right 5.487054e-02	k: 504	n:10000
KS ci ratio: 6.758888e-02	ci left: 2.431184e-01	ci right 2.602265e-01	k: 2516	n:10000
SND1   10000 perm   2 sec   (5655 perm/sec)   p_kst 2.516000e-01   p_cons 5.040000e-02   p_joint 4.582000e-01

Joint ci ratio: 1.284842e-02	ci left: 8.177903e-01	ci right 8.284155e-01	k: 16463	n:20000
Cons ci ratio: 1.170486e-01	ci left: 4.998388e-02	ci right 5.624684e-02	k: 1061	n:20000
KS ci ratio: 4.798401e-02	ci left: 2.441593e-01	ci right 2.562134e-01	k: 5003	n:20000
SND1   20000 perm   4 sec   (5127 perm/sec)   p_kst 2.501500e-01   p_cons 5.305000e-02   p_joint 8.231500e-01

Joint ci ratio: 1.113913e-02	ci left: 8.004705e-01	ci right 8.094703e-01	k: 24150	n:30000
Cons ci ratio: 9.576109e-02	ci left: 5.036128e-02	ci right 5.545908e-02	k: 1586	n:30000
KS ci ratio: 3.921024e-02	ci left: 2.449754e-01	ci right 2.548064e-01	k: 7496	n:30000
SND1   30000 perm   6 sec   (4921 perm/sec)   p_kst 2.498667e-01   p_cons 5.286667e-02   p_joint 8.050000e-01

Outputting figure to mutsig2_images.part000000000163/SND1.2_2829_30000_0.24987_0.052867_0.805.png
                gene_name: SND1
               theta_stop: 0.096 
                    nperm: 30000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.053 
      ci_cons_bounds_left: 0.050 
     ci_cons_bounds_right: 0.055 
                  p_joint: 0.81 
     ci_joint_bounds_left: 0.80 
    ci_joint_bounds_right: 0.81 

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.165.3896/
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/181708/iteration1/scatter.0000000163
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 163 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120267: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000164> was used as the working directory.
Started at Wed Oct 10 10:45:15 2012
Results reported at Wed Oct 10 10:47:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000164.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000164.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 164  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    127.64 sec.
    Max Memory :      1118 MB
    Max Swap   :      3830 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.165.3896/
-whichjob
164
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 164: processing genes 14748 - 14837
Calculating significance of each gene.
Using projection method.
14748	SNX21	1
14749	SNX22	3.808716e-02
14750	SNX24	1
14751	SNX25	6.419727e-02
14752	SNX27	1
14753	SNX29	1
14754	SNX3	1
14755	SNX30	1
14756	SNX31	9.776467e-02
14757	SNX32	1.103447e-01
14758	SNX33	5.432333e-02
14759	SNX4	1
14760	SNX5	1
14761	SNX6	1
14762	SNX7	1
14763	SNX8	1
14764	SNX9	1
14765	SOAT1	1
14766	SOAT2	1
14767	SOBP	1
14768	SOCS1	1
14769	SOCS2	1
14770	SOCS3	1
14771	SOCS4	1
14772	SOCS5	1
14773	SOCS6	1
14774	SOCS7	1
14775	SOD1	1
14776	SOD2	1
14777	SOD3	1
14778	SOHLH1	1
14779	SOHLH2	2.921229e-02
14780	SOLH	1
14781	SON	4.220520e-01
14782	SORBS1	1
14783	SORBS2	1
14784	SORBS3	1
14785	SORCS1	2.468733e-01
14786	SORCS2	1
14787	SORCS3	5.891001e-02
14788	SORD	1
14789	SORL1	1
14790	SORT1	1
14791	SOS1	1.748274e-01
14792	SOS2	1
14793	SOST	1
14794	SOSTDC1	1
14795	SOX1	1
14796	SOX10	1
14797	SOX11	1
14798	SOX12	1
14799	SOX13	1
14800	SOX14	1
14801	SOX15	1
14802	SOX17	1
14803	SOX18	1
14804	SOX2	1
14805	SOX21	1
14806	SOX3	1
14807	SOX30	2.711551e-01
14808	SOX4	1
14809	SOX5	1
14810	SOX6	1
14811	SOX7	1.296746e-01
14812	SOX8	1
14813	SOX9	1
14814	SP1	1
14815	SP100	4.062108e-01
14816	SP110	1
14817	SP140	1
14818	SP140L	1
14819	SP2	1.702843e-01
14820	SP3	3.056304e-02
14821	SP4	1
14822	SP5	1
14823	SP6	1
14824	SP7	1
14825	SP8	1
14826	SPA17	1
14827	SPACA1	1
14828	SPACA3	1
14829	SPACA4	1
14830	SPAG1	1
14831	SPAG11A	1
14832	SPAG11B	6.152166e-02
14833	SPAG16	1
14834	SPAG17	4.320929e-01
14835	SPAG4	1
14836	SPAG5	1
14837	SPAG6	1
Done

Running MutSig 2:
Scatter job 164: processing genes 14748 - 14837
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SNX25
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.624806e-01	ci left: 5.051566e-02	ci right 5.954576e-02	k: 549	n:10000
Cons ci ratio: 1.805768e-01	ci left: 4.092429e-02	ci right 4.914339e-02	k: 449	n:10000
KS ci ratio: 1.339460e-02	ci left: 8.893387e-01	ci right 9.014299e-01	k: 8955	n:10000
SNX25   10000 perm   2 sec   (5417 perm/sec)   p_kst 8.955000e-01   p_cons 4.490000e-02   p_joint 5.490000e-02

Joint ci ratio: 1.103976e-01	ci left: 5.601725e-02	ci right 6.261160e-02	k: 1185	n:20000
Cons ci ratio: 1.292004e-01	ci left: 4.115060e-02	ci right 4.688292e-02	k: 879	n:20000
KS ci ratio: 9.487815e-03	ci left: 8.908216e-01	ci right 8.993632e-01	k: 17903	n:20000
SNX25   20000 perm   6 sec   (3307 perm/sec)   p_kst 8.951500e-01   p_cons 4.395000e-02   p_joint 5.925000e-02

Joint ci ratio: 9.354131e-02	ci left: 5.270749e-02	ci right 5.791238e-02	k: 1658	n:30000
Cons ci ratio: 1.066815e-01	ci left: 4.076467e-02	ci right 4.539102e-02	k: 1291	n:30000
KS ci ratio: 7.744356e-03	ci left: 8.916790e-01	ci right 8.986443e-01	k: 26856	n:30000
SNX25   30000 perm   8 sec   (3636 perm/sec)   p_kst 8.952000e-01   p_cons 4.303333e-02   p_joint 5.526667e-02

Joint ci ratio: 8.060522e-02	ci left: 5.357041e-02	ci right 5.809435e-02	k: 2232	n:40000
Cons ci ratio: 9.237989e-02	ci left: 4.108167e-02	ci right 4.508501e-02	k: 1722	n:40000
KS ci ratio: 6.643051e-03	ci left: 8.939546e-01	ci right 8.999377e-01	k: 35879	n:40000
SNX25   40000 perm   11 sec   (3806 perm/sec)   p_kst 8.969750e-01   p_cons 4.305000e-02   p_joint 5.580000e-02

Outputting figure to mutsig2_images.part000000000164/SNX25.2_2595_40000_0.89697_0.04305_0.0558.png
                gene_name: SNX25
               theta_stop: 0.092 
                    nperm: 40000 
                     p_ks: 0.90 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   p_cons: 0.043 
      ci_cons_bounds_left: 0.041 
     ci_cons_bounds_right: 0.045 
                  p_joint: 0.056 
     ci_joint_bounds_left: 0.054 
    ci_joint_bounds_right: 0.058 

Current progress: 25 percent done.
SORCS3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.783063e-02	ci left: 5.078524e-01	ci right 5.275373e-01	k: 5177	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: 4.091696e-02	ci left: 4.686667e-01	ci right 4.883458e-01	k: 4785	n:10000
SORCS3   10000 perm   2 sec   (5533 perm/sec)   p_kst 4.785000e-01   p_cons 2.195000e-01   p_joint 5.177000e-01

Outputting figure to mutsig2_images.part000000000164/SORCS3.2_3777_10000_0.4785_0.2195_0.5177.png
                gene_name: SORCS3
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.52 
     ci_joint_bounds_left: 0.51 
    ci_joint_bounds_right: 0.53 

Current progress: 50 percent done.
SOS1
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: 5.821045e-02	ci left: 3.028259e-01	ci right 3.210837e-01	k: 3119	n:10000
KS ci ratio: 3.515339e-02	ci left: 5.443933e-01	ci right 5.639751e-01	k: 5542	n:10000
SOS1   10000 perm   2 sec   (5323 perm/sec)   p_kst 5.542000e-01   p_cons 3.119000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000164/SOS1.2_4094_10000_0.5542_0.3119_1.png
                gene_name: SOS1
               theta_stop: 0.058 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   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.
SP3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.083156e-01	ci left: 1.094933e-01	ci right 1.221314e-01	k: 1157	n:10000
Cons ci ratio: 4.102367e-02	ci left: 4.673682e-01	ci right 4.870451e-01	k: 4772	n:10000
KS ci ratio: 1.552890e-01	ci left: 5.523135e-02	ci right 6.462705e-02	k: 598	n:10000
SP3   10000 perm   2 sec   (6089 perm/sec)   p_kst 5.980000e-02   p_cons 4.772000e-01   p_joint 1.157000e-01

Joint ci ratio: 6.854230e-02	ci left: 1.357114e-01	ci right 1.453933e-01	k: 2810	n:20000
Cons ci ratio: 2.896106e-02	ci left: 4.711058e-01	ci right 4.850006e-01	k: 9561	n:20000
KS ci ratio: 1.060452e-01	ci left: 6.054901e-02	ci right 6.737843e-02	k: 1278	n:20000
SP3   20000 perm   4 sec   (5414 perm/sec)   p_kst 6.390000e-02   p_cons 4.780500e-01   p_joint 1.405000e-01

Joint ci ratio: 4.463246e-02	ci left: 1.999480e-01	ci right 2.091093e-01	k: 6135	n:30000
Cons ci ratio: 2.340769e-02	ci left: 4.774638e-01	ci right 4.888061e-01	k: 14494	n:30000
KS ci ratio: 8.681601e-02	ci left: 6.086418e-02	ci right 6.642069e-02	k: 1908	n:30000
SP3   30000 perm   6 sec   (5155 perm/sec)   p_kst 6.360000e-02   p_cons 4.831333e-01   p_joint 2.045000e-01

Outputting figure to mutsig2_images.part000000000164/SP3.2_2374_30000_0.0636_0.48313_0.2045.png
                gene_name: SP3
               theta_stop: 0.087 
                    nperm: 30000 
                     p_ks: 0.064 
        ci_ks_bounds_left: 0.061 
       ci_ks_bounds_right: 0.066 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.21 

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.165.3896/
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/181708/iteration1/scatter.0000000164
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 164 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120271: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000165> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 13:39:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000165.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000165.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 165  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :  10585.42 sec.
    Max Memory :      1544 MB
    Max Swap   :      3992 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.165.3896/
-whichjob
165
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 165: processing genes 14838 - 14928
Calculating significance of each gene.
Using projection method.
14838	SPAG7	2.730470e-02
14839	SPAG8	1
14840	SPAG9	1
14841	SPAM1	1.574475e-01
14842	SPANXC	1
14843	SPANXD	1
14844	SPANXE	2.855208e-02
14845	SPANXN1	1
14846	SPANXN2	1
14847	SPANXN3	4.676444e-02
14848	SPANXN4	1
14849	SPANXN5	1
14850	SPARC	1
14851	SPARCL1	1
14852	SPAST	1
14853	SPATA1	1
14854	SPATA12	1
14855	SPATA13	1
14856	SPATA16	1
14857	SPATA17	1.256164e-01
14858	SPATA18	1
14859	SPATA19	1
14860	SPATA2	1
14861	SPATA20	1
14862	SPATA21	2.066127e-02
14863	SPATA22	1
14864	SPATA2L	1
14865	SPATA4	1
14866	SPATA5	1
14867	SPATA5L1	1
14868	SPATA6	1
14869	SPATA7	1
14870	SPATA8	1
14871	SPATA9	1
14872	SPATC1	1
14873	SPATS1	8.452645e-02
14874	SPATS2	1.753214e-02
14875	SPATS2L	1
14876	SPC24	1
14877	SPC25	1
14878	SPCS1	1
14879	SPCS2	1
14880	SPCS3	1
14881	SPDEF	1
14882	SPDYA	1
14883	SPDYC	1
14884	SPDYE1	1
14885	SPDYE3	1
14886	SPDYE4	1
14887	SPDYE5	1
14888	SPDYE6	4.281366e-02
14889	SPEF1	1
14890	SPEF2	3.890320e-01
14891	SPEG	1
14892	SPEM1	1
14893	SPEN	1
14894	SPERT	1
14895	SPESP1	5.516629e-02
14896	SPG11	3.866497e-01
14897	SPG20	1
14898	SPG21	1
14899	SPG7	1
14900	SPHAR	1
14901	SPHK1	1
14902	SPHK2	2.820292e-01
14903	SPHKAP	5.152498e-01
14904	SPI1	1
14905	SPIB	1
14906	SPIC	1
14907	SPIN1	1
14908	SPIN2A	1
14909	SPIN2B	1
14910	SPIN3	1
14911	SPIN4	1
14912	SPINK1	1
14913	SPINK13	1
14914	SPINK14	1
14915	SPINK2	1
14916	SPINK4	1
14917	SPINK5	1
14918	SPINK6	1
14919	SPINK7	1
14920	SPINK8	1
14921	SPINK9	1
14922	SPINLW1	1
14923	SPINT1	1
14924	SPINT2	1
14925	SPINT4	1
14926	SPIRE1	1
14927	SPIRE2	1.278743e-01
14928	SPN	1
Done

Running MutSig 2:
Scatter job 165: processing genes 14838 - 14928
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SPATS2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.609790e-02	ci left: 2.016579e-01	ci right 2.177115e-01	k: 2096	n:10000
Cons ci ratio: 6.573861e-02	ci left: 2.535997e-01	ci right 2.709390e-01	k: 2622	n:10000
KS ci ratio: 6.251794e-02	ci left: 2.732942e-01	ci right 2.910328e-01	k: 2821	n:10000
SPATS2   10000 perm   2 sec   (5955 perm/sec)   p_kst 2.821000e-01   p_cons 2.622000e-01   p_joint 2.096000e-01

Outputting figure to mutsig2_images.part000000000165/SPATS2.4_1686_10000_0.2821_0.2622_0.2096.png
                gene_name: SPATS2
               theta_stop: 0.076 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.27 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.25 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.22 

Current progress: 20 percent done.
SPATA21
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.373646e-02	ci left: 7.228992e-01	ci right 7.403656e-01	k: 7317	n:10000
Cons ci ratio: 8.307184e-03	ci left: 9.529432e-01	ci right 9.609878e-01	k: 9571	n:10000
KS ci ratio: 3.250553e-02	ci left: 5.827935e-01	ci right 6.021526e-01	k: 5925	n:10000
SPATA21   10000 perm   2 sec   (6588 perm/sec)   p_kst 5.925000e-01   p_cons 9.571000e-01   p_joint 7.317000e-01

Outputting figure to mutsig2_images.part000000000165/SPATA21.2_1454_10000_0.5925_0.9571_0.7317.png
                gene_name: SPATA21
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.96 
      ci_cons_bounds_left: 0.95 
     ci_cons_bounds_right: 0.96 
                  p_joint: 0.73 
     ci_joint_bounds_left: 0.72 
    ci_joint_bounds_right: 0.74 

Current progress: 40 percent done.
SPEG
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.773547e-02	ci left: 1.590500e-01	ci right 1.737448e-01	k: 1663	n:10000
Cons ci ratio: 1.256428e-01	ci left: 8.310086e-02	ci right 9.434008e-02	k: 886	n:10000
KS ci ratio: 1.680366e-02	ci left: 8.375528e-01	ci right 8.518458e-01	k: 8448	n:10000
SPEG   10000 perm   2 sec   (4074 perm/sec)   p_kst 8.448000e-01   p_cons 8.860000e-02   p_joint 1.663000e-01

Joint ci ratio: 4.650859e-02	ci left: 2.559654e-01	ci right 2.682038e-01	k: 5241	n:20000
Cons ci ratio: 8.723533e-02	ci left: 8.768580e-02	ci right 9.573336e-02	k: 1833	n:20000
KS ci ratio: 1.193110e-02	ci left: 8.385923e-01	ci right 8.487075e-01	k: 16874	n:20000
SPEG   20000 perm   5 sec   (3731 perm/sec)   p_kst 8.437000e-01   p_cons 9.165000e-02   p_joint 2.620500e-01

Outputting figure to mutsig2_images.part000000000165/SPEG.2_9980_20000_0.8437_0.09165_0.26205.png
                gene_name: SPEG
               theta_stop: 0.087 
                    nperm: 20000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.092 
      ci_cons_bounds_left: 0.088 
     ci_cons_bounds_right: 0.096 
                  p_joint: 0.26 
     ci_joint_bounds_left: 0.26 
    ci_joint_bounds_right: 0.27 

Current progress: 60 percent done.
SPG11
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: 3.725901e-02	ci left: 5.154566e-01	ci right 5.351287e-01	k: 5253	n:10000
KS ci ratio: 1.959510e+00	ci left: 6.187149e-05	ci right 8.764745e-04	k: 3	n:10000
SPG11   10000 perm   2 sec   (4614 perm/sec)   p_kst 3.000000e-04   p_cons 5.253000e-01   p_joint 4.000000e-04

Joint ci ratio: 1.239272e+00	ci left: 2.057886e-04	ci right 8.540675e-04	k: 9	n:20000
Cons ci ratio: 2.609808e-02	ci left: 5.231041e-01	ci right 5.369872e-01	k: 10601	n:20000
KS ci ratio: 1.481324e+00	ci left: 1.101024e-04	ci right 6.528585e-04	k: 6	n:20000
SPG11   20000 perm   5 sec   (4015 perm/sec)   p_kst 3.000000e-04   p_cons 5.300500e-01   p_joint 4.500000e-04

Joint ci ratio: 7.404523e-01	ci left: 5.931868e-04	ci right 1.309185e-03	k: 27	n:30000
Cons ci ratio: 2.125323e-02	ci left: 5.257004e-01	ci right 5.370269e-01	k: 15941	n:30000
KS ci ratio: 1.131361e+00	ci left: 1.830524e-04	ci right 6.559730e-04	k: 11	n:30000
SPG11   30000 perm   8 sec   (3925 perm/sec)   p_kst 3.666667e-04   p_cons 5.313667e-01   p_joint 9.000000e-04

Joint ci ratio: 6.719803e-01	ci left: 5.679580e-04	ci right 1.158413e-03	k: 33	n:40000
Cons ci ratio: 1.850112e-02	ci left: 5.238938e-01	ci right 5.337020e-01	k: 21152	n:40000
KS ci ratio: 1.011937e+00	ci left: 1.913610e-04	ci right 5.871709e-04	k: 14	n:40000
SPG11   40000 perm   10 sec   (3853 perm/sec)   p_kst 3.500000e-04   p_cons 5.288000e-01   p_joint 8.250000e-04

Joint ci ratio: 7.685677e-01	ci left: 3.235989e-04	ci right 7.380108e-04	k: 25	n:50000
Cons ci ratio: 1.652280e-02	ci left: 5.251734e-01	ci right 5.339431e-01	k: 26478	n:50000
KS ci ratio: 8.991298e-01	ci left: 2.133723e-04	ci right 5.688958e-04	k: 18	n:50000
SPG11   50000 perm   13 sec   (3792 perm/sec)   p_kst 3.600000e-04   p_cons 5.295600e-01   p_joint 5.000000e-04

Joint ci ratio: 7.999999e-01	ci left: 2.430155e-04	ci right 5.751330e-04	k: 23	n:60000
Cons ci ratio: 1.507952e-02	ci left: 5.256799e-01	ci right 5.336839e-01	k: 31781	n:60000
KS ci ratio: 8.552573e-01	ci left: 2.036202e-04	ci right 5.147596e-04	k: 20	n:60000
SPG11   60000 perm   16 sec   (3733 perm/sec)   p_kst 3.333333e-04   p_cons 5.296833e-01   p_joint 3.833333e-04

Joint ci ratio: 8.000238e-01	ci left: 2.082971e-04	ci right 4.929779e-04	k: 23	n:70000
Cons ci ratio: 1.395970e-02	ci left: 5.260228e-01	ci right 5.334318e-01	k: 37081	n:70000
KS ci ratio: 8.552797e-01	ci left: 1.745302e-04	ci right 4.412282e-04	k: 20	n:70000
SPG11   70000 perm   19 sec   (3680 perm/sec)   p_kst 2.857143e-04   p_cons 5.297286e-01   p_joint 3.285714e-04

Joint ci ratio: 9.506327e-01	ci left: 1.143215e-04	ci right 3.247672e-04	k: 16	n:80000
Cons ci ratio: 1.305790e-02	ci left: 5.262716e-01	ci right 5.332012e-01	k: 42379	n:80000
KS ci ratio: 8.552965e-01	ci left: 1.527130e-04	ci right 3.860784e-04	k: 20	n:80000
SPG11   80000 perm   22 sec   (3628 perm/sec)   p_kst 2.500000e-04   p_cons 5.297375e-01   p_joint 2.000000e-04

Joint ci ratio: 9.238553e-01	ci left: 1.100385e-04	ci right 3.024122e-04	k: 17	n:90000
Cons ci ratio: 1.232442e-02	ci left: 5.259325e-01	ci right 5.324656e-01	k: 47628	n:90000
KS ci ratio: 7.838868e-01	ci left: 1.708656e-04	ci right 3.967530e-04	k: 24	n:90000
SPG11   90000 perm   25 sec   (3575 perm/sec)   p_kst 2.666667e-04   p_cons 5.292000e-01   p_joint 1.888889e-04

Joint ci ratio: 8.992197e-01	ci left: 1.066828e-04	ci right 2.844627e-04	k: 18	n:100000
Cons ci ratio: 1.168612e-02	ci left: 5.263506e-01	ci right 5.325477e-01	k: 52945	n:100000
KS ci ratio: 7.686715e-01	ci left: 1.617931e-04	ci right 3.690273e-04	k: 25	n:100000
SPG11   100000 perm   28 sec   (3521 perm/sec)   p_kst 2.500000e-04   p_cons 5.294500e-01   p_joint 1.800000e-04

Joint ci ratio: 8.764550e-01	ci left: 1.039962e-04	ci right 2.697219e-04	k: 19	n:110000
Cons ci ratio: 1.115297e-02	ci left: 5.260177e-01	ci right 5.319263e-01	k: 58187	n:110000
KS ci ratio: 7.407127e-01	ci left: 1.617621e-04	ci right 3.571035e-04	k: 27	n:110000
SPG11   110000 perm   32 sec   (3471 perm/sec)   p_kst 2.454545e-04   p_cons 5.289727e-01   p_joint 1.727273e-04

Joint ci ratio: 8.172948e-01	ci left: 1.148975e-04	ci right 2.775558e-04	k: 22	n:120000
Cons ci ratio: 1.069027e-02	ci left: 5.255791e-01	ci right 5.312362e-01	k: 63409	n:120000
KS ci ratio: 6.822877e-01	ci left: 1.824067e-04	ci right 3.764331e-04	k: 32	n:120000
SPG11   120000 perm   35 sec   (3433 perm/sec)   p_kst 2.666667e-04   p_cons 5.284083e-01   p_joint 1.833333e-04

Joint ci ratio: 8.173011e-01	ci left: 1.060590e-04	ci right 2.562063e-04	k: 22	n:130000
Cons ci ratio: 9.892164e-03	ci left: 5.443738e-01	ci right 5.497933e-01	k: 71121	n:130000
KS ci ratio: 6.822952e-01	ci left: 1.683749e-04	ci right 3.474782e-04	k: 32	n:130000
SPG11   130000 perm   38 sec   (3394 perm/sec)   p_kst 2.461538e-04   p_cons 5.470846e-01   p_joint 1.692308e-04

Joint ci ratio: 7.687011e-01	ci left: 1.155652e-04	ci right 2.635954e-04	k: 25	n:140000
Cons ci ratio: 9.534649e-03	ci left: 5.443522e-01	ci right 5.495744e-01	k: 76575	n:140000
KS ci ratio: 6.276127e-01	ci left: 1.920859e-04	ci right 3.725381e-04	k: 38	n:140000
SPG11   140000 perm   42 sec   (3356 perm/sec)   p_kst 2.714286e-04   p_cons 5.469643e-01   p_joint 1.785714e-04

Joint ci ratio: 7.543339e-01	ci left: 1.132301e-04	ci right 2.539633e-04	k: 26	n:150000
Cons ci ratio: 9.211803e-03	ci left: 5.444167e-01	ci right 5.494615e-01	k: 82041	n:150000
KS ci ratio: 6.197217e-01	ci left: 1.848917e-04	ci right 3.554116e-04	k: 39	n:150000
SPG11   150000 perm   45 sec   (3317 perm/sec)   p_kst 2.600000e-04   p_cons 5.469400e-01   p_joint 1.733333e-04

Joint ci ratio: 7.543383e-01	ci left: 1.061531e-04	ci right 2.380912e-04	k: 26	n:160000
Cons ci ratio: 8.921928e-03	ci left: 5.443506e-01	ci right 5.492352e-01	k: 87487	n:160000
KS ci ratio: 6.047878e-01	ci left: 1.838955e-04	ci right 3.476162e-04	k: 41	n:160000
SPG11   160000 perm   49 sec   (3278 perm/sec)   p_kst 2.562500e-04   p_cons 5.467937e-01   p_joint 1.625000e-04

Joint ci ratio: 6.928974e-01	ci left: 1.239032e-04	ci right 2.588255e-04	k: 31	n:170000
Cons ci ratio: 8.643013e-03	ci left: 5.451420e-01	ci right 5.498799e-01	k: 93077	n:170000
KS ci ratio: 5.542886e-01	ci left: 2.132454e-04	ci right 3.810447e-04	k: 49	n:170000
SPG11   170000 perm   52 sec   (3242 perm/sec)   p_kst 2.882353e-04   p_cons 5.475118e-01   p_joint 1.823529e-04

Joint ci ratio: 6.625347e-01	ci left: 1.308145e-04	ci right 2.639434e-04	k: 34	n:180000
Cons ci ratio: 8.397630e-03	ci left: 5.453194e-01	ci right 5.499236e-01	k: 98572	n:180000
KS ci ratio: 5.333629e-01	ci left: 2.205666e-04	ci right 3.851231e-04	k: 53	n:180000
SPG11   180000 perm   56 sec   (3207 perm/sec)   p_kst 2.944444e-04   p_cons 5.476222e-01   p_joint 1.888889e-04

Joint ci ratio: 6.443796e-01	ci left: 1.327085e-04	ci right 2.623019e-04	k: 36	n:190000
Cons ci ratio: 8.172460e-03	ci left: 5.454534e-01	ci right 5.499346e-01	k: 104062	n:190000
KS ci ratio: 5.191374e-01	ci left: 2.226485e-04	ci right 3.827235e-04	k: 56	n:190000
SPG11   190000 perm   60 sec   (3171 perm/sec)   p_kst 2.947368e-04   p_cons 5.476947e-01   p_joint 1.894737e-04

Joint ci ratio: 5.059926e-01	ci left: 2.245750e-04	ci right 3.805122e-04	k: 59	n:200000
Cons ci ratio: 7.962795e-03	ci left: 5.456806e-01	ci right 5.500480e-01	k: 109573	n:200000
KS ci ratio: 5.059926e-01	ci left: 2.245750e-04	ci right 3.805122e-04	k: 59	n:200000
SPG11   200000 perm   64 sec   (3136 perm/sec)   p_kst 2.950000e-04   p_cons 5.478650e-01   p_joint 2.950000e-04

Joint ci ratio: 5.018305e-01	ci left: 2.180370e-04	ci right 3.677558e-04	k: 60	n:210000
Cons ci ratio: 7.768478e-03	ci left: 5.458874e-01	ci right 5.501494e-01	k: 115084	n:210000
KS ci ratio: 5.018305e-01	ci left: 2.180370e-04	ci right 3.677558e-04	k: 60	n:210000
SPG11   210000 perm   68 sec   (3102 perm/sec)   p_kst 2.857143e-04   p_cons 5.480190e-01   p_joint 2.857143e-04

Joint ci ratio: 4.977692e-01	ci left: 2.120981e-04	ci right 3.561544e-04	k: 61	n:220000
Cons ci ratio: 7.591207e-03	ci left: 5.458492e-01	ci right 5.500132e-01	k: 120545	n:220000
KS ci ratio: 4.977692e-01	ci left: 2.120981e-04	ci right 3.561544e-04	k: 61	n:220000
SPG11   220000 perm   72 sec   (3069 perm/sec)   p_kst 2.772727e-04   p_cons 5.479318e-01   p_joint 2.772727e-04

Joint ci ratio: 6.048126e-01	ci left: 1.279260e-04	ci right 2.418233e-04	k: 41	n:230000
Cons ci ratio: 7.427042e-03	ci left: 5.457153e-01	ci right 5.497878e-01	k: 125983	n:230000
KS ci ratio: 4.899308e-01	ci left: 2.104885e-04	ci right 3.504404e-04	k: 63	n:230000
SPG11   230000 perm   76 sec   (3037 perm/sec)   p_kst 2.739130e-04   p_cons 5.477522e-01   p_joint 1.782609e-04

Joint ci ratio: 5.909068e-01	ci left: 1.296667e-04	ci right 2.413288e-04	k: 43	n:240000
Cons ci ratio: 7.269599e-03	ci left: 5.458311e-01	ci right 5.498177e-01	k: 131478	n:240000
KS ci ratio: 4.824513e-01	ci left: 2.090295e-04	ci right 3.451865e-04	k: 65	n:240000
SPG11   240000 perm   80 sec   (3004 perm/sec)   p_kst 2.708333e-04   p_cons 5.478250e-01   p_joint 1.791667e-04

Joint ci ratio: 5.599440e-01	ci left: 1.415689e-04	ci right 2.545562e-04	k: 48	n:250000
Cons ci ratio: 7.122279e-03	ci left: 5.459025e-01	ci right 5.498084e-01	k: 136964	n:250000
KS ci ratio: 4.651514e-01	ci left: 2.182800e-04	ci right 3.537501e-04	k: 70	n:250000
SPG11   250000 perm   84 sec   (2973 perm/sec)   p_kst 2.800000e-04   p_cons 5.478560e-01   p_joint 1.920000e-04

Joint ci ratio: 5.488549e-01	ci left: 1.427377e-04	ci right 2.535260e-04	k: 50	n:260000
Cons ci ratio: 6.983784e-03	ci left: 5.459537e-01	ci right 5.497837e-01	k: 142446	n:260000
KS ci ratio: 4.556250e-01	ci left: 2.200845e-04	ci right 3.530124e-04	k: 73	n:260000
SPG11   260000 perm   88 sec   (2942 perm/sec)   p_kst 2.807692e-04   p_cons 5.478692e-01   p_joint 1.923077e-04

Joint ci ratio: 5.435528e-01	ci left: 1.406433e-04	ci right 2.483466e-04	k: 51	n:270000
Cons ci ratio: 6.852912e-03	ci left: 5.460129e-01	ci right 5.497712e-01	k: 147931	n:270000
KS ci ratio: 4.495907e-01	ci left: 2.184959e-04	ci right 3.481846e-04	k: 75	n:270000
SPG11   270000 perm   93 sec   (2910 perm/sec)   p_kst 2.777778e-04   p_cons 5.478926e-01   p_joint 1.888889e-04

Joint ci ratio: 5.285198e-01	ci left: 1.448834e-04	ci right 2.516293e-04	k: 54	n:280000
Cons ci ratio: 6.730346e-03	ci left: 5.459792e-01	ci right 5.496698e-01	k: 153391	n:280000
KS ci ratio: 4.409714e-01	ci left: 2.202052e-04	ci right 3.476577e-04	k: 78	n:280000
SPG11   280000 perm   97 sec   (2880 perm/sec)   p_kst 2.785714e-04   p_cons 5.478250e-01   p_joint 1.928571e-04

Joint ci ratio: 5.191648e-01	ci left: 1.458715e-04	ci right 2.507537e-04	k: 56	n:290000
Cons ci ratio: 6.614819e-03	ci left: 5.458967e-01	ci right 5.495231e-01	k: 158836	n:290000
KS ci ratio: 4.354940e-01	ci left: 2.187473e-04	ci right 3.433226e-04	k: 80	n:290000
SPG11   290000 perm   102 sec   (2849 perm/sec)   p_kst 2.758621e-04   p_cons 5.477103e-01   p_joint 1.931034e-04

Joint ci ratio: 5.146706e-01	ci left: 1.439072e-04	ci right 2.461601e-04	k: 57	n:300000
Cons ci ratio: 6.505963e-03	ci left: 5.457501e-01	ci right 5.493156e-01	k: 164260	n:300000
KS ci ratio: 4.302157e-01	ci left: 2.173958e-04	ci right 3.392675e-04	k: 82	n:300000
SPG11   300000 perm   106 sec   (2819 perm/sec)   p_kst 2.733333e-04   p_cons 5.475333e-01   p_joint 1.900000e-04

Joint ci ratio: 5.060200e-01	ci left: 1.448854e-04	ci right 2.454955e-04	k: 59	n:310000
Cons ci ratio: 6.399599e-03	ci left: 5.458233e-01	ci right 5.493307e-01	k: 169749	n:310000
KS ci ratio: 4.251247e-01	ci left: 2.161401e-04	ci right 3.354657e-04	k: 84	n:310000
SPG11   310000 perm   111 sec   (2788 perm/sec)   p_kst 2.709677e-04   p_cons 5.475774e-01   p_joint 1.903226e-04

Joint ci ratio: 4.977915e-01	ci left: 1.458161e-04	ci right 2.448591e-04	k: 61	n:320000
Cons ci ratio: 6.297453e-03	ci left: 5.459579e-01	ci right 5.494100e-01	k: 175259	n:320000
KS ci ratio: 4.178153e-01	ci left: 2.177663e-04	ci right 3.353462e-04	k: 87	n:320000
SPG11   320000 perm   116 sec   (2759 perm/sec)   p_kst 2.718750e-04   p_cons 5.476844e-01   p_joint 1.906250e-04

Joint ci ratio: 4.086307e-01	ci left: 2.220284e-04	ci right 3.385586e-04	k: 91	n:330000
Cons ci ratio: 6.200274e-03	ci left: 5.460666e-01	ci right 5.494659e-01	k: 180763	n:330000
KS ci ratio: 4.086307e-01	ci left: 2.220284e-04	ci right 3.385586e-04	k: 91	n:330000
SPG11   330000 perm   121 sec   (2733 perm/sec)   p_kst 2.757576e-04   p_cons 5.477667e-01   p_joint 2.757576e-04

Joint ci ratio: 4.042606e-01	ci left: 2.207790e-04	ci right 3.350817e-04	k: 93	n:340000
Cons ci ratio: 6.107350e-03	ci left: 5.461781e-01	ci right 5.495269e-01	k: 186270	n:340000
KS ci ratio: 4.042606e-01	ci left: 2.207790e-04	ci right 3.350817e-04	k: 93	n:340000
SPG11   340000 perm   126 sec   (2706 perm/sec)   p_kst 2.735294e-04   p_cons 5.478529e-01   p_joint 2.735294e-04

Joint ci ratio: 4.021284e-01	ci left: 2.170383e-04	ci right 3.286535e-04	k: 94	n:350000
Cons ci ratio: 6.019003e-03	ci left: 5.462408e-01	ci right 5.495413e-01	k: 191762	n:350000
KS ci ratio: 4.021284e-01	ci left: 2.170383e-04	ci right 3.286535e-04	k: 94	n:350000
SPG11   350000 perm   131 sec   (2675 perm/sec)   p_kst 2.685714e-04   p_cons 5.478914e-01   p_joint 2.685714e-04

Joint ci ratio: 3.959253e-01	ci left: 2.185066e-04	ci right 3.286896e-04	k: 97	n:360000
Cons ci ratio: 5.936046e-03	ci left: 5.461613e-01	ci right 5.494157e-01	k: 197204	n:360000
KS ci ratio: 3.959253e-01	ci left: 2.185066e-04	ci right 3.286896e-04	k: 97	n:360000
SPG11   360000 perm   136 sec   (2648 perm/sec)   p_kst 2.694444e-04   p_cons 5.477889e-01   p_joint 2.694444e-04

Joint ci ratio: 3.824980e-01	ci left: 2.296692e-04	ci right 3.405666e-04	k: 104	n:370000
Cons ci ratio: 5.855947e-03	ci left: 5.461270e-01	ci right 5.493371e-01	k: 202661	n:370000
KS ci ratio: 3.824980e-01	ci left: 2.296692e-04	ci right 3.405666e-04	k: 104	n:370000
SPG11   370000 perm   141 sec   (2624 perm/sec)   p_kst 2.810811e-04   p_cons 5.477324e-01   p_joint 2.810811e-04

Joint ci ratio: 3.737027e-01	ci left: 2.355329e-04	ci right 3.460067e-04	k: 109	n:380000
Cons ci ratio: 5.777410e-03	ci left: 5.462317e-01	ci right 5.493992e-01	k: 208170	n:380000
KS ci ratio: 3.737027e-01	ci left: 2.355329e-04	ci right 3.460067e-04	k: 109	n:380000
SPG11   380000 perm   146 sec   (2602 perm/sec)   p_kst 2.868421e-04   p_cons 5.478158e-01   p_joint 2.868421e-04

Joint ci ratio: 3.703515e-01	ci left: 2.341423e-04	ci right 3.427404e-04	k: 111	n:390000
Cons ci ratio: 5.703869e-03	ci left: 5.461645e-01	ci right 5.492912e-01	k: 213614	n:390000
KS ci ratio: 3.703515e-01	ci left: 2.341423e-04	ci right 3.427404e-04	k: 111	n:390000
SPG11   390000 perm   151 sec   (2578 perm/sec)   p_kst 2.846154e-04   p_cons 5.477282e-01   p_joint 2.846154e-04

Joint ci ratio: 3.639096e-01	ci left: 2.373664e-04	ci right 3.450903e-04	k: 115	n:400000
Cons ci ratio: 5.629854e-03	ci left: 5.463836e-01	ci right 5.494708e-01	k: 219171	n:400000
KS ci ratio: 3.639096e-01	ci left: 2.373664e-04	ci right 3.450903e-04	k: 115	n:400000
SPG11   400000 perm   157 sec   (2554 perm/sec)   p_kst 2.875000e-04   p_cons 5.479275e-01   p_joint 2.875000e-04

Joint ci ratio: 3.608129e-01	ci left: 2.360109e-04	ci right 3.419938e-04	k: 117	n:410000
Cons ci ratio: 5.559796e-03	ci left: 5.464897e-01	ci right 5.495389e-01	k: 224686	n:410000
KS ci ratio: 3.608129e-01	ci left: 2.360109e-04	ci right 3.419938e-04	k: 117	n:410000
SPG11   410000 perm   162 sec   (2526 perm/sec)   p_kst 2.853659e-04   p_cons 5.480146e-01   p_joint 2.853659e-04

Joint ci ratio: 4.788655e-01	ci left: 1.215363e-04	ci right 1.999200e-04	k: 66	n:420000
Cons ci ratio: 5.494217e-03	ci left: 5.464171e-01	ci right 5.494298e-01	k: 230128	n:420000
KS ci ratio: 3.548482e-01	ci left: 2.390594e-04	ci right 3.442274e-04	k: 121	n:420000
SPG11   420000 perm   168 sec   (2501 perm/sec)   p_kst 2.880952e-04   p_cons 5.479238e-01   p_joint 1.571429e-04

Joint ci ratio: 4.718741e-01	ci left: 1.228036e-04	ci right 2.004753e-04	k: 68	n:430000
Cons ci ratio: 5.430012e-03	ci left: 5.464295e-01	ci right 5.494070e-01	k: 235605	n:430000
KS ci ratio: 3.491698e-01	ci left: 2.419798e-04	ci right 3.463435e-04	k: 125	n:430000
SPG11   430000 perm   174 sec   (2477 perm/sec)   p_kst 2.906977e-04   p_cons 5.479186e-01   p_joint 1.581395e-04

Joint ci ratio: 4.651803e-01	ci left: 1.240212e-04	ci right 2.009976e-04	k: 70	n:440000
Cons ci ratio: 5.369189e-03	ci left: 5.463325e-01	ci right 5.492760e-01	k: 241034	n:440000
KS ci ratio: 3.464315e-01	ci left: 2.406286e-04	ci right 3.434131e-04	k: 127	n:440000
SPG11   440000 perm   179 sec   (2453 perm/sec)   p_kst 2.886364e-04   p_cons 5.478045e-01   p_joint 1.590909e-04

Joint ci ratio: 3.411418e-01	ci left: 2.434029e-04	ci right 3.454350e-04	k: 131	n:450000
Cons ci ratio: 5.311675e-03	ci left: 5.461177e-01	ci right 5.490284e-01	k: 246408	n:450000
KS ci ratio: 3.411418e-01	ci left: 2.434029e-04	ci right 3.454350e-04	k: 131	n:450000
SPG11   450000 perm   185 sec   (2427 perm/sec)   p_kst 2.911111e-04   p_cons 5.475733e-01   p_joint 2.911111e-04

Joint ci ratio: 3.373300e-01	ci left: 2.440778e-04	ci right 3.450007e-04	k: 134	n:460000
Cons ci ratio: 5.253639e-03	ci left: 5.461320e-01	ci right 5.490109e-01	k: 251883	n:460000
KS ci ratio: 3.373300e-01	ci left: 2.440778e-04	ci right 3.450007e-04	k: 134	n:460000
SPG11   460000 perm   191 sec   (2404 perm/sec)   p_kst 2.913043e-04   p_cons 5.475717e-01   p_joint 2.913043e-04

Joint ci ratio: 3.324405e-01	ci left: 2.466798e-04	ci right 3.468838e-04	k: 138	n:470000
Cons ci ratio: 5.198001e-03	ci left: 5.460948e-01	ci right 5.489429e-01	k: 257334	n:470000
KS ci ratio: 3.324405e-01	ci left: 2.466798e-04	ci right 3.468838e-04	k: 138	n:470000
SPG11   470000 perm   197 sec   (2382 perm/sec)   p_kst 2.936170e-04   p_cons 5.475191e-01   p_joint 2.936170e-04

Joint ci ratio: 3.312518e-01	ci left: 2.434503e-04	ci right 3.419135e-04	k: 139	n:480000
Cons ci ratio: 5.142342e-03	ci left: 5.462281e-01	ci right 5.490463e-01	k: 262866	n:480000
KS ci ratio: 3.312518e-01	ci left: 2.434503e-04	ci right 3.419135e-04	k: 139	n:480000
SPG11   480000 perm   203 sec   (2361 perm/sec)   p_kst 2.895833e-04   p_cons 5.476375e-01   p_joint 2.895833e-04

Joint ci ratio: 3.300757e-01	ci left: 2.403533e-04	ci right 3.371454e-04	k: 140	n:490000
Cons ci ratio: 5.090299e-03	ci left: 5.461745e-01	ci right 5.489637e-01	k: 268309	n:490000
KS ci ratio: 3.300757e-01	ci left: 2.403533e-04	ci right 3.371454e-04	k: 140	n:490000
SPG11   490000 perm   209 sec   (2340 perm/sec)   p_kst 2.857143e-04   p_cons 5.475694e-01   p_joint 2.857143e-04

Joint ci ratio: 3.254907e-01	ci left: 2.428881e-04	ci right 3.390584e-04	k: 144	n:500000
Cons ci ratio: 5.038258e-03	ci left: 5.462751e-01	ci right 5.490363e-01	k: 273828	n:500000
KS ci ratio: 3.254907e-01	ci left: 2.428881e-04	ci right 3.390584e-04	k: 144	n:500000
SPG11   500000 perm   216 sec   (2318 perm/sec)   p_kst 2.880000e-04   p_cons 5.476560e-01   p_joint 2.880000e-04

Joint ci ratio: 3.243748e-01	ci left: 2.399264e-04	ci right 3.345304e-04	k: 145	n:510000
Cons ci ratio: 4.987979e-03	ci left: 5.463524e-01	ci right 5.490863e-01	k: 279337	n:510000
KS ci ratio: 3.243748e-01	ci left: 2.399264e-04	ci right 3.345304e-04	k: 145	n:510000
SPG11   510000 perm   222 sec   (2297 perm/sec)   p_kst 2.843137e-04   p_cons 5.477196e-01   p_joint 2.843137e-04

Joint ci ratio: 4.276721e-01	ci left: 1.271347e-04	ci right 1.978635e-04	k: 83	n:520000
Cons ci ratio: 4.939827e-03	ci left: 5.463614e-01	ci right 5.490689e-01	k: 284812	n:520000
KS ci ratio: 3.210926e-01	ci left: 2.406143e-04	ci right 3.343321e-04	k: 148	n:520000
SPG11   520000 perm   228 sec   (2278 perm/sec)   p_kst 2.846154e-04   p_cons 5.477154e-01   p_joint 1.596154e-04

Joint ci ratio: 4.202332e-01	ci left: 1.297924e-04	ci right 2.003911e-04	k: 86	n:530000
Cons ci ratio: 4.892764e-03	ci left: 5.463985e-01	ci right 5.490803e-01	k: 290302	n:530000
KS ci ratio: 3.158364e-01	ci left: 2.447545e-04	ci right 3.382093e-04	k: 153	n:530000
SPG11   530000 perm   235 sec   (2259 perm/sec)   p_kst 2.886792e-04   p_cons 5.477396e-01   p_joint 1.622642e-04

Joint ci ratio: 4.202339e-01	ci left: 1.273888e-04	ci right 1.966802e-04	k: 86	n:540000
Cons ci ratio: 4.848289e-03	ci left: 5.463046e-01	ci right 5.489615e-01	k: 295722	n:540000
KS ci ratio: 3.158373e-01	ci left: 2.402219e-04	ci right 3.319463e-04	k: 153	n:540000
SPG11   540000 perm   241 sec   (2240 perm/sec)   p_kst 2.833333e-04   p_cons 5.476333e-01   p_joint 1.592593e-04

Joint ci ratio: 4.178396e-01	ci left: 1.266990e-04	ci right 1.951131e-04	k: 87	n:550000
Cons ci ratio: 4.804317e-03	ci left: 5.462853e-01	ci right 5.489179e-01	k: 301181	n:550000
KS ci ratio: 3.128051e-01	ci left: 2.408786e-04	ci right 3.317944e-04	k: 156	n:550000
SPG11   550000 perm   247 sec   (2222 perm/sec)   p_kst 2.836364e-04   p_cons 5.476018e-01   p_joint 1.581818e-04

Joint ci ratio: 4.178402e-01	ci left: 1.244365e-04	ci right 1.916290e-04	k: 87	n:560000
Cons ci ratio: 4.762361e-03	ci left: 5.461792e-01	ci right 5.487882e-01	k: 306591	n:560000
KS ci ratio: 3.128059e-01	ci left: 2.365771e-04	ci right 3.258696e-04	k: 156	n:560000
SPG11   560000 perm   254 sec   (2204 perm/sec)   p_kst 2.785714e-04   p_cons 5.474839e-01   p_joint 1.553571e-04

Joint ci ratio: 4.131713e-01	ci left: 1.253953e-04	ci right 1.921407e-04	k: 89	n:570000
Cons ci ratio: 4.720315e-03	ci left: 5.461997e-01	ci right 5.487858e-01	k: 312071	n:570000
KS ci ratio: 3.108326e-01	ci left: 2.356609e-04	ci right 3.239351e-04	k: 158	n:570000
SPG11   570000 perm   261 sec   (2186 perm/sec)   p_kst 2.771930e-04   p_cons 5.474930e-01   p_joint 1.561404e-04

Joint ci ratio: 4.021502e-01	ci left: 1.309701e-04	ci right 1.983278e-04	k: 94	n:580000
Cons ci ratio: 4.680618e-03	ci left: 5.460869e-01	ci right 5.486506e-01	k: 317474	n:580000
KS ci ratio: 3.060570e-01	ci left: 2.395514e-04	ci right 3.276357e-04	k: 163	n:580000
SPG11   580000 perm   268 sec   (2168 perm/sec)   p_kst 2.810345e-04   p_cons 5.473690e-01   p_joint 1.620690e-04

Joint ci ratio: 3.979826e-01	ci left: 1.317991e-04	ci right 1.986955e-04	k: 96	n:590000
Cons ci ratio: 4.639857e-03	ci left: 5.461967e-01	ci right 5.487385e-01	k: 323006	n:590000
KS ci ratio: 3.042079e-01	ci left: 2.386215e-04	ci right 3.257311e-04	k: 165	n:590000
SPG11   590000 perm   275 sec   (2147 perm/sec)   p_kst 2.796610e-04   p_cons 5.474678e-01   p_joint 1.627119e-04

Joint ci ratio: 3.939420e-01	ci left: 1.326038e-04	ci right 1.990475e-04	k: 98	n:600000
Cons ci ratio: 4.602076e-03	ci left: 5.460945e-01	ci right 5.486151e-01	k: 328413	n:600000
KS ci ratio: 3.006074e-01	ci left: 2.408054e-04	ci right 3.274731e-04	k: 169	n:600000
SPG11   600000 perm   282 sec   (2130 perm/sec)   p_kst 2.816667e-04   p_cons 5.473550e-01   p_joint 1.633333e-04

Joint ci ratio: 3.881051e-01	ci left: 1.348645e-04	ci right 2.011836e-04	k: 101	n:610000
Cons ci ratio: 4.563588e-03	ci left: 5.461712e-01	ci right 5.486710e-01	k: 333927	n:610000
KS ci ratio: 2.971318e-01	ci left: 2.429236e-04	ci right 3.291522e-04	k: 173	n:610000
SPG11   610000 perm   289 sec   (2113 perm/sec)   p_kst 2.836066e-04   p_cons 5.474213e-01   p_joint 1.655738e-04

Joint ci ratio: 3.862167e-01	ci left: 1.341452e-04	ci right 1.997078e-04	k: 102	n:620000
Cons ci ratio: 4.525681e-03	ci left: 5.462858e-01	ci right 5.487653e-01	k: 339466	n:620000
KS ci ratio: 2.962821e-01	ci left: 2.404983e-04	ci right 3.255760e-04	k: 174	n:620000
SPG11   620000 perm   296 sec   (2096 perm/sec)   p_kst 2.806452e-04   p_cons 5.475258e-01   p_joint 1.645161e-04

Joint ci ratio: 3.825206e-01	ci left: 1.348837e-04	ci right 2.000178e-04	k: 104	n:630000
Cons ci ratio: 4.489537e-03	ci left: 5.463048e-01	ci right 5.487646e-01	k: 344947	n:630000
KS ci ratio: 2.937747e-01	ci left: 2.410904e-04	ci right 3.255214e-04	k: 177	n:630000
SPG11   630000 perm   303 sec   (2079 perm/sec)   p_kst 2.809524e-04   p_cons 5.475349e-01   p_joint 1.650794e-04

Joint ci ratio: 3.807122e-01	ci left: 1.341888e-04	ci right 1.986042e-04	k: 105	n:640000
Cons ci ratio: 4.454020e-03	ci left: 5.463483e-01	ci right 5.487887e-01	k: 350444	n:640000
KS ci ratio: 2.921382e-01	ci left: 2.402187e-04	ci right 3.237892e-04	k: 179	n:640000
SPG11   640000 perm   310 sec   (2063 perm/sec)   p_kst 2.796875e-04   p_cons 5.475688e-01   p_joint 1.640625e-04

Joint ci ratio: 2.905288e-01	ci left: 2.393751e-04	ci right 3.221090e-04	k: 181	n:650000
Cons ci ratio: 4.419072e-03	ci left: 5.464198e-01	ci right 5.488413e-01	k: 355960	n:650000
KS ci ratio: 2.905288e-01	ci left: 2.393751e-04	ci right 3.221090e-04	k: 181	n:650000
SPG11   650000 perm   318 sec   (2047 perm/sec)   p_kst 2.784615e-04   p_cons 5.476308e-01   p_joint 2.784615e-04

Joint ci ratio: 2.873876e-01	ci left: 2.413697e-04	ci right 3.237271e-04	k: 185	n:660000
Cons ci ratio: 4.385364e-03	ci left: 5.464407e-01	ci right 5.488438e-01	k: 361444	n:660000
KS ci ratio: 2.873876e-01	ci left: 2.413697e-04	ci right 3.237271e-04	k: 185	n:660000
SPG11   660000 perm   325 sec   (2031 perm/sec)   p_kst 2.803030e-04   p_cons 5.476424e-01   p_joint 2.803030e-04

Joint ci ratio: 2.873882e-01	ci left: 2.377671e-04	ci right 3.188955e-04	k: 185	n:670000
Cons ci ratio: 4.353267e-03	ci left: 5.463640e-01	ci right 5.487491e-01	k: 366863	n:670000
KS ci ratio: 2.873882e-01	ci left: 2.377671e-04	ci right 3.188955e-04	k: 185	n:670000
SPG11   670000 perm   333 sec   (2011 perm/sec)   p_kst 2.761194e-04   p_cons 5.475567e-01   p_joint 2.761194e-04

Joint ci ratio: 2.858556e-01	ci left: 2.370003e-04	ci right 3.173579e-04	k: 187	n:680000
Cons ci ratio: 4.322019e-03	ci left: 5.462719e-01	ci right 5.486395e-01	k: 372270	n:680000
KS ci ratio: 2.858556e-01	ci left: 2.370003e-04	ci right 3.173579e-04	k: 187	n:680000
SPG11   680000 perm   341 sec   (1993 perm/sec)   p_kst 2.750000e-04   p_cons 5.474559e-01   p_joint 2.750000e-04

Joint ci ratio: 2.843473e-01	ci left: 2.362568e-04	ci right 3.158638e-04	k: 189	n:690000
Cons ci ratio: 4.291082e-03	ci left: 5.462232e-01	ci right 5.485735e-01	k: 377705	n:690000
KS ci ratio: 2.843473e-01	ci left: 2.362568e-04	ci right 3.158638e-04	k: 189	n:690000
SPG11   690000 perm   349 sec   (1979 perm/sec)   p_kst 2.739130e-04   p_cons 5.473986e-01   p_joint 2.739130e-04

Joint ci ratio: 2.806777e-01	ci left: 2.395186e-04	ci right 3.189989e-04	k: 194	n:700000
Cons ci ratio: 4.260702e-03	ci left: 5.461873e-01	ci right 5.485208e-01	k: 383148	n:700000
KS ci ratio: 2.806777e-01	ci left: 2.395186e-04	ci right 3.189989e-04	k: 194	n:700000
SPG11   700000 perm   356 sec   (1964 perm/sec)   p_kst 2.771429e-04   p_cons 5.473543e-01   p_joint 2.771429e-04

Joint ci ratio: 2.792495e-01	ci left: 2.387643e-04	ci right 3.175201e-04	k: 196	n:710000
Cons ci ratio: 4.230321e-03	ci left: 5.462272e-01	ci right 5.485442e-01	k: 388644	n:710000
KS ci ratio: 2.792495e-01	ci left: 2.387643e-04	ci right 3.175201e-04	k: 196	n:710000
SPG11   710000 perm   364 sec   (1949 perm/sec)   p_kst 2.760563e-04   p_cons 5.473859e-01   p_joint 2.760563e-04

Joint ci ratio: 2.771472e-01	ci left: 2.393241e-04	ci right 3.175667e-04	k: 199	n:720000
Cons ci ratio: 4.199662e-03	ci left: 5.463744e-01	ci right 5.486752e-01	k: 394218	n:720000
KS ci ratio: 2.771472e-01	ci left: 2.393241e-04	ci right 3.175667e-04	k: 199	n:720000
SPG11   720000 perm   372 sec   (1935 perm/sec)   p_kst 2.763889e-04   p_cons 5.475250e-01   p_joint 2.763889e-04

Joint ci ratio: 2.764572e-01	ci left: 2.373205e-04	ci right 3.146812e-04	k: 200	n:730000
Cons ci ratio: 4.171228e-03	ci left: 5.463313e-01	ci right 5.486163e-01	k: 399656	n:730000
KS ci ratio: 2.764572e-01	ci left: 2.373205e-04	ci right 3.146812e-04	k: 200	n:730000
SPG11   730000 perm   380 sec   (1920 perm/sec)   p_kst 2.739726e-04   p_cons 5.474740e-01   p_joint 2.739726e-04

Joint ci ratio: 2.750921e-01	ci left: 2.366292e-04	ci right 3.133179e-04	k: 202	n:740000
Cons ci ratio: 4.143137e-03	ci left: 5.463164e-01	ci right 5.485859e-01	k: 405114	n:740000
KS ci ratio: 2.750921e-01	ci left: 2.366292e-04	ci right 3.133179e-04	k: 202	n:740000
SPG11   740000 perm   388 sec   (1907 perm/sec)   p_kst 2.729730e-04   p_cons 5.474514e-01   p_joint 2.729730e-04

Joint ci ratio: 2.737471e-01	ci left: 2.359574e-04	ci right 3.119901e-04	k: 204	n:750000
Cons ci ratio: 4.115308e-03	ci left: 5.463380e-01	ci right 5.485923e-01	k: 410599	n:750000
KS ci ratio: 2.737471e-01	ci left: 2.359574e-04	ci right 3.119901e-04	k: 204	n:750000
SPG11   750000 perm   397 sec   (1889 perm/sec)   p_kst 2.720000e-04   p_cons 5.474653e-01   p_joint 2.720000e-04

Joint ci ratio: 2.724215e-01	ci left: 2.353041e-04	ci right 3.106963e-04	k: 206	n:760000
Cons ci ratio: 4.088042e-03	ci left: 5.463578e-01	ci right 5.485971e-01	k: 416083	n:760000
KS ci ratio: 2.724215e-01	ci left: 2.353041e-04	ci right 3.106963e-04	k: 206	n:760000
SPG11   760000 perm   405 sec   (1876 perm/sec)   p_kst 2.710526e-04   p_cons 5.474776e-01   p_joint 2.710526e-04

Joint ci ratio: 2.698268e-01	ci left: 2.370899e-04	ci right 3.122083e-04	k: 210	n:770000
Cons ci ratio: 4.061588e-03	ci left: 5.463433e-01	ci right 5.485681e-01	k: 421541	n:770000
KS ci ratio: 2.698268e-01	ci left: 2.370899e-04	ci right 3.122083e-04	k: 210	n:770000
SPG11   770000 perm   414 sec   (1862 perm/sec)   p_kst 2.727273e-04   p_cons 5.474558e-01   p_joint 2.727273e-04

Joint ci ratio: 2.673048e-01	ci left: 2.388333e-04	ci right 3.136782e-04	k: 214	n:780000
Cons ci ratio: 4.035495e-03	ci left: 5.463471e-01	ci right 5.485576e-01	k: 427013	n:780000
KS ci ratio: 2.673048e-01	ci left: 2.388333e-04	ci right 3.136782e-04	k: 214	n:780000
SPG11   780000 perm   422 sec   (1848 perm/sec)   p_kst 2.743590e-04   p_cons 5.474526e-01   p_joint 2.743590e-04

Joint ci ratio: 2.618787e-01	ci left: 2.464471e-04	ci right 3.218537e-04	k: 223	n:790000
Cons ci ratio: 4.009919e-03	ci left: 5.463484e-01	ci right 5.485449e-01	k: 432483	n:790000
KS ci ratio: 2.618787e-01	ci left: 2.464471e-04	ci right 3.218537e-04	k: 223	n:790000
SPG11   790000 perm   430 sec   (1835 perm/sec)   p_kst 2.822785e-04   p_cons 5.474468e-01   p_joint 2.822785e-04

Joint ci ratio: 2.595712e-01	ci left: 2.480398e-04	ci right 3.231565e-04	k: 227	n:800000
Cons ci ratio: 3.984060e-03	ci left: 5.464448e-01	ci right 5.486274e-01	k: 438029	n:800000
KS ci ratio: 2.595712e-01	ci left: 2.480398e-04	ci right 3.231565e-04	k: 227	n:800000
SPG11   800000 perm   439 sec   (1821 perm/sec)   p_kst 2.837500e-04   p_cons 5.475362e-01   p_joint 2.837500e-04

Joint ci ratio: 2.567706e-01	ci left: 2.507511e-04	ci right 3.257382e-04	k: 232	n:810000
Cons ci ratio: 3.959552e-03	ci left: 5.464313e-01	ci right 5.486004e-01	k: 443488	n:810000
KS ci ratio: 2.567706e-01	ci left: 2.507511e-04	ci right 3.257382e-04	k: 232	n:810000
SPG11   810000 perm   448 sec   (1807 perm/sec)   p_kst 2.864198e-04   p_cons 5.475160e-01   p_joint 2.864198e-04

Joint ci ratio: 2.556758e-01	ci left: 2.499755e-04	ci right 3.243612e-04	k: 234	n:820000
Cons ci ratio: 3.935055e-03	ci left: 5.464731e-01	ci right 5.486290e-01	k: 448992	n:820000
KS ci ratio: 2.556758e-01	ci left: 2.499755e-04	ci right 3.243612e-04	k: 234	n:820000
SPG11   820000 perm   458 sec   (1791 perm/sec)   p_kst 2.853659e-04   p_cons 5.475512e-01   p_joint 2.853659e-04

Joint ci ratio: 2.524726e-01	ci left: 2.537324e-04	ci right 3.281413e-04	k: 240	n:830000
Cons ci ratio: 3.910883e-03	ci left: 5.465297e-01	ci right 5.486724e-01	k: 454509	n:830000
KS ci ratio: 2.524726e-01	ci left: 2.537324e-04	ci right 3.281413e-04	k: 240	n:830000
SPG11   830000 perm   467 sec   (1778 perm/sec)   p_kst 2.891566e-04   p_cons 5.476012e-01   p_joint 2.891566e-04

Joint ci ratio: 2.498933e-01	ci left: 2.562896e-04	ci right 3.305611e-04	k: 245	n:840000
Cons ci ratio: 3.887656e-03	ci left: 5.465206e-01	ci right 5.486505e-01	k: 459972	n:840000
KS ci ratio: 2.498933e-01	ci left: 2.562896e-04	ci right 3.305611e-04	k: 245	n:840000
SPG11   840000 perm   476 sec   (1766 perm/sec)   p_kst 2.916667e-04   p_cons 5.475857e-01   p_joint 2.916667e-04

Joint ci ratio: 2.488838e-01	ci left: 2.554803e-04	ci right 3.291719e-04	k: 247	n:850000
Cons ci ratio: 3.864361e-03	ci left: 5.465729e-01	ci right 5.486903e-01	k: 465487	n:850000
KS ci ratio: 2.488838e-01	ci left: 2.554803e-04	ci right 3.291719e-04	k: 247	n:850000
SPG11   850000 perm   485 sec   (1753 perm/sec)   p_kst 2.905882e-04   p_cons 5.476318e-01   p_joint 2.905882e-04

Joint ci ratio: 2.821359e-01	ci left: 1.927948e-04	ci right 2.571621e-04	k: 192	n:860000
Cons ci ratio: 3.842056e-03	ci left: 5.465496e-01	ci right 5.486547e-01	k: 470938	n:860000
KS ci ratio: 2.483838e-01	ci left: 2.535999e-04	ci right 3.265795e-04	k: 248	n:860000
SPG11   860000 perm   494 sec   (1741 perm/sec)   p_kst 2.883721e-04   p_cons 5.476023e-01   p_joint 2.232558e-04

Joint ci ratio: 2.459266e-01	ci left: 2.560762e-04	ci right 3.289280e-04	k: 253	n:870000
Cons ci ratio: 3.820355e-03	ci left: 5.464982e-01	ci right 5.485911e-01	k: 476364	n:870000
KS ci ratio: 2.459266e-01	ci left: 2.560762e-04	ci right 3.289280e-04	k: 253	n:870000
SPG11   870000 perm   503 sec   (1728 perm/sec)   p_kst 2.908046e-04   p_cons 5.475448e-01   p_joint 2.908046e-04

Joint ci ratio: 2.430720e-01	ci left: 2.595668e-04	ci right 3.324251e-04	k: 259	n:880000
Cons ci ratio: 3.799017e-03	ci left: 5.464480e-01	ci right 5.485290e-01	k: 481790	n:880000
KS ci ratio: 2.430720e-01	ci left: 2.595668e-04	ci right 3.324251e-04	k: 259	n:880000
SPG11   880000 perm   513 sec   (1717 perm/sec)   p_kst 2.943182e-04   p_cons 5.474886e-01   p_joint 2.943182e-04

Joint ci ratio: 2.426062e-01	ci left: 2.577055e-04	ci right 3.298819e-04	k: 260	n:890000
Cons ci ratio: 3.776628e-03	ci left: 5.465832e-01	ci right 5.486524e-01	k: 487380	n:890000
KS ci ratio: 2.426062e-01	ci left: 2.577055e-04	ci right 3.298819e-04	k: 260	n:890000
SPG11   890000 perm   522 sec   (1706 perm/sec)   p_kst 2.921348e-04   p_cons 5.476180e-01   p_joint 2.921348e-04

Joint ci ratio: 2.412238e-01	ci left: 2.579734e-04	ci right 3.297515e-04	k: 263	n:900000
Cons ci ratio: 3.755169e-03	ci left: 5.466443e-01	ci right 5.487020e-01	k: 492906	n:900000
KS ci ratio: 2.412238e-01	ci left: 2.579734e-04	ci right 3.297515e-04	k: 263	n:900000
SPG11   900000 perm   531 sec   (1694 perm/sec)   p_kst 2.922222e-04   p_cons 5.476733e-01   p_joint 2.922222e-04

Joint ci ratio: 2.398648e-01	ci left: 2.582366e-04	ci right 3.296229e-04	k: 266	n:910000
Cons ci ratio: 3.734460e-03	ci left: 5.466525e-01	ci right 5.486988e-01	k: 498385	n:910000
KS ci ratio: 2.398648e-01	ci left: 2.582366e-04	ci right 3.296229e-04	k: 266	n:910000
SPG11   910000 perm   541 sec   (1683 perm/sec)   p_kst 2.923077e-04   p_cons 5.476758e-01   p_joint 2.923077e-04

Joint ci ratio: 2.394171e-01	ci left: 2.564513e-04	ci right 3.271922e-04	k: 267	n:920000
Cons ci ratio: 3.714058e-03	ci left: 5.466649e-01	ci right 5.487000e-01	k: 503868	n:920000
KS ci ratio: 2.394171e-01	ci left: 2.564513e-04	ci right 3.271922e-04	k: 267	n:920000
SPG11   920000 perm   550 sec   (1672 perm/sec)   p_kst 2.902174e-04   p_cons 5.476826e-01   p_joint 2.902174e-04

Joint ci ratio: 2.372142e-01	ci left: 2.587491e-04	ci right 3.293707e-04	k: 272	n:930000
Cons ci ratio: 3.693939e-03	ci left: 5.466835e-01	ci right 5.487076e-01	k: 509357	n:930000
KS ci ratio: 2.372142e-01	ci left: 2.587491e-04	ci right 3.293707e-04	k: 272	n:930000
SPG11   930000 perm   560 sec   (1662 perm/sec)   p_kst 2.924731e-04   p_cons 5.476957e-01   p_joint 2.924731e-04

Joint ci ratio: 2.367812e-01	ci left: 2.569971e-04	ci right 3.269937e-04	k: 273	n:940000
Cons ci ratio: 3.674095e-03	ci left: 5.467081e-01	ci right 5.487214e-01	k: 514852	n:940000
KS ci ratio: 2.367812e-01	ci left: 2.569971e-04	ci right 3.269937e-04	k: 273	n:940000
SPG11   940000 perm   569 sec   (1651 perm/sec)   p_kst 2.904255e-04   p_cons 5.477149e-01   p_joint 2.904255e-04

Joint ci ratio: 2.363506e-01	ci left: 2.552821e-04	ci right 3.246666e-04	k: 274	n:950000
Cons ci ratio: 3.654335e-03	ci left: 5.467638e-01	ci right 5.487665e-01	k: 520377	n:950000
KS ci ratio: 2.363506e-01	ci left: 2.552821e-04	ci right 3.246666e-04	k: 274	n:950000
SPG11   950000 perm   579 sec   (1641 perm/sec)   p_kst 2.884211e-04   p_cons 5.477653e-01   p_joint 2.884211e-04

Joint ci ratio: 2.333982e-01	ci left: 2.594856e-04	ci right 3.290045e-04	k: 281	n:960000
Cons ci ratio: 3.634807e-03	ci left: 5.468298e-01	ci right 5.488220e-01	k: 525913	n:960000
KS ci ratio: 2.333982e-01	ci left: 2.594856e-04	ci right 3.290045e-04	k: 281	n:960000
SPG11   960000 perm   588 sec   (1631 perm/sec)   p_kst 2.927083e-04   p_cons 5.478260e-01   p_joint 2.927083e-04

Joint ci ratio: 2.325750e-01	ci left: 2.587520e-04	ci right 3.277947e-04	k: 283	n:970000
Cons ci ratio: 3.616415e-03	ci left: 5.467810e-01	ci right 5.487630e-01	k: 531339	n:970000
KS ci ratio: 2.325750e-01	ci left: 2.587520e-04	ci right 3.277947e-04	k: 283	n:970000
SPG11   970000 perm   598 sec   (1621 perm/sec)   p_kst 2.917526e-04   p_cons 5.477722e-01   p_joint 2.917526e-04

Joint ci ratio: 2.313563e-01	ci left: 2.589950e-04	ci right 3.276887e-04	k: 286	n:980000
Cons ci ratio: 3.597863e-03	ci left: 5.467935e-01	ci right 5.487654e-01	k: 536824	n:980000
KS ci ratio: 2.313563e-01	ci left: 2.589950e-04	ci right 3.276887e-04	k: 286	n:980000
SPG11   980000 perm   608 sec   (1611 perm/sec)   p_kst 2.918367e-04   p_cons 5.477796e-01   p_joint 2.918367e-04

Joint ci ratio: 2.293667e-01	ci left: 2.611380e-04	ci right 3.297201e-04	k: 291	n:990000
Cons ci ratio: 3.579498e-03	ci left: 5.468189e-01	ci right 5.487808e-01	k: 542322	n:990000
KS ci ratio: 2.293667e-01	ci left: 2.611380e-04	ci right 3.297201e-04	k: 291	n:990000
SPG11   990000 perm   618 sec   (1602 perm/sec)   p_kst 2.939394e-04   p_cons 5.478000e-01   p_joint 2.939394e-04

Joint ci ratio: 2.278115e-01	ci left: 2.622976e-04	ci right 3.306515e-04	k: 295	n:1000000
Cons ci ratio: 3.561276e-03	ci left: 5.468629e-01	ci right 5.488148e-01	k: 547839	n:1000000
KS ci ratio: 2.278115e-01	ci left: 2.622976e-04	ci right 3.306515e-04	k: 295	n:1000000
SPG11   1000000 perm   628 sec   (1592 perm/sec)   p_kst 2.950000e-04   p_cons 5.478390e-01   p_joint 2.950000e-04

Joint ci ratio: 2.266658e-01	ci left: 2.625018e-04	ci right 3.305168e-04	k: 298	n:1010000
Cons ci ratio: 3.544376e-03	ci left: 5.467594e-01	ci right 5.487017e-01	k: 553208	n:1010000
KS ci ratio: 2.266658e-01	ci left: 2.625018e-04	ci right 3.305168e-04	k: 298	n:1010000
SPG11   1010000 perm   638 sec   (1582 perm/sec)   p_kst 2.950495e-04   p_cons 5.477307e-01   p_joint 2.950495e-04

Joint ci ratio: 2.247938e-01	ci left: 2.645531e-04	ci right 3.324551e-04	k: 303	n:1020000
Cons ci ratio: 3.527136e-03	ci left: 5.467394e-01	ci right 5.486721e-01	k: 558660	n:1020000
KS ci ratio: 2.247938e-01	ci left: 2.645531e-04	ci right 3.324551e-04	k: 303	n:1020000
SPG11   1020000 perm   648 sec   (1573 perm/sec)   p_kst 2.970588e-04   p_cons 5.477059e-01   p_joint 2.970588e-04

Joint ci ratio: 2.240581e-01	ci left: 2.638172e-04	ci right 3.312781e-04	k: 305	n:1030000
Cons ci ratio: 3.509863e-03	ci left: 5.467595e-01	ci right 5.486829e-01	k: 564153	n:1030000
KS ci ratio: 2.240581e-01	ci left: 2.638172e-04	ci right 3.312781e-04	k: 305	n:1030000
SPG11   1030000 perm   658 sec   (1564 perm/sec)   p_kst 2.961165e-04   p_cons 5.477214e-01   p_joint 2.961165e-04

Joint ci ratio: 2.215380e-01	ci left: 2.676357e-04	ci right 3.351984e-04	k: 312	n:1040000
Cons ci ratio: 3.493274e-03	ci left: 5.467178e-01	ci right 5.486319e-01	k: 569582	n:1040000
KS ci ratio: 2.215380e-01	ci left: 2.676357e-04	ci right 3.351984e-04	k: 312	n:1040000
SPG11   1040000 perm   669 sec   (1555 perm/sec)   p_kst 3.000000e-04   p_cons 5.476750e-01   p_joint 3.000000e-04

Joint ci ratio: 2.201358e-01	ci left: 2.686857e-04	ci right 3.360260e-04	k: 316	n:1050000
Cons ci ratio: 3.476177e-03	ci left: 5.467826e-01	ci right 5.486876e-01	k: 575122	n:1050000
KS ci ratio: 2.201358e-01	ci left: 2.686857e-04	ci right 3.360260e-04	k: 316	n:1050000
SPG11   1050000 perm   679 sec   (1547 perm/sec)   p_kst 3.009524e-04   p_cons 5.477352e-01   p_joint 3.009524e-04

Joint ci ratio: 2.180813e-01	ci left: 2.715007e-04	ci right 3.388264e-04	k: 322	n:1060000
Cons ci ratio: 3.459783e-03	ci left: 5.467811e-01	ci right 5.486771e-01	k: 580593	n:1060000
KS ci ratio: 2.180813e-01	ci left: 2.715007e-04	ci right 3.388264e-04	k: 322	n:1060000
SPG11   1060000 perm   689 sec   (1538 perm/sec)   p_kst 3.037736e-04   p_cons 5.477292e-01   p_joint 3.037736e-04

Joint ci ratio: 2.167433e-01	ci left: 2.724981e-04	ci right 3.396013e-04	k: 326	n:1070000
Cons ci ratio: 3.443612e-03	ci left: 5.467806e-01	ci right 5.486677e-01	k: 586065	n:1070000
KS ci ratio: 2.167433e-01	ci left: 2.724981e-04	ci right 3.396013e-04	k: 326	n:1070000
SPG11   1070000 perm   700 sec   (1530 perm/sec)   p_kst 3.046729e-04   p_cons 5.477243e-01   p_joint 3.046729e-04

Joint ci ratio: 2.154296e-01	ci left: 2.734782e-04	ci right 3.403607e-04	k: 330	n:1080000
Cons ci ratio: 3.427468e-03	ci left: 5.468089e-01	ci right 5.486872e-01	k: 591568	n:1080000
KS ci ratio: 2.154296e-01	ci left: 2.734782e-04	ci right 3.403607e-04	k: 330	n:1080000
SPG11   1080000 perm   710 sec   (1521 perm/sec)   p_kst 3.055556e-04   p_cons 5.477481e-01   p_joint 3.055556e-04

Joint ci ratio: 2.128720e-01	ci left: 2.779152e-04	ci right 3.449705e-04	k: 338	n:1090000
Cons ci ratio: 3.411592e-03	ci left: 5.468302e-01	ci right 5.486998e-01	k: 597064	n:1090000
KS ci ratio: 2.128720e-01	ci left: 2.779152e-04	ci right 3.449705e-04	k: 338	n:1090000
SPG11   1090000 perm   721 sec   (1512 perm/sec)   p_kst 3.100917e-04   p_cons 5.477651e-01   p_joint 3.100917e-04

Joint ci ratio: 2.125589e-01	ci left: 2.762493e-04	ci right 3.427919e-04	k: 339	n:1100000
Cons ci ratio: 3.395892e-03	ci left: 5.468575e-01	ci right 5.487186e-01	k: 602567	n:1100000
KS ci ratio: 2.125589e-01	ci left: 2.762493e-04	ci right 3.427919e-04	k: 339	n:1100000
SPG11   1100000 perm   732 sec   (1503 perm/sec)   p_kst 3.081818e-04   p_cons 5.477882e-01   p_joint 3.081818e-04

Joint ci ratio: 2.113194e-01	ci left: 2.771729e-04	ci right 3.434982e-04	k: 343	n:1110000
Cons ci ratio: 3.380025e-03	ci left: 5.469402e-01	ci right 5.487929e-01	k: 608132	n:1110000
KS ci ratio: 2.113194e-01	ci left: 2.771729e-04	ci right 3.434982e-04	k: 343	n:1110000
SPG11   1110000 perm   743 sec   (1495 perm/sec)   p_kst 3.090090e-04   p_cons 5.478667e-01   p_joint 3.090090e-04

Joint ci ratio: 2.107079e-01	ci left: 2.763895e-04	ci right 3.423112e-04	k: 345	n:1120000
Cons ci ratio: 3.364948e-03	ci left: 5.469375e-01	ci right 5.487819e-01	k: 613603	n:1120000
KS ci ratio: 2.107079e-01	ci left: 2.763895e-04	ci right 3.423112e-04	k: 345	n:1120000
SPG11   1120000 perm   754 sec   (1486 perm/sec)   p_kst 3.080357e-04   p_cons 5.478598e-01   p_joint 3.080357e-04

Joint ci ratio: 2.098003e-01	ci left: 2.764587e-04	ci right 3.420764e-04	k: 348	n:1130000
Cons ci ratio: 3.350436e-03	ci left: 5.468809e-01	ci right 5.487171e-01	k: 619013	n:1130000
KS ci ratio: 2.098003e-01	ci left: 2.764587e-04	ci right 3.420764e-04	k: 348	n:1130000
SPG11   1130000 perm   766 sec   (1476 perm/sec)   p_kst 3.079646e-04   p_cons 5.477991e-01   p_joint 3.079646e-04

Joint ci ratio: 2.092018e-01	ci left: 2.756959e-04	ci right 3.409220e-04	k: 350	n:1140000
Cons ci ratio: 3.336270e-03	ci left: 5.468016e-01	ci right 5.486298e-01	k: 624396	n:1140000
KS ci ratio: 2.092018e-01	ci left: 2.756959e-04	ci right 3.409220e-04	k: 350	n:1140000
SPG11   1140000 perm   778 sec   (1466 perm/sec)   p_kst 3.070175e-04   p_cons 5.477158e-01   p_joint 3.070175e-04

Joint ci ratio: 2.092021e-01	ci left: 2.732985e-04	ci right 3.379575e-04	k: 350	n:1150000
Cons ci ratio: 3.321804e-03	ci left: 5.467950e-01	ci right 5.486152e-01	k: 629861	n:1150000
KS ci ratio: 2.092021e-01	ci left: 2.732985e-04	ci right 3.379575e-04	k: 350	n:1150000
SPG11   1150000 perm   789 sec   (1458 perm/sec)   p_kst 3.043478e-04   p_cons 5.477052e-01   p_joint 3.043478e-04

Joint ci ratio: 2.080201e-01	ci left: 2.742107e-04	ci right 3.386722e-04	k: 354	n:1160000
Cons ci ratio: 3.307904e-03	ci left: 5.467316e-01	ci right 5.485440e-01	k: 635260	n:1160000
KS ci ratio: 2.080201e-01	ci left: 2.742107e-04	ci right 3.386722e-04	k: 354	n:1160000
SPG11   1160000 perm   800 sec   (1450 perm/sec)   p_kst 3.051724e-04   p_cons 5.476379e-01   p_joint 3.051724e-04

Joint ci ratio: 2.074367e-01	ci left: 2.734875e-04	ci right 3.375758e-04	k: 356	n:1170000
Cons ci ratio: 3.293433e-03	ci left: 5.467814e-01	ci right 5.485859e-01	k: 640790	n:1170000
KS ci ratio: 2.074367e-01	ci left: 2.734875e-04	ci right 3.375758e-04	k: 356	n:1170000
SPG11   1170000 perm   811 sec   (1442 perm/sec)   p_kst 3.042735e-04   p_cons 5.476838e-01   p_joint 3.042735e-04

Joint ci ratio: 2.071469e-01	ci left: 2.719732e-04	ci right 3.356064e-04	k: 357	n:1180000
Cons ci ratio: 3.279296e-03	ci left: 5.468082e-01	ci right 5.486051e-01	k: 646294	n:1180000
KS ci ratio: 2.071469e-01	ci left: 2.719732e-04	ci right 3.356064e-04	k: 357	n:1180000
SPG11   1180000 perm   824 sec   (1433 perm/sec)   p_kst 3.025424e-04   p_cons 5.477068e-01   p_joint 3.025424e-04

Joint ci ratio: 2.062844e-01	ci left: 2.720782e-04	ci right 3.354375e-04	k: 360	n:1190000
Cons ci ratio: 3.265289e-03	ci left: 5.468422e-01	ci right 5.486315e-01	k: 651807	n:1190000
KS ci ratio: 2.062844e-01	ci left: 2.720782e-04	ci right 3.354375e-04	k: 360	n:1190000
SPG11   1190000 perm   838 sec   (1420 perm/sec)   p_kst 3.025210e-04   p_cons 5.477370e-01   p_joint 3.025210e-04

Joint ci ratio: 2.057154e-01	ci left: 2.713916e-04	ci right 3.343948e-04	k: 362	n:1200000
Cons ci ratio: 3.251674e-03	ci left: 5.468431e-01	ci right 5.486250e-01	k: 657281	n:1200000
KS ci ratio: 2.057154e-01	ci left: 2.713916e-04	ci right 3.343948e-04	k: 362	n:1200000
SPG11   1200000 perm   851 sec   (1411 perm/sec)   p_kst 3.016667e-04   p_cons 5.477342e-01   p_joint 3.016667e-04

Joint ci ratio: 2.037599e-01	ci left: 2.746373e-04	ci right 3.377124e-04	k: 369	n:1210000
Cons ci ratio: 3.237876e-03	ci left: 5.468978e-01	ci right 5.486722e-01	k: 662820	n:1210000
KS ci ratio: 2.037599e-01	ci left: 2.746373e-04	ci right 3.377124e-04	k: 369	n:1210000
SPG11   1210000 perm   862 sec   (1403 perm/sec)   p_kst 3.049587e-04   p_cons 5.477851e-01   p_joint 3.049587e-04

Joint ci ratio: 2.026672e-01	ci left: 2.754981e-04	ci right 3.383895e-04	k: 373	n:1220000
Cons ci ratio: 3.224935e-03	ci left: 5.468466e-01	ci right 5.486138e-01	k: 668231	n:1220000
KS ci ratio: 2.026672e-01	ci left: 2.754981e-04	ci right 3.383895e-04	k: 373	n:1220000
SPG11   1220000 perm   875 sec   (1394 perm/sec)   p_kst 3.057377e-04   p_cons 5.477303e-01   p_joint 3.057377e-04

Joint ci ratio: 2.018592e-01	ci left: 2.755737e-04	ci right 3.382008e-04	k: 376	n:1230000
Cons ci ratio: 3.211790e-03	ci left: 5.468516e-01	ci right 5.486116e-01	k: 673710	n:1230000
KS ci ratio: 2.018592e-01	ci left: 2.755737e-04	ci right 3.382008e-04	k: 376	n:1230000
SPG11   1230000 perm   887 sec   (1386 perm/sec)   p_kst 3.056911e-04   p_cons 5.477317e-01   p_joint 3.056911e-04

Joint ci ratio: 2.015922e-01	ci left: 2.741171e-04	ci right 3.363205e-04	k: 377	n:1240000
Cons ci ratio: 3.198279e-03	ci left: 5.469380e-01	ci right 5.486908e-01	k: 679290	n:1240000
KS ci ratio: 2.015922e-01	ci left: 2.741171e-04	ci right 3.363205e-04	k: 377	n:1240000
SPG11   1240000 perm   901 sec   (1376 perm/sec)   p_kst 3.040323e-04   p_cons 5.478145e-01   p_joint 3.040323e-04

Joint ci ratio: 2.015925e-01	ci left: 2.719241e-04	ci right 3.336300e-04	k: 377	n:1250000
Cons ci ratio: 3.185173e-03	ci left: 5.469862e-01	ci right 5.487320e-01	k: 684824	n:1250000
KS ci ratio: 2.015925e-01	ci left: 2.719241e-04	ci right 3.336300e-04	k: 377	n:1250000
SPG11   1250000 perm   914 sec   (1368 perm/sec)   p_kst 3.016000e-04   p_cons 5.478592e-01   p_joint 3.016000e-04

Joint ci ratio: 2.010614e-01	ci left: 2.712732e-04	ci right 3.326494e-04	k: 379	n:1260000
Cons ci ratio: 3.172384e-03	ci left: 5.470090e-01	ci right 5.487479e-01	k: 690327	n:1260000
KS ci ratio: 2.010614e-01	ci left: 2.712732e-04	ci right 3.326494e-04	k: 379	n:1260000
SPG11   1260000 perm   927 sec   (1359 perm/sec)   p_kst 3.007937e-04   p_cons 5.478786e-01   p_joint 3.007937e-04

Joint ci ratio: 1.997513e-01	ci left: 2.728767e-04	ci right 3.341644e-04	k: 384	n:1270000
Cons ci ratio: 3.160099e-03	ci left: 5.469764e-01	ci right 5.487084e-01	k: 695760	n:1270000
KS ci ratio: 1.997513e-01	ci left: 2.728767e-04	ci right 3.341644e-04	k: 384	n:1270000
SPG11   1270000 perm   941 sec   (1350 perm/sec)   p_kst 3.023622e-04   p_cons 5.478425e-01   p_joint 3.023622e-04

Joint ci ratio: 1.984666e-01	ci left: 2.744564e-04	ci right 3.356544e-04	k: 389	n:1280000
Cons ci ratio: 3.147510e-03	ci left: 5.470146e-01	ci right 5.487398e-01	k: 701283	n:1280000
KS ci ratio: 1.984666e-01	ci left: 2.744564e-04	ci right 3.356544e-04	k: 389	n:1280000
SPG11   1280000 perm   954 sec   (1342 perm/sec)   p_kst 3.039062e-04   p_cons 5.478773e-01   p_joint 3.039062e-04

Joint ci ratio: 1.979597e-01	ci left: 2.738023e-04	ci right 3.346797e-04	k: 391	n:1290000
Cons ci ratio: 3.135428e-03	ci left: 5.469957e-01	ci right 5.487142e-01	k: 706733	n:1290000
KS ci ratio: 1.979597e-01	ci left: 2.738023e-04	ci right 3.346797e-04	k: 391	n:1290000
SPG11   1290000 perm   967 sec   (1334 perm/sec)   p_kst 3.031008e-04   p_cons 5.478550e-01   p_joint 3.031008e-04

Joint ci ratio: 1.964617e-01	ci left: 2.760836e-04	ci right 3.369482e-04	k: 397	n:1300000
Cons ci ratio: 3.123488e-03	ci left: 5.469763e-01	ci right 5.486881e-01	k: 712182	n:1300000
KS ci ratio: 1.964617e-01	ci left: 2.760836e-04	ci right 3.369482e-04	k: 397	n:1300000
SPG11   1300000 perm   981 sec   (1326 perm/sec)   p_kst 3.053846e-04   p_cons 5.478323e-01   p_joint 3.053846e-04

Joint ci ratio: 1.962155e-01	ci left: 2.747019e-04	ci right 3.351769e-04	k: 398	n:1310000
Cons ci ratio: 3.111555e-03	ci left: 5.469778e-01	ci right 5.486831e-01	k: 717658	n:1310000
KS ci ratio: 1.962155e-01	ci left: 2.747019e-04	ci right 3.351769e-04	k: 398	n:1310000
SPG11   1310000 perm   994 sec   (1317 perm/sec)   p_kst 3.038168e-04   p_cons 5.478305e-01   p_joint 3.038168e-04

Joint ci ratio: 1.952392e-01	ci left: 2.755027e-04	ci right 3.358163e-04	k: 402	n:1320000
Cons ci ratio: 3.099828e-03	ci left: 5.469679e-01	ci right 5.486668e-01	k: 723119	n:1320000
KS ci ratio: 1.952392e-01	ci left: 2.755027e-04	ci right 3.358163e-04	k: 402	n:1320000
SPG11   1320000 perm   1008 sec   (1310 perm/sec)   p_kst 3.045455e-04   p_cons 5.478174e-01   p_joint 3.045455e-04

Joint ci ratio: 1.940391e-01	ci left: 2.770075e-04	ci right 3.372337e-04	k: 407	n:1330000
Cons ci ratio: 3.088346e-03	ci left: 5.469401e-01	ci right 5.486326e-01	k: 728556	n:1330000
KS ci ratio: 1.940391e-01	ci left: 2.770075e-04	ci right 3.372337e-04	k: 407	n:1330000
SPG11   1330000 perm   1023 sec   (1300 perm/sec)   p_kst 3.060150e-04   p_cons 5.477865e-01   p_joint 3.060150e-04

Joint ci ratio: 1.928608e-01	ci left: 2.784909e-04	ci right 3.386288e-04	k: 412	n:1340000
Cons ci ratio: 3.076856e-03	ci left: 5.469344e-01	ci right 5.486206e-01	k: 734022	n:1340000
KS ci ratio: 1.928608e-01	ci left: 2.784909e-04	ci right 3.386288e-04	k: 412	n:1340000
SPG11   1340000 perm   1038 sec   (1291 perm/sec)   p_kst 3.074627e-04   p_cons 5.477776e-01   p_joint 3.074627e-04

Joint ci ratio: 1.919335e-01	ci left: 2.792483e-04	ci right 3.392260e-04	k: 416	n:1350000
Cons ci ratio: 3.065484e-03	ci left: 5.469303e-01	ci right 5.486102e-01	k: 739490	n:1350000
KS ci ratio: 1.919335e-01	ci left: 2.792483e-04	ci right 3.392260e-04	k: 416	n:1350000
SPG11   1350000 perm   1052 sec   (1283 perm/sec)   p_kst 3.081481e-04   p_cons 5.477704e-01   p_joint 3.081481e-04

Joint ci ratio: 1.905672e-01	ci left: 2.813955e-04	ci right 3.413544e-04	k: 422	n:1360000
Cons ci ratio: 3.054119e-03	ci left: 5.469454e-01	ci right 5.486191e-01	k: 744984	n:1360000
KS ci ratio: 1.905672e-01	ci left: 2.813955e-04	ci right 3.413544e-04	k: 422	n:1360000
SPG11   1360000 perm   1065 sec   (1277 perm/sec)   p_kst 3.102941e-04   p_cons 5.477824e-01   p_joint 3.102941e-04

Joint ci ratio: 1.901184e-01	ci left: 2.807318e-04	ci right 3.403921e-04	k: 424	n:1370000
Cons ci ratio: 3.042624e-03	ci left: 5.470019e-01	ci right 5.486694e-01	k: 750535	n:1370000
KS ci ratio: 1.901184e-01	ci left: 2.807318e-04	ci right 3.403921e-04	k: 424	n:1370000
SPG11   1370000 perm   1080 sec   (1268 perm/sec)   p_kst 3.094891e-04   p_cons 5.478358e-01   p_joint 3.094891e-04

Joint ci ratio: 1.892299e-01	ci left: 2.814585e-04	ci right 3.409615e-04	k: 428	n:1380000
Cons ci ratio: 3.032056e-03	ci left: 5.469271e-01	ci right 5.485886e-01	k: 755906	n:1380000
KS ci ratio: 1.892299e-01	ci left: 2.814585e-04	ci right 3.409615e-04	k: 428	n:1380000
SPG11   1380000 perm   1094 sec   (1261 perm/sec)   p_kst 3.101449e-04   p_cons 5.477580e-01   p_joint 3.101449e-04

Joint ci ratio: 1.881366e-01	ci left: 2.828608e-04	ci right 3.422753e-04	k: 433	n:1390000
Cons ci ratio: 3.021220e-03	ci left: 5.469153e-01	ci right 5.485708e-01	k: 761363	n:1390000
KS ci ratio: 1.881366e-01	ci left: 2.828608e-04	ci right 3.422753e-04	k: 433	n:1390000
SPG11   1390000 perm   1111 sec   (1251 perm/sec)   p_kst 3.115108e-04   p_cons 5.477432e-01   p_joint 3.115108e-04

Joint ci ratio: 1.872755e-01	ci left: 2.835633e-04	ci right 3.428217e-04	k: 437	n:1400000
Cons ci ratio: 3.010664e-03	ci left: 5.468765e-01	ci right 5.485261e-01	k: 766782	n:1400000
KS ci ratio: 1.872755e-01	ci left: 2.835633e-04	ci right 3.428217e-04	k: 437	n:1400000
SPG11   1400000 perm   1126 sec   (1244 perm/sec)   p_kst 3.121429e-04   p_cons 5.477014e-01   p_joint 3.121429e-04

Joint ci ratio: 1.855880e-01	ci left: 2.869612e-04	ci right 3.463286e-04	k: 445	n:1410000
Cons ci ratio: 3.000150e-03	ci left: 5.468496e-01	ci right 5.484934e-01	k: 772217	n:1410000
KS ci ratio: 1.855880e-01	ci left: 2.869612e-04	ci right 3.463286e-04	k: 445	n:1410000
SPG11   1410000 perm   1140 sec   (1237 perm/sec)   p_kst 3.156028e-04   p_cons 5.476716e-01   p_joint 3.156028e-04

Joint ci ratio: 1.849669e-01	ci left: 2.869551e-04	ci right 3.461002e-04	k: 448	n:1420000
Cons ci ratio: 2.989481e-03	ci left: 5.468668e-01	ci right 5.485048e-01	k: 777714	n:1420000
KS ci ratio: 1.849669e-01	ci left: 2.869551e-04	ci right 3.461002e-04	k: 448	n:1420000
SPG11   1420000 perm   1154 sec   (1230 perm/sec)   p_kst 3.154930e-04   p_cons 5.476859e-01   p_joint 3.154930e-04

Joint ci ratio: 1.843521e-01	ci left: 2.869493e-04	ci right 3.458747e-04	k: 451	n:1430000
Cons ci ratio: 2.979135e-03	ci left: 5.468488e-01	ci right 5.484811e-01	k: 783161	n:1430000
KS ci ratio: 1.843521e-01	ci left: 2.869493e-04	ci right 3.458747e-04	k: 451	n:1430000
SPG11   1430000 perm   1168 sec   (1224 perm/sec)   p_kst 3.153846e-04   p_cons 5.476650e-01   p_joint 3.153846e-04

Joint ci ratio: 1.835417e-01	ci left: 2.876065e-04	ci right 3.463783e-04	k: 455	n:1440000
Cons ci ratio: 2.968697e-03	ci left: 5.468644e-01	ci right 5.484910e-01	k: 788656	n:1440000
KS ci ratio: 1.835417e-01	ci left: 2.876065e-04	ci right 3.463783e-04	k: 455	n:1440000
SPG11   1440000 perm   1181 sec   (1219 perm/sec)   p_kst 3.159722e-04   p_cons 5.476778e-01   p_joint 3.159722e-04

Joint ci ratio: 1.827419e-01	ci left: 2.882552e-04	ci right 3.468744e-04	k: 459	n:1450000
Cons ci ratio: 2.958618e-03	ci left: 5.468377e-01	ci right 5.484587e-01	k: 794090	n:1450000
KS ci ratio: 1.827419e-01	ci left: 2.882552e-04	ci right 3.468744e-04	k: 459	n:1450000
SPG11   1450000 perm   1195 sec   (1213 perm/sec)   p_kst 3.165517e-04   p_cons 5.476483e-01   p_joint 3.165517e-04

Joint ci ratio: 1.825437e-01	ci left: 2.869344e-04	ci right 3.452148e-04	k: 460	n:1460000
Cons ci ratio: 2.948308e-03	ci left: 5.468676e-01	ci right 5.484829e-01	k: 799606	n:1460000
KS ci ratio: 1.825437e-01	ci left: 2.869344e-04	ci right 3.452148e-04	k: 460	n:1460000
SPG11   1460000 perm   1209 sec   (1207 perm/sec)   p_kst 3.150685e-04   p_cons 5.476753e-01   p_joint 3.150685e-04

Joint ci ratio: 1.823462e-01	ci left: 2.856317e-04	ci right 3.435777e-04	k: 461	n:1470000
Cons ci ratio: 2.938293e-03	ci left: 5.468650e-01	ci right 5.484749e-01	k: 805075	n:1470000
KS ci ratio: 1.823462e-01	ci left: 2.856317e-04	ci right 3.435777e-04	k: 461	n:1470000
SPG11   1470000 perm   1223 sec   (1202 perm/sec)   p_kst 3.136054e-04   p_cons 5.476701e-01   p_joint 3.136054e-04

Joint ci ratio: 1.817570e-01	ci left: 2.856364e-04	ci right 3.433756e-04	k: 464	n:1480000
Cons ci ratio: 2.928057e-03	ci left: 5.469173e-01	ci right 5.485217e-01	k: 810625	n:1480000
KS ci ratio: 1.817570e-01	ci left: 2.856364e-04	ci right 3.433756e-04	k: 464	n:1480000
SPG11   1480000 perm   1236 sec   (1197 perm/sec)   p_kst 3.135135e-04   p_cons 5.477196e-01   p_joint 3.135135e-04

Joint ci ratio: 1.813675e-01	ci left: 2.850006e-04	ci right 3.424743e-04	k: 466	n:1490000
Cons ci ratio: 2.918342e-03	ci left: 5.468984e-01	ci right 5.484974e-01	k: 816070	n:1490000
KS ci ratio: 1.813675e-01	ci left: 2.850006e-04	ci right 3.424743e-04	k: 466	n:1490000
SPG11   1490000 perm   1250 sec   (1192 perm/sec)   p_kst 3.127517e-04   p_cons 5.476980e-01   p_joint 3.127517e-04

Joint ci ratio: 1.805956e-01	ci left: 2.856465e-04	ci right 3.429784e-04	k: 470	n:1500000
Cons ci ratio: 2.908567e-03	ci left: 5.469064e-01	ci right 5.485001e-01	k: 821555	n:1500000
KS ci ratio: 1.805956e-01	ci left: 2.856465e-04	ci right 3.429784e-04	k: 470	n:1500000
SPG11   1500000 perm   1265 sec   (1186 perm/sec)   p_kst 3.133333e-04   p_cons 5.477033e-01   p_joint 3.133333e-04

Joint ci ratio: 2.309661e-01	ci left: 1.687124e-04	ci right 2.133740e-04	k: 287	n:1510000
Cons ci ratio: 2.898874e-03	ci left: 5.469170e-01	ci right 5.485054e-01	k: 827044	n:1510000
KS ci ratio: 1.798336e-01	ci left: 2.862843e-04	ci right 3.434754e-04	k: 474	n:1510000
SPG11   1510000 perm   1280 sec   (1180 perm/sec)   p_kst 3.139073e-04   p_cons 5.477113e-01   p_joint 1.900662e-04

Joint ci ratio: 2.305662e-01	ci left: 1.682224e-04	ci right 2.126661e-04	k: 288	n:1520000
Cons ci ratio: 2.889296e-03	ci left: 5.469241e-01	ci right 5.485073e-01	k: 832528	n:1520000
KS ci ratio: 1.796447e-01	ci left: 2.850291e-04	ci right 3.419032e-04	k: 475	n:1520000
SPG11   1520000 perm   1295 sec   (1173 perm/sec)   p_kst 3.125000e-04   p_cons 5.477158e-01   p_joint 1.894737e-04

Joint ci ratio: 2.301684e-01	ci left: 1.677387e-04	ci right 2.119674e-04	k: 289	n:1530000
Cons ci ratio: 2.992068e-03	ci left: 5.279230e-01	ci right 5.295056e-01	k: 808933	n:1530000
KS ci ratio: 1.792686e-01	ci left: 2.844147e-04	ci right 3.410344e-04	k: 477	n:1530000
SPG11   1530000 perm   1310 sec   (1168 perm/sec)   p_kst 3.117647e-04   p_cons 5.287144e-01   p_joint 1.888889e-04

Joint ci ratio: 1.785231e-01	ci left: 2.850489e-04	ci right 3.415335e-04	k: 481	n:1540000
Cons ci ratio: 2.982078e-03	ci left: 5.279690e-01	ci right 5.295464e-01	k: 814287	n:1540000
KS ci ratio: 1.785231e-01	ci left: 2.850489e-04	ci right 3.415335e-04	k: 481	n:1540000
SPG11   1540000 perm   1326 sec   (1161 perm/sec)   p_kst 3.123377e-04   p_cons 5.287578e-01   p_joint 3.123377e-04

Joint ci ratio: 1.781539e-01	ci left: 2.844426e-04	ci right 3.406779e-04	k: 483	n:1550000
Cons ci ratio: 2.972553e-03	ci left: 5.279531e-01	ci right 5.295255e-01	k: 819546	n:1550000
KS ci ratio: 1.781539e-01	ci left: 2.844426e-04	ci right 3.406779e-04	k: 483	n:1550000
SPG11   1550000 perm   1341 sec   (1155 perm/sec)   p_kst 3.116129e-04   p_cons 5.287394e-01   p_joint 3.116129e-04

Joint ci ratio: 1.774222e-01	ci left: 2.850693e-04	ci right 3.411721e-04	k: 487	n:1560000
Cons ci ratio: 2.963096e-03	ci left: 5.279413e-01	ci right 5.295086e-01	k: 824811	n:1560000
KS ci ratio: 1.774222e-01	ci left: 2.850693e-04	ci right 3.411721e-04	k: 487	n:1560000
SPG11   1560000 perm   1356 sec   (1150 perm/sec)   p_kst 3.121795e-04   p_cons 5.287250e-01   p_joint 3.121795e-04

Joint ci ratio: 1.765201e-01	ci left: 2.862972e-04	ci right 3.423247e-04	k: 492	n:1570000
Cons ci ratio: 2.953211e-03	ci left: 5.280169e-01	ci right 5.295792e-01	k: 830213	n:1570000
KS ci ratio: 1.765201e-01	ci left: 2.862972e-04	ci right 3.423247e-04	k: 492	n:1570000
SPG11   1570000 perm   1371 sec   (1145 perm/sec)   p_kst 3.133758e-04   p_cons 5.287981e-01   p_joint 3.133758e-04

Joint ci ratio: 1.763415e-01	ci left: 2.850901e-04	ci right 3.408189e-04	k: 493	n:1580000
Cons ci ratio: 2.943719e-03	ci left: 5.280415e-01	ci right 5.295989e-01	k: 835536	n:1580000
KS ci ratio: 1.763415e-01	ci left: 2.850901e-04	ci right 3.408189e-04	k: 493	n:1580000
SPG11   1580000 perm   1389 sec   (1138 perm/sec)   p_kst 3.120253e-04   p_cons 5.288203e-01   p_joint 3.120253e-04

Joint ci ratio: 1.756318e-01	ci left: 2.857020e-04	ci right 3.413018e-04	k: 497	n:1590000
Cons ci ratio: 2.934426e-03	ci left: 5.280476e-01	ci right 5.296000e-01	k: 840830	n:1590000
KS ci ratio: 1.756318e-01	ci left: 2.857020e-04	ci right 3.413018e-04	k: 497	n:1590000
SPG11   1590000 perm   1407 sec   (1130 perm/sec)   p_kst 3.125786e-04   p_cons 5.288239e-01   p_joint 3.125786e-04

Joint ci ratio: 1.749307e-01	ci left: 2.863067e-04	ci right 3.417783e-04	k: 501	n:1600000
Cons ci ratio: 2.925390e-03	ci left: 5.280249e-01	ci right 5.295725e-01	k: 846078	n:1600000
KS ci ratio: 1.749307e-01	ci left: 2.863067e-04	ci right 3.417783e-04	k: 501	n:1600000
SPG11   1600000 perm   1422 sec   (1125 perm/sec)   p_kst 3.131250e-04   p_cons 5.287987e-01   p_joint 3.131250e-04

Joint ci ratio: 1.742378e-01	ci left: 2.869043e-04	ci right 3.422483e-04	k: 505	n:1610000
Cons ci ratio: 2.916279e-03	ci left: 5.280292e-01	ci right 5.295719e-01	k: 851369	n:1610000
KS ci ratio: 1.742378e-01	ci left: 2.869043e-04	ci right 3.422483e-04	k: 505	n:1610000
SPG11   1610000 perm   1439 sec   (1119 perm/sec)   p_kst 3.136646e-04   p_cons 5.288006e-01   p_joint 3.136646e-04

Joint ci ratio: 1.737236e-01	ci left: 2.869045e-04	ci right 3.420681e-04	k: 508	n:1620000
Cons ci ratio: 2.906977e-03	ci left: 5.280810e-01	ci right 5.296189e-01	k: 856737	n:1620000
KS ci ratio: 1.737236e-01	ci left: 2.869045e-04	ci right 3.420681e-04	k: 508	n:1620000
SPG11   1620000 perm   1455 sec   (1114 perm/sec)   p_kst 3.135802e-04   p_cons 5.288500e-01   p_joint 3.135802e-04

Joint ci ratio: 1.733834e-01	ci left: 2.863181e-04	ci right 3.412498e-04	k: 510	n:1630000
Cons ci ratio: 2.897691e-03	ci left: 5.281444e-01	ci right 5.296776e-01	k: 862125	n:1630000
KS ci ratio: 1.733834e-01	ci left: 2.863181e-04	ci right 3.412498e-04	k: 510	n:1630000
SPG11   1630000 perm   1470 sec   (1109 perm/sec)   p_kst 3.128834e-04   p_cons 5.289110e-01   p_joint 3.128834e-04

Joint ci ratio: 1.730451e-01	ci left: 2.857389e-04	ci right 3.404413e-04	k: 512	n:1640000
Cons ci ratio: 2.888864e-03	ci left: 5.281430e-01	ci right 5.296715e-01	k: 867408	n:1640000
KS ci ratio: 1.730451e-01	ci left: 2.857389e-04	ci right 3.404413e-04	k: 512	n:1640000
SPG11   1640000 perm   1486 sec   (1104 perm/sec)   p_kst 3.121951e-04   p_cons 5.289073e-01   p_joint 3.121951e-04

Joint ci ratio: 1.720418e-01	ci left: 2.874865e-04	ci right 3.421713e-04	k: 518	n:1650000
Cons ci ratio: 2.880381e-03	ci left: 5.280962e-01	ci right 5.296201e-01	k: 872616	n:1650000
KS ci ratio: 1.720418e-01	ci left: 2.874865e-04	ci right 3.421713e-04	k: 518	n:1650000
SPG11   1650000 perm   1502 sec   (1099 perm/sec)   p_kst 3.139394e-04   p_cons 5.288582e-01   p_joint 3.139394e-04

Joint ci ratio: 1.710557e-01	ci left: 2.892139e-04	ci right 3.438794e-04	k: 524	n:1660000
Cons ci ratio: 2.871836e-03	ci left: 5.280734e-01	ci right 5.295927e-01	k: 877863	n:1660000
KS ci ratio: 1.710557e-01	ci left: 2.892139e-04	ci right 3.438794e-04	k: 524	n:1660000
SPG11   1660000 perm   1517 sec   (1094 perm/sec)   p_kst 3.156627e-04   p_cons 5.288331e-01   p_joint 3.156627e-04

Joint ci ratio: 1.707309e-01	ci left: 2.886285e-04	ci right 3.430691e-04	k: 526	n:1670000
Cons ci ratio: 2.863058e-03	ci left: 5.281049e-01	ci right 5.296196e-01	k: 883200	n:1670000
KS ci ratio: 1.707309e-01	ci left: 2.886285e-04	ci right 3.430691e-04	k: 526	n:1670000
SPG11   1670000 perm   1533 sec   (1089 perm/sec)   p_kst 3.149701e-04   p_cons 5.288623e-01   p_joint 3.149701e-04

Joint ci ratio: 1.699266e-01	ci left: 2.897598e-04	ci right 3.441299e-04	k: 531	n:1680000
Cons ci ratio: 2.854380e-03	ci left: 5.281323e-01	ci right 5.296426e-01	k: 888531	n:1680000
KS ci ratio: 1.699266e-01	ci left: 2.897598e-04	ci right 3.441299e-04	k: 531	n:1680000
SPG11   1680000 perm   1550 sec   (1084 perm/sec)   p_kst 3.160714e-04   p_cons 5.288875e-01   p_joint 3.160714e-04

Joint ci ratio: 1.696081e-01	ci left: 2.891784e-04	ci right 3.433273e-04	k: 533	n:1690000
Cons ci ratio: 2.845756e-03	ci left: 5.281637e-01	ci right 5.296694e-01	k: 893869	n:1690000
KS ci ratio: 1.696081e-01	ci left: 2.891784e-04	ci right 3.433273e-04	k: 533	n:1690000
SPG11   1690000 perm   1566 sec   (1079 perm/sec)   p_kst 3.153846e-04   p_cons 5.289166e-01   p_joint 3.153846e-04

Joint ci ratio: 1.692915e-01	ci left: 2.886039e-04	ci right 3.425341e-04	k: 535	n:1700000
Cons ci ratio: 2.837341e-03	ci left: 5.281717e-01	ci right 5.296730e-01	k: 899168	n:1700000
KS ci ratio: 1.692915e-01	ci left: 2.886039e-04	ci right 3.425341e-04	k: 535	n:1700000
SPG11   1700000 perm   1591 sec   (1068 perm/sec)   p_kst 3.147059e-04   p_cons 5.289224e-01   p_joint 3.147059e-04

Joint ci ratio: 1.686633e-01	ci left: 2.891564e-04	ci right 3.429690e-04	k: 539	n:1710000
Cons ci ratio: 2.828794e-03	ci left: 5.282158e-01	ci right 5.297127e-01	k: 904529	n:1710000
KS ci ratio: 1.686633e-01	ci left: 2.891564e-04	ci right 3.429690e-04	k: 539	n:1710000
SPG11   1710000 perm   1611 sec   (1061 perm/sec)   p_kst 3.152047e-04   p_cons 5.289643e-01   p_joint 3.152047e-04

Joint ci ratio: 1.680420e-01	ci left: 2.897029e-04	ci right 3.433984e-04	k: 543	n:1720000
Cons ci ratio: 2.820400e-03	ci left: 5.282461e-01	ci right 5.297387e-01	k: 909867	n:1720000
KS ci ratio: 1.680420e-01	ci left: 2.897029e-04	ci right 3.433984e-04	k: 543	n:1720000
SPG11   1720000 perm   1628 sec   (1057 perm/sec)   p_kst 3.156977e-04   p_cons 5.289924e-01   p_joint 3.156977e-04

Joint ci ratio: 1.677340e-01	ci left: 2.891358e-04	ci right 3.426181e-04	k: 545	n:1730000
Cons ci ratio: 2.812426e-03	ci left: 5.282148e-01	ci right 5.297030e-01	k: 915099	n:1730000
KS ci ratio: 1.677340e-01	ci left: 2.891358e-04	ci right 3.426181e-04	k: 545	n:1730000
SPG11   1730000 perm   1646 sec   (1051 perm/sec)   p_kst 3.150289e-04   p_cons 5.289590e-01   p_joint 3.150289e-04

Joint ci ratio: 1.672751e-01	ci left: 2.891259e-04	ci right 3.424454e-04	k: 548	n:1740000
Cons ci ratio: 2.804580e-03	ci left: 5.281729e-01	ci right 5.296569e-01	k: 920312	n:1740000
KS ci ratio: 1.672751e-01	ci left: 2.891259e-04	ci right 3.424454e-04	k: 548	n:1740000
SPG11   1740000 perm   1662 sec   (1047 perm/sec)   p_kst 3.149425e-04   p_cons 5.289149e-01   p_joint 3.149425e-04

Joint ci ratio: 1.671230e-01	ci left: 2.880213e-04	ci right 3.410839e-04	k: 549	n:1750000
Cons ci ratio: 2.796293e-03	ci left: 5.282218e-01	ci right 5.297015e-01	k: 925683	n:1750000
KS ci ratio: 1.671230e-01	ci left: 2.880213e-04	ci right 3.410839e-04	k: 549	n:1750000
SPG11   1750000 perm   1678 sec   (1043 perm/sec)   p_kst 3.137143e-04   p_cons 5.289617e-01   p_joint 3.137143e-04

Joint ci ratio: 1.668201e-01	ci left: 2.874737e-04	ci right 3.403297e-04	k: 551	n:1760000
Cons ci ratio: 2.788413e-03	ci left: 5.282105e-01	ci right 5.296860e-01	k: 930949	n:1760000
KS ci ratio: 1.668201e-01	ci left: 2.874737e-04	ci right 3.403297e-04	k: 551	n:1760000
SPG11   1760000 perm   1697 sec   (1037 perm/sec)   p_kst 3.130682e-04   p_cons 5.289483e-01   p_joint 3.130682e-04

Joint ci ratio: 1.665187e-01	ci left: 2.869323e-04	ci right 3.395840e-04	k: 553	n:1770000
Cons ci ratio: 2.780593e-03	ci left: 5.282005e-01	ci right 5.296718e-01	k: 936217	n:1770000
KS ci ratio: 1.665187e-01	ci left: 2.869323e-04	ci right 3.395840e-04	k: 553	n:1770000
SPG11   1770000 perm   1714 sec   (1033 perm/sec)   p_kst 3.124294e-04   p_cons 5.289362e-01   p_joint 3.124294e-04

Joint ci ratio: 1.657723e-01	ci left: 2.880126e-04	ci right 3.406019e-04	k: 558	n:1780000
Cons ci ratio: 2.772847e-03	ci left: 5.281888e-01	ci right 5.296560e-01	k: 941482	n:1780000
KS ci ratio: 1.657723e-01	ci left: 2.880126e-04	ci right 3.406019e-04	k: 558	n:1780000
SPG11   1780000 perm   1731 sec   (1028 perm/sec)   p_kst 3.134831e-04   p_cons 5.289225e-01   p_joint 3.134831e-04

Joint ci ratio: 1.653292e-01	ci left: 2.880101e-04	ci right 3.404444e-04	k: 561	n:1790000
Cons ci ratio: 2.765284e-03	ci left: 5.281561e-01	ci right 5.296192e-01	k: 946709	n:1790000
KS ci ratio: 1.653292e-01	ci left: 2.880101e-04	ci right 3.404444e-04	k: 561	n:1790000
SPG11   1790000 perm   1752 sec   (1022 perm/sec)   p_kst 3.134078e-04   p_cons 5.288877e-01   p_joint 3.134078e-04

Joint ci ratio: 1.650359e-01	ci left: 2.874752e-04	ci right 3.397101e-04	k: 563	n:1800000
Cons ci ratio: 2.757551e-03	ci left: 5.281655e-01	ci right 5.296244e-01	k: 952011	n:1800000
KS ci ratio: 1.650359e-01	ci left: 2.874752e-04	ci right 3.397101e-04	k: 563	n:1800000
SPG11   1800000 perm   1770 sec   (1017 perm/sec)   p_kst 3.127778e-04   p_cons 5.288950e-01   p_joint 3.127778e-04

Joint ci ratio: 1.647441e-01	ci left: 2.869463e-04	ci right 3.389838e-04	k: 565	n:1810000
Cons ci ratio: 2.749896e-03	ci left: 5.281725e-01	ci right 5.296274e-01	k: 957309	n:1810000
KS ci ratio: 1.647441e-01	ci left: 2.869463e-04	ci right 3.389838e-04	k: 565	n:1810000
SPG11   1810000 perm   1786 sec   (1013 perm/sec)   p_kst 3.121547e-04   p_cons 5.289000e-01   p_joint 3.121547e-04

Joint ci ratio: 1.645988e-01	ci left: 2.858965e-04	ci right 3.376933e-04	k: 566	n:1820000
Cons ci ratio: 2.742216e-03	ci left: 5.281954e-01	ci right 5.296463e-01	k: 962636	n:1820000
KS ci ratio: 1.645988e-01	ci left: 2.858965e-04	ci right 3.376933e-04	k: 566	n:1820000
SPG11   1820000 perm   1803 sec   (1009 perm/sec)   p_kst 3.109890e-04   p_cons 5.289209e-01   p_joint 3.109890e-04

Joint ci ratio: 1.643094e-01	ci left: 2.853821e-04	ci right 3.369858e-04	k: 568	n:1830000
Cons ci ratio: 2.734933e-03	ci left: 5.281573e-01	ci right 5.296043e-01	k: 967852	n:1830000
KS ci ratio: 1.643094e-01	ci left: 2.853821e-04	ci right 3.369858e-04	k: 568	n:1830000
SPG11   1830000 perm   1819 sec   (1006 perm/sec)   p_kst 3.103825e-04   p_cons 5.288809e-01   p_joint 3.103825e-04

Joint ci ratio: 1.641653e-01	ci left: 2.843523e-04	ci right 3.357202e-04	k: 569	n:1840000
Cons ci ratio: 2.727431e-03	ci left: 5.281703e-01	ci right 5.296133e-01	k: 973161	n:1840000
KS ci ratio: 1.641653e-01	ci left: 2.843523e-04	ci right 3.357202e-04	k: 569	n:1840000
SPG11   1840000 perm   1835 sec   (1002 perm/sec)   p_kst 3.092391e-04   p_cons 5.288918e-01   p_joint 3.092391e-04

Joint ci ratio: 1.635922e-01	ci left: 2.848887e-04	ci right 3.361562e-04	k: 573	n:1850000
Cons ci ratio: 2.719949e-03	ci left: 5.281907e-01	ci right 5.296298e-01	k: 978484	n:1850000
KS ci ratio: 1.635922e-01	ci left: 2.848887e-04	ci right 3.361562e-04	k: 573	n:1850000
SPG11   1850000 perm   1851 sec   (999 perm/sec)   p_kst 3.097297e-04   p_cons 5.289103e-01   p_joint 3.097297e-04

Joint ci ratio: 1.631664e-01	ci left: 2.849040e-04	ci right 3.360277e-04	k: 576	n:1860000
Cons ci ratio: 2.712484e-03	ci left: 5.282189e-01	ci right 5.296541e-01	k: 983822	n:1860000
KS ci ratio: 1.631664e-01	ci left: 2.849040e-04	ci right 3.360277e-04	k: 576	n:1860000
SPG11   1860000 perm   1867 sec   (996 perm/sec)   p_kst 3.096774e-04   p_cons 5.289366e-01   p_joint 3.096774e-04

Joint ci ratio: 1.630253e-01	ci left: 2.838934e-04	ci right 3.347874e-04	k: 577	n:1870000
Cons ci ratio: 2.705194e-03	ci left: 5.282260e-01	ci right 5.296574e-01	k: 989121	n:1870000
KS ci ratio: 1.630253e-01	ci left: 2.838934e-04	ci right 3.347874e-04	k: 577	n:1870000
SPG11   1870000 perm   1884 sec   (993 perm/sec)   p_kst 3.085561e-04   p_cons 5.289417e-01   p_joint 3.085561e-04

Joint ci ratio: 1.628845e-01	ci left: 2.828935e-04	ci right 3.335602e-04	k: 578	n:1880000
Cons ci ratio: 2.698152e-03	ci left: 5.281979e-01	ci right 5.296255e-01	k: 994354	n:1880000
KS ci ratio: 1.628845e-01	ci left: 2.828935e-04	ci right 3.335602e-04	k: 578	n:1880000
SPG11   1880000 perm   1900 sec   (989 perm/sec)   p_kst 3.074468e-04   p_cons 5.289117e-01   p_joint 3.074468e-04

Joint ci ratio: 1.626040e-01	ci left: 2.824118e-04	ci right 3.328966e-04	k: 580	n:1890000
Cons ci ratio: 2.690888e-03	ci left: 5.282214e-01	ci right 5.296452e-01	k: 999684	n:1890000
KS ci ratio: 1.626040e-01	ci left: 2.824118e-04	ci right 3.328966e-04	k: 580	n:1890000
SPG11   1890000 perm   1916 sec   (986 perm/sec)   p_kst 3.068783e-04   p_cons 5.289333e-01   p_joint 3.068783e-04

Joint ci ratio: 1.619087e-01	ci left: 2.834502e-04	ci right 3.338828e-04	k: 585	n:1900000
Cons ci ratio: 2.683707e-03	ci left: 5.282399e-01	ci right 5.296600e-01	k: 1005005	n:1900000
KS ci ratio: 1.619087e-01	ci left: 2.834502e-04	ci right 3.338828e-04	k: 585	n:1900000
SPG11   1900000 perm   1933 sec   (983 perm/sec)   p_kst 3.078947e-04   p_cons 5.289500e-01   p_joint 3.078947e-04

Joint ci ratio: 1.613589e-01	ci left: 2.839757e-04	ci right 3.343136e-04	k: 589	n:1910000
Cons ci ratio: 2.676463e-03	ci left: 5.282808e-01	ci right 5.296971e-01	k: 1010369	n:1910000
KS ci ratio: 1.613589e-01	ci left: 2.839757e-04	ci right 3.343136e-04	k: 589	n:1910000
SPG11   1910000 perm   1949 sec   (980 perm/sec)   p_kst 3.083770e-04   p_cons 5.289890e-01   p_joint 3.083770e-04

Joint ci ratio: 1.613590e-01	ci left: 2.824966e-04	ci right 3.325724e-04	k: 589	n:1920000
Cons ci ratio: 2.669344e-03	ci left: 5.283088e-01	ci right 5.297214e-01	k: 1015709	n:1920000
KS ci ratio: 1.613590e-01	ci left: 2.824966e-04	ci right 3.325724e-04	k: 589	n:1920000
SPG11   1920000 perm   1966 sec   (976 perm/sec)   p_kst 3.067708e-04   p_cons 5.290151e-01   p_joint 3.067708e-04

Joint ci ratio: 1.610863e-01	ci left: 2.820274e-04	ci right 3.319273e-04	k: 591	n:1930000
Cons ci ratio: 2.662155e-03	ci left: 5.283603e-01	ci right 5.297692e-01	k: 1021095	n:1930000
KS ci ratio: 1.610863e-01	ci left: 2.820274e-04	ci right 3.319273e-04	k: 591	n:1930000
SPG11   1930000 perm   1984 sec   (973 perm/sec)   p_kst 3.062176e-04   p_cons 5.290648e-01   p_joint 3.062176e-04

Joint ci ratio: 1.606796e-01	ci left: 2.820578e-04	ci right 3.318249e-04	k: 594	n:1940000
Cons ci ratio: 2.655322e-03	ci left: 5.283550e-01	ci right 5.297603e-01	k: 1026372	n:1940000
KS ci ratio: 1.606796e-01	ci left: 2.820578e-04	ci right 3.318249e-04	k: 594	n:1940000
SPG11   1940000 perm   2001 sec   (969 perm/sec)   p_kst 3.061856e-04   p_cons 5.290577e-01   p_joint 3.061856e-04

Joint ci ratio: 1.601422e-01	ci left: 2.825803e-04	ci right 3.322568e-04	k: 598	n:1950000
Cons ci ratio: 2.648604e-03	ci left: 5.283381e-01	ci right 5.297398e-01	k: 1031626	n:1950000
KS ci ratio: 1.601422e-01	ci left: 2.825803e-04	ci right 3.322568e-04	k: 598	n:1950000
SPG11   1950000 perm   2019 sec   (966 perm/sec)   p_kst 3.066667e-04   p_cons 5.290390e-01   p_joint 3.066667e-04

Joint ci ratio: 1.600088e-01	ci left: 2.816283e-04	ci right 3.310923e-04	k: 599	n:1960000
Cons ci ratio: 2.642076e-03	ci left: 5.282953e-01	ci right 5.296934e-01	k: 1036829	n:1960000
KS ci ratio: 1.600088e-01	ci left: 2.816283e-04	ci right 3.310923e-04	k: 599	n:1960000
SPG11   1960000 perm   2037 sec   (962 perm/sec)   p_kst 3.056122e-04   p_cons 5.289944e-01   p_joint 3.056122e-04

Joint ci ratio: 1.597428e-01	ci left: 2.811733e-04	ci right 3.304674e-04	k: 601	n:1970000
Cons ci ratio: 2.635530e-03	ci left: 5.282651e-01	ci right 5.296597e-01	k: 1042056	n:1970000
KS ci ratio: 1.597428e-01	ci left: 2.811733e-04	ci right 3.304674e-04	k: 601	n:1970000
SPG11   1970000 perm   2054 sec   (959 perm/sec)   p_kst 3.050761e-04   p_cons 5.289624e-01   p_joint 3.050761e-04

Joint ci ratio: 1.596104e-01	ci left: 2.802381e-04	ci right 3.293236e-04	k: 602	n:1980000
Cons ci ratio: 2.628855e-03	ci left: 5.282691e-01	ci right 5.296601e-01	k: 1047350	n:1980000
KS ci ratio: 1.596104e-01	ci left: 2.802381e-04	ci right 3.293236e-04	k: 602	n:1980000
SPG11   1980000 perm   2071 sec   (956 perm/sec)   p_kst 3.040404e-04   p_cons 5.289646e-01   p_joint 3.040404e-04

Joint ci ratio: 1.593464e-01	ci left: 2.797948e-04	ci right 3.287138e-04	k: 604	n:1990000
Cons ci ratio: 2.621960e-03	ci left: 5.283243e-01	ci right 5.297118e-01	k: 1052746	n:1990000
KS ci ratio: 1.593464e-01	ci left: 2.797948e-04	ci right 3.287138e-04	k: 604	n:1990000
SPG11   1990000 perm   2089 sec   (953 perm/sec)   p_kst 3.035176e-04   p_cons 5.290181e-01   p_joint 3.035176e-04

Joint ci ratio: 1.593465e-01	ci left: 2.783958e-04	ci right 3.270703e-04	k: 604	n:2000000
Cons ci ratio: 2.615206e-03	ci left: 5.283624e-01	ci right 5.297465e-01	k: 1058109	n:2000000
KS ci ratio: 1.593465e-01	ci left: 2.783958e-04	ci right 3.270703e-04	k: 604	n:2000000
SPG11   2000000 perm   2107 sec   (949 perm/sec)   p_kst 3.020000e-04   p_cons 5.290545e-01   p_joint 3.020000e-04

Joint ci ratio: 1.590838e-01	ci left: 2.779661e-04	ci right 3.264777e-04	k: 606	n:2010000
Cons ci ratio: 2.608394e-03	ci left: 5.284211e-01	ci right 5.298017e-01	k: 1063514	n:2010000
KS ci ratio: 1.590838e-01	ci left: 2.779661e-04	ci right 3.264777e-04	k: 606	n:2010000
SPG11   2010000 perm   2124 sec   (946 perm/sec)   p_kst 3.014925e-04   p_cons 5.291114e-01   p_joint 3.014925e-04

Joint ci ratio: 1.589530e-01	ci left: 2.770654e-04	ci right 3.253762e-04	k: 607	n:2020000
Cons ci ratio: 2.601966e-03	ci left: 5.284158e-01	ci right 5.297930e-01	k: 1068791	n:2020000
KS ci ratio: 1.589530e-01	ci left: 2.770654e-04	ci right 3.253762e-04	k: 607	n:2020000
SPG11   2020000 perm   2142 sec   (943 perm/sec)   p_kst 3.004950e-04   p_cons 5.291045e-01   p_joint 3.004950e-04

Joint ci ratio: 1.589531e-01	ci left: 2.757005e-04	ci right 3.237734e-04	k: 607	n:2030000
Cons ci ratio: 2.595442e-03	ci left: 5.284382e-01	ci right 5.298120e-01	k: 1074124	n:2030000
KS ci ratio: 1.589531e-01	ci left: 2.757005e-04	ci right 3.237734e-04	k: 607	n:2030000
SPG11   2030000 perm   2159 sec   (940 perm/sec)   p_kst 2.990148e-04   p_cons 5.291251e-01   p_joint 2.990148e-04

Joint ci ratio: 1.586924e-01	ci left: 2.752905e-04	ci right 3.232056e-04	k: 609	n:2040000
Cons ci ratio: 2.589124e-03	ci left: 5.284299e-01	ci right 5.298004e-01	k: 1079395	n:2040000
KS ci ratio: 1.586924e-01	ci left: 2.752905e-04	ci right 3.232056e-04	k: 609	n:2040000
SPG11   2040000 perm   2177 sec   (937 perm/sec)   p_kst 2.985294e-04   p_cons 5.291152e-01   p_joint 2.985294e-04

Joint ci ratio: 1.584329e-01	ci left: 2.748845e-04	ci right 3.226433e-04	k: 611	n:2050000
Cons ci ratio: 2.582969e-03	ci left: 5.283994e-01	ci right 5.297664e-01	k: 1084620	n:2050000
KS ci ratio: 1.584329e-01	ci left: 2.748845e-04	ci right 3.226433e-04	k: 611	n:2050000
SPG11   2050000 perm   2194 sec   (934 perm/sec)   p_kst 2.980488e-04   p_cons 5.290829e-01   p_joint 2.980488e-04

Joint ci ratio: 1.580460e-01	ci left: 2.749487e-04	ci right 3.225910e-04	k: 614	n:2060000
Cons ci ratio: 2.576817e-03	ci left: 5.283768e-01	ci right 5.297406e-01	k: 1089861	n:2060000
KS ci ratio: 1.580460e-01	ci left: 2.749487e-04	ci right 3.225910e-04	k: 614	n:2060000
SPG11   2060000 perm   2212 sec   (931 perm/sec)   p_kst 2.980583e-04   p_cons 5.290587e-01   p_joint 2.980583e-04

Joint ci ratio: 1.574074e-01	ci left: 2.759406e-04	ci right 3.235433e-04	k: 619	n:2070000
Cons ci ratio: 2.570579e-03	ci left: 5.283796e-01	ci right 5.297401e-01	k: 1095154	n:2070000
KS ci ratio: 1.574074e-01	ci left: 2.759406e-04	ci right 3.235433e-04	k: 619	n:2070000
SPG11   2070000 perm   2230 sec   (928 perm/sec)   p_kst 2.990338e-04   p_cons 5.290599e-01   p_joint 2.990338e-04

Joint ci ratio: 1.567764e-01	ci left: 2.769233e-04	ci right 3.244861e-04	k: 624	n:2080000
Cons ci ratio: 2.564312e-03	ci left: 5.283969e-01	ci right 5.297540e-01	k: 1100477	n:2080000
KS ci ratio: 1.567764e-01	ci left: 2.769233e-04	ci right 3.244861e-04	k: 624	n:2080000
SPG11   2080000 perm   2248 sec   (925 perm/sec)   p_kst 3.000000e-04   p_cons 5.290755e-01   p_joint 3.000000e-04

Joint ci ratio: 1.559056e-01	ci left: 2.788166e-04	ci right 3.264137e-04	k: 631	n:2090000
Cons ci ratio: 2.557959e-03	ci left: 5.284397e-01	ci right 5.297937e-01	k: 1105854	n:2090000
KS ci ratio: 1.559056e-01	ci left: 2.788166e-04	ci right 3.264137e-04	k: 631	n:2090000
SPG11   2090000 perm   2267 sec   (922 perm/sec)   p_kst 3.019139e-04   p_cons 5.291167e-01   p_joint 3.019139e-04

Joint ci ratio: 1.554145e-01	ci left: 2.793195e-04	ci right 3.268382e-04	k: 635	n:2100000
Cons ci ratio: 2.551869e-03	ci left: 5.284399e-01	ci right 5.297905e-01	k: 1111142	n:2100000
KS ci ratio: 1.554145e-01	ci left: 2.793195e-04	ci right 3.268382e-04	k: 635	n:2100000
SPG11   2100000 perm   2285 sec   (919 perm/sec)   p_kst 3.023810e-04   p_cons 5.291152e-01   p_joint 3.023810e-04

Joint ci ratio: 1.549281e-01	ci left: 2.798178e-04	ci right 3.272585e-04	k: 639	n:2110000
Cons ci ratio: 2.545735e-03	ci left: 5.284570e-01	ci right 5.298045e-01	k: 1116466	n:2110000
KS ci ratio: 1.549281e-01	ci left: 2.798178e-04	ci right 3.272585e-04	k: 639	n:2110000
SPG11   2110000 perm   2303 sec   (916 perm/sec)   p_kst 3.028436e-04   p_cons 5.291308e-01   p_joint 3.028436e-04

Joint ci ratio: 1.548072e-01	ci left: 2.789514e-04	ci right 3.262048e-04	k: 640	n:2120000
Cons ci ratio: 2.539859e-03	ci left: 5.284321e-01	ci right 5.297764e-01	k: 1121701	n:2120000
KS ci ratio: 1.548072e-01	ci left: 2.789514e-04	ci right 3.262048e-04	k: 640	n:2120000
SPG11   2120000 perm   2321 sec   (913 perm/sec)   p_kst 3.018868e-04   p_cons 5.291042e-01   p_joint 3.018868e-04

Joint ci ratio: 1.543264e-01	ci left: 2.794470e-04	ci right 3.266238e-04	k: 644	n:2130000
Cons ci ratio: 2.533761e-03	ci left: 5.284590e-01	ci right 5.298001e-01	k: 1127046	n:2130000
KS ci ratio: 1.543264e-01	ci left: 2.794470e-04	ci right 3.266238e-04	k: 644	n:2130000
SPG11   2130000 perm   2339 sec   (911 perm/sec)   p_kst 3.023474e-04   p_cons 5.291296e-01   p_joint 3.023474e-04

Joint ci ratio: 1.538501e-01	ci left: 2.799383e-04	ci right 3.270387e-04	k: 648	n:2140000
Cons ci ratio: 2.527705e-03	ci left: 5.284861e-01	ci right 5.298241e-01	k: 1132392	n:2140000
KS ci ratio: 1.538501e-01	ci left: 2.799383e-04	ci right 3.270387e-04	k: 648	n:2140000
SPG11   2140000 perm   2358 sec   (908 perm/sec)   p_kst 3.028037e-04   p_cons 5.291551e-01   p_joint 3.028037e-04

Joint ci ratio: 1.536136e-01	ci left: 2.795307e-04	ci right 3.264836e-04	k: 650	n:2150000
Cons ci ratio: 2.521837e-03	ci left: 5.284842e-01	ci right 5.298190e-01	k: 1137676	n:2150000
KS ci ratio: 1.536136e-01	ci left: 2.795307e-04	ci right 3.264836e-04	k: 650	n:2150000
SPG11   2150000 perm   2376 sec   (905 perm/sec)   p_kst 3.023256e-04   p_cons 5.291516e-01   p_joint 3.023256e-04

Joint ci ratio: 1.532609e-01	ci left: 2.795722e-04	ci right 3.264143e-04	k: 653	n:2160000
Cons ci ratio: 2.516050e-03	ci left: 5.284743e-01	ci right 5.298061e-01	k: 1142943	n:2160000
KS ci ratio: 1.532609e-01	ci left: 2.795722e-04	ci right 3.264143e-04	k: 653	n:2160000
SPG11   2160000 perm   2394 sec   (902 perm/sec)   p_kst 3.023148e-04   p_cons 5.291403e-01   p_joint 3.023148e-04

Joint ci ratio: 1.527943e-01	ci left: 2.800565e-04	ci right 3.268239e-04	k: 657	n:2170000
Cons ci ratio: 2.510170e-03	ci left: 5.284909e-01	ci right 5.298196e-01	k: 1148267	n:2170000
KS ci ratio: 1.527943e-01	ci left: 2.800565e-04	ci right 3.268239e-04	k: 657	n:2170000
SPG11   2170000 perm   2411 sec   (900 perm/sec)   p_kst 3.027650e-04   p_cons 5.291553e-01   p_joint 3.027650e-04

Joint ci ratio: 1.525627e-01	ci left: 2.796543e-04	ci right 3.262772e-04	k: 659	n:2180000
Cons ci ratio: 2.504518e-03	ci left: 5.284702e-01	ci right 5.297958e-01	k: 1153510	n:2180000
KS ci ratio: 1.525627e-01	ci left: 2.796543e-04	ci right 3.262772e-04	k: 659	n:2180000
SPG11   2180000 perm   2429 sec   (897 perm/sec)   p_kst 3.022936e-04   p_cons 5.291330e-01   p_joint 3.022936e-04

Joint ci ratio: 1.518738e-01	ci left: 2.810127e-04	ci right 3.276313e-04	k: 665	n:2190000
Cons ci ratio: 2.498719e-03	ci left: 5.284866e-01	ci right 5.298092e-01	k: 1158834	n:2190000
KS ci ratio: 1.518738e-01	ci left: 2.810127e-04	ci right 3.276313e-04	k: 665	n:2190000
SPG11   2190000 perm   2448 sec   (894 perm/sec)   p_kst 3.036530e-04   p_cons 5.291479e-01   p_joint 3.036530e-04

Joint ci ratio: 1.515329e-01	ci left: 2.810472e-04	ci right 3.275574e-04	k: 668	n:2200000
Cons ci ratio: 2.492839e-03	ci left: 5.285270e-01	ci right 5.298466e-01	k: 1164211	n:2200000
KS ci ratio: 1.515329e-01	ci left: 2.810472e-04	ci right 3.275574e-04	k: 668	n:2200000
SPG11   2200000 perm   2466 sec   (892 perm/sec)   p_kst 3.036364e-04   p_cons 5.291868e-01   p_joint 3.036364e-04

Joint ci ratio: 1.510819e-01	ci left: 2.815170e-04	ci right 3.279537e-04	k: 672	n:2210000
Cons ci ratio: 2.487249e-03	ci left: 5.285172e-01	ci right 5.298338e-01	k: 1169478	n:2210000
KS ci ratio: 1.510819e-01	ci left: 2.815170e-04	ci right 3.279537e-04	k: 672	n:2210000
SPG11   2210000 perm   2484 sec   (890 perm/sec)   p_kst 3.040724e-04   p_cons 5.291756e-01   p_joint 3.040724e-04

Joint ci ratio: 1.505237e-01	ci left: 2.824161e-04	ci right 3.288136e-04	k: 677	n:2220000
Cons ci ratio: 2.481777e-03	ci left: 5.284913e-01	ci right 5.298050e-01	k: 1174709	n:2220000
KS ci ratio: 1.505237e-01	ci left: 2.824161e-04	ci right 3.288136e-04	k: 677	n:2220000
SPG11   2220000 perm   2502 sec   (887 perm/sec)   p_kst 3.049550e-04   p_cons 5.291482e-01   p_joint 3.049550e-04

Joint ci ratio: 1.499716e-01	ci left: 2.833076e-04	ci right 3.296654e-04	k: 682	n:2230000
Cons ci ratio: 2.476210e-03	ci left: 5.284921e-01	ci right 5.298028e-01	k: 1179999	n:2230000
KS ci ratio: 1.499716e-01	ci left: 2.833076e-04	ci right 3.296654e-04	k: 682	n:2230000
SPG11   2230000 perm   2520 sec   (885 perm/sec)   p_kst 3.058296e-04   p_cons 5.291475e-01   p_joint 3.058296e-04

Joint ci ratio: 1.498620e-01	ci left: 2.824725e-04	ci right 3.286569e-04	k: 683	n:2240000
Cons ci ratio: 2.470666e-03	ci left: 5.284956e-01	ci right 5.298034e-01	k: 1185295	n:2240000
KS ci ratio: 1.498620e-01	ci left: 2.824725e-04	ci right 3.286569e-04	k: 683	n:2240000
SPG11   2240000 perm   2539 sec   (882 perm/sec)   p_kst 3.049107e-04   p_cons 5.291496e-01   p_joint 3.049107e-04

Joint ci ratio: 1.496434e-01	ci left: 2.820726e-04	ci right 3.281184e-04	k: 685	n:2250000
Cons ci ratio: 2.465235e-03	ci left: 5.284840e-01	ci right 5.297888e-01	k: 1190557	n:2250000
KS ci ratio: 1.496434e-01	ci left: 2.820726e-04	ci right 3.281184e-04	k: 685	n:2250000
SPG11   2250000 perm   2557 sec   (880 perm/sec)   p_kst 3.044444e-04   p_cons 5.291364e-01   p_joint 3.044444e-04

Joint ci ratio: 1.492090e-01	ci left: 2.825283e-04	ci right 3.285026e-04	k: 689	n:2260000
Cons ci ratio: 2.459673e-03	ci left: 5.285061e-01	ci right 5.298080e-01	k: 1195895	n:2260000
KS ci ratio: 1.492090e-01	ci left: 2.825283e-04	ci right 3.285026e-04	k: 689	n:2260000
SPG11   2260000 perm   2575 sec   (878 perm/sec)   p_kst 3.048673e-04   p_cons 5.291571e-01   p_joint 3.048673e-04

Joint ci ratio: 1.489933e-01	ci left: 2.821318e-04	ci right 3.279693e-04	k: 691	n:2270000
Cons ci ratio: 2.454211e-03	ci left: 5.285152e-01	ci right 5.298143e-01	k: 1201204	n:2270000
KS ci ratio: 1.489933e-01	ci left: 2.821318e-04	ci right 3.279693e-04	k: 691	n:2270000
SPG11   2270000 perm   2594 sec   (875 perm/sec)   p_kst 3.044053e-04   p_cons 5.291648e-01   p_joint 3.044053e-04

Joint ci ratio: 1.484579e-01	ci left: 2.830058e-04	ci right 3.288054e-04	k: 696	n:2280000
Cons ci ratio: 2.448835e-03	ci left: 5.285141e-01	ci right 5.298104e-01	k: 1206490	n:2280000
KS ci ratio: 1.484579e-01	ci left: 2.830058e-04	ci right 3.288054e-04	k: 696	n:2280000
SPG11   2280000 perm   2613 sec   (873 perm/sec)   p_kst 3.052632e-04   p_cons 5.291623e-01   p_joint 3.052632e-04

Joint ci ratio: 1.480337e-01	ci left: 2.834519e-04	ci right 3.291810e-04	k: 700	n:2290000
Cons ci ratio: 2.443527e-03	ci left: 5.285065e-01	ci right 5.297999e-01	k: 1211761	n:2290000
KS ci ratio: 1.480337e-01	ci left: 2.834519e-04	ci right 3.291810e-04	k: 700	n:2290000
SPG11   2290000 perm   2631 sec   (870 perm/sec)   p_kst 3.056769e-04   p_cons 5.291533e-01   p_joint 3.056769e-04

Joint ci ratio: 1.472999e-01	ci left: 2.851506e-04	ci right 3.309056e-04	k: 707	n:2300000
Cons ci ratio: 2.438314e-03	ci left: 5.284864e-01	ci right 5.297770e-01	k: 1217003	n:2300000
KS ci ratio: 1.472999e-01	ci left: 2.851506e-04	ci right 3.309056e-04	k: 707	n:2300000
SPG11   2300000 perm   2649 sec   (868 perm/sec)   p_kst 3.073913e-04   p_cons 5.291317e-01   p_joint 3.073913e-04

Joint ci ratio: 1.470923e-01	ci left: 2.847500e-04	ci right 3.303708e-04	k: 709	n:2310000
Cons ci ratio: 2.433002e-03	ci left: 5.284937e-01	ci right 5.297815e-01	k: 1222308	n:2310000
KS ci ratio: 1.470923e-01	ci left: 2.847500e-04	ci right 3.303708e-04	k: 709	n:2310000
SPG11   2310000 perm   2668 sec   (866 perm/sec)   p_kst 3.069264e-04   p_cons 5.291377e-01   p_joint 3.069264e-04

Joint ci ratio: 1.466797e-01	ci left: 2.851835e-04	ci right 3.307342e-04	k: 713	n:2320000
Cons ci ratio: 2.427754e-03	ci left: 5.284950e-01	ci right 5.297800e-01	k: 1227599	n:2320000
KS ci ratio: 1.466797e-01	ci left: 2.851835e-04	ci right 3.307342e-04	k: 713	n:2320000
SPG11   2320000 perm   2686 sec   (864 perm/sec)   p_kst 3.073276e-04   p_cons 5.291375e-01   p_joint 3.073276e-04

Joint ci ratio: 1.460672e-01	ci left: 2.864403e-04	ci right 3.319841e-04	k: 719	n:2330000
Cons ci ratio: 2.422574e-03	ci left: 5.284889e-01	ci right 5.297711e-01	k: 1232873	n:2330000
KS ci ratio: 1.460672e-01	ci left: 2.864403e-04	ci right 3.319841e-04	k: 719	n:2330000
SPG11   2330000 perm   2705 sec   (861 perm/sec)   p_kst 3.085837e-04   p_cons 5.291300e-01   p_joint 3.085837e-04

Joint ci ratio: 1.458648e-01	ci left: 2.860397e-04	ci right 3.314513e-04	k: 721	n:2340000
Cons ci ratio: 2.417316e-03	ci left: 5.285059e-01	ci right 5.297854e-01	k: 1238201	n:2340000
KS ci ratio: 1.458648e-01	ci left: 2.860397e-04	ci right 3.314513e-04	k: 721	n:2340000
SPG11   2340000 perm   2724 sec   (859 perm/sec)   p_kst 3.081197e-04   p_cons 5.291457e-01   p_joint 3.081197e-04

Joint ci ratio: 1.455627e-01	ci left: 2.860525e-04	ci right 3.313639e-04	k: 724	n:2350000
Cons ci ratio: 2.412080e-03	ci left: 5.285254e-01	ci right 5.298022e-01	k: 1243535	n:2350000
KS ci ratio: 1.455627e-01	ci left: 2.860525e-04	ci right 3.313639e-04	k: 724	n:2350000
SPG11   2350000 perm   2743 sec   (857 perm/sec)   p_kst 3.080851e-04   p_cons 5.291638e-01   p_joint 3.080851e-04

Joint ci ratio: 1.453623e-01	ci left: 2.856571e-04	ci right 3.308381e-04	k: 726	n:2360000
Cons ci ratio: 2.406884e-03	ci left: 5.285434e-01	ci right 5.298175e-01	k: 1248866	n:2360000
KS ci ratio: 1.453623e-01	ci left: 2.856571e-04	ci right 3.308381e-04	k: 726	n:2360000
SPG11   2360000 perm   2762 sec   (854 perm/sec)   p_kst 3.076271e-04   p_cons 5.291805e-01   p_joint 3.076271e-04

Joint ci ratio: 1.452625e-01	ci left: 2.848584e-04	ci right 3.298795e-04	k: 727	n:2370000
Cons ci ratio: 2.401719e-03	ci left: 5.285617e-01	ci right 5.298331e-01	k: 1254198	n:2370000
KS ci ratio: 1.452625e-01	ci left: 2.848584e-04	ci right 3.298795e-04	k: 727	n:2370000
SPG11   2370000 perm   2782 sec   (852 perm/sec)   p_kst 3.067511e-04   p_cons 5.291975e-01   p_joint 3.067511e-04

Joint ci ratio: 1.448651e-01	ci left: 2.852811e-04	ci right 3.302351e-04	k: 731	n:2380000
Cons ci ratio: 2.396549e-03	ci left: 5.285879e-01	ci right 5.298566e-01	k: 1259549	n:2380000
KS ci ratio: 1.448651e-01	ci left: 2.852811e-04	ci right 3.302351e-04	k: 731	n:2380000
SPG11   2380000 perm   2801 sec   (850 perm/sec)   p_kst 3.071429e-04   p_cons 5.292223e-01   p_joint 3.071429e-04

Joint ci ratio: 1.442749e-01	ci left: 2.865072e-04	ci right 3.314545e-04	k: 737	n:2390000
Cons ci ratio: 2.391470e-03	ci left: 5.286017e-01	ci right 5.298677e-01	k: 1264871	n:2390000
KS ci ratio: 1.442749e-01	ci left: 2.865072e-04	ci right 3.314545e-04	k: 737	n:2390000
SPG11   2390000 perm   2820 sec   (848 perm/sec)   p_kst 3.083682e-04   p_cons 5.292347e-01   p_joint 3.083682e-04

Joint ci ratio: 1.440798e-01	ci left: 2.861167e-04	ci right 3.309368e-04	k: 739	n:2400000
Cons ci ratio: 2.386421e-03	ci left: 5.286158e-01	ci right 5.298792e-01	k: 1270194	n:2400000
KS ci ratio: 1.440798e-01	ci left: 2.861167e-04	ci right 3.309368e-04	k: 739	n:2400000
SPG11   2400000 perm   2840 sec   (845 perm/sec)   p_kst 3.079167e-04   p_cons 5.292475e-01   p_joint 3.079167e-04

Joint ci ratio: 1.435955e-01	ci left: 2.869295e-04	ci right 3.317129e-04	k: 744	n:2410000
Cons ci ratio: 2.381644e-03	ci left: 5.285795e-01	ci right 5.298403e-01	k: 1275396	n:2410000
KS ci ratio: 1.435955e-01	ci left: 2.869295e-04	ci right 3.317129e-04	k: 744	n:2410000
SPG11   2410000 perm   2860 sec   (843 perm/sec)   p_kst 3.087137e-04   p_cons 5.292100e-01   p_joint 3.087137e-04

Joint ci ratio: 1.433072e-01	ci left: 2.869390e-04	ci right 3.316264e-04	k: 747	n:2420000
Cons ci ratio: 2.376790e-03	ci left: 5.285659e-01	ci right 5.298241e-01	k: 1280652	n:2420000
KS ci ratio: 1.433072e-01	ci left: 2.869390e-04	ci right 3.316264e-04	k: 747	n:2420000
SPG11   2420000 perm   2879 sec   (840 perm/sec)   p_kst 3.086777e-04   p_cons 5.291950e-01   p_joint 3.086777e-04

Joint ci ratio: 1.430207e-01	ci left: 2.869485e-04	ci right 3.315404e-04	k: 750	n:2430000
Cons ci ratio: 2.372037e-03	ci left: 5.285372e-01	ci right 5.297928e-01	k: 1285871	n:2430000
KS ci ratio: 1.430207e-01	ci left: 2.869485e-04	ci right 3.315404e-04	k: 750	n:2430000
SPG11   2430000 perm   2899 sec   (838 perm/sec)   p_kst 3.086420e-04   p_cons 5.291650e-01   p_joint 3.086420e-04

Joint ci ratio: 1.428307e-01	ci left: 2.865629e-04	ci right 3.310306e-04	k: 752	n:2440000
Cons ci ratio: 2.367328e-03	ci left: 5.285054e-01	ci right 5.297584e-01	k: 1291082	n:2440000
KS ci ratio: 1.428307e-01	ci left: 2.865629e-04	ci right 3.310306e-04	k: 752	n:2440000
SPG11   2440000 perm   2919 sec   (836 perm/sec)   p_kst 3.081967e-04   p_cons 5.291320e-01   p_joint 3.081967e-04

Joint ci ratio: 1.425470e-01	ci left: 2.865740e-04	ci right 3.309476e-04	k: 755	n:2450000
Cons ci ratio: 2.362617e-03	ci left: 5.284805e-01	ci right 5.297309e-01	k: 1296309	n:2450000
KS ci ratio: 1.425470e-01	ci left: 2.865740e-04	ci right 3.309476e-04	k: 755	n:2450000
SPG11   2450000 perm   2939 sec   (834 perm/sec)   p_kst 3.081633e-04   p_cons 5.291057e-01   p_joint 3.081633e-04

Joint ci ratio: 1.418915e-01	ci left: 2.881534e-04	ci right 3.325490e-04	k: 762	n:2460000
Cons ci ratio: 2.357602e-03	ci left: 5.285256e-01	ci right 5.297735e-01	k: 1301708	n:2460000
KS ci ratio: 1.418915e-01	ci left: 2.881534e-04	ci right 3.325490e-04	k: 762	n:2460000
SPG11   2460000 perm   2959 sec   (831 perm/sec)   p_kst 3.097561e-04   p_cons 5.291496e-01   p_joint 3.097561e-04

Joint ci ratio: 1.417987e-01	ci left: 2.873772e-04	ci right 3.316219e-04	k: 763	n:2470000
Cons ci ratio: 2.352944e-03	ci left: 5.285016e-01	ci right 5.297469e-01	k: 1306937	n:2470000
KS ci ratio: 1.417987e-01	ci left: 2.873772e-04	ci right 3.316219e-04	k: 763	n:2470000
SPG11   2470000 perm   2979 sec   (829 perm/sec)   p_kst 3.089069e-04   p_cons 5.291243e-01   p_joint 3.089069e-04

Joint ci ratio: 1.414289e-01	ci left: 2.877742e-04	ci right 3.319547e-04	k: 767	n:2480000
Cons ci ratio: 2.348170e-03	ci left: 5.285084e-01	ci right 5.297512e-01	k: 1312242	n:2480000
KS ci ratio: 1.414289e-01	ci left: 2.877742e-04	ci right 3.319547e-04	k: 767	n:2480000
SPG11   2480000 perm   2998 sec   (827 perm/sec)   p_kst 3.092742e-04   p_cons 5.291298e-01   p_joint 3.092742e-04

Joint ci ratio: 1.412451e-01	ci left: 2.873933e-04	ci right 3.314531e-04	k: 769	n:2490000
Cons ci ratio: 2.343503e-03	ci left: 5.284983e-01	ci right 5.297386e-01	k: 1317505	n:2490000
KS ci ratio: 1.412451e-01	ci left: 2.873933e-04	ci right 3.314531e-04	k: 769	n:2490000
SPG11   2490000 perm   3019 sec   (825 perm/sec)   p_kst 3.088353e-04   p_cons 5.291185e-01   p_joint 3.088353e-04

Joint ci ratio: 1.408796e-01	ci left: 2.877873e-04	ci right 3.317838e-04	k: 773	n:2500000
Cons ci ratio: 2.338673e-03	ci left: 5.285290e-01	ci right 5.297669e-01	k: 1322870	n:2500000
KS ci ratio: 1.408796e-01	ci left: 2.877873e-04	ci right 3.317838e-04	k: 773	n:2500000
SPG11   2500000 perm   3038 sec   (823 perm/sec)   p_kst 3.092000e-04   p_cons 5.291480e-01   p_joint 3.092000e-04

Joint ci ratio: 1.406074e-01	ci left: 2.877938e-04	ci right 3.316992e-04	k: 776	n:2510000
Cons ci ratio: 2.333975e-03	ci left: 5.285376e-01	ci right 5.297731e-01	k: 1328180	n:2510000
KS ci ratio: 1.406074e-01	ci left: 2.877938e-04	ci right 3.316992e-04	k: 776	n:2510000
SPG11   2510000 perm   3059 sec   (821 perm/sec)   p_kst 3.091633e-04   p_cons 5.291554e-01   p_joint 3.091633e-04

Joint ci ratio: 1.404268e-01	ci left: 2.874175e-04	ci right 3.312045e-04	k: 778	n:2520000
Cons ci ratio: 2.329431e-03	ci left: 5.285192e-01	ci right 5.297522e-01	k: 1333422	n:2520000
KS ci ratio: 1.404268e-01	ci left: 2.874175e-04	ci right 3.312045e-04	k: 778	n:2520000
SPG11   2520000 perm   3078 sec   (819 perm/sec)   p_kst 3.087302e-04   p_cons 5.291357e-01   p_joint 3.087302e-04

Joint ci ratio: 1.403368e-01	ci left: 2.866629e-04	ci right 3.303045e-04	k: 779	n:2530000
Cons ci ratio: 2.324733e-03	ci left: 5.285396e-01	ci right 5.297702e-01	k: 1338762	n:2530000
KS ci ratio: 1.403368e-01	ci left: 2.866629e-04	ci right 3.303045e-04	k: 779	n:2530000
SPG11   2530000 perm   3099 sec   (816 perm/sec)   p_kst 3.079051e-04   p_cons 5.291549e-01   p_joint 3.079051e-04

Joint ci ratio: 1.399784e-01	ci left: 2.870539e-04	ci right 3.306341e-04	k: 783	n:2540000
Cons ci ratio: 2.320216e-03	ci left: 5.285273e-01	ci right 5.297554e-01	k: 1344019	n:2540000
KS ci ratio: 1.399784e-01	ci left: 2.870539e-04	ci right 3.306341e-04	k: 783	n:2540000
SPG11   2540000 perm   3120 sec   (814 perm/sec)   p_kst 3.082677e-04   p_cons 5.291413e-01   p_joint 3.082677e-04

Joint ci ratio: 1.396226e-01	ci left: 2.874419e-04	ci right 3.309609e-04	k: 787	n:2550000
Cons ci ratio: 2.315681e-03	ci left: 5.285244e-01	ci right 5.297501e-01	k: 1349300	n:2550000
KS ci ratio: 1.396226e-01	ci left: 2.874419e-04	ci right 3.309609e-04	k: 787	n:2550000
SPG11   2550000 perm   3140 sec   (812 perm/sec)   p_kst 3.086275e-04   p_cons 5.291373e-01   p_joint 3.086275e-04

Joint ci ratio: 1.391817e-01	ci left: 2.882041e-04	ci right 3.316893e-04	k: 792	n:2560000
Cons ci ratio: 2.311390e-03	ci left: 5.284746e-01	ci right 5.296979e-01	k: 1354461	n:2560000
KS ci ratio: 1.391817e-01	ci left: 2.882041e-04	ci right 3.316893e-04	k: 792	n:2560000
SPG11   2560000 perm   3161 sec   (810 perm/sec)   p_kst 3.093750e-04   p_cons 5.290863e-01   p_joint 3.093750e-04

Joint ci ratio: 1.390065e-01	ci left: 2.878338e-04	ci right 3.312039e-04	k: 794	n:2570000
Cons ci ratio: 2.307168e-03	ci left: 5.284156e-01	ci right 5.296365e-01	k: 1359597	n:2570000
KS ci ratio: 1.390065e-01	ci left: 2.878338e-04	ci right 3.312039e-04	k: 794	n:2570000
SPG11   2570000 perm   3181 sec   (808 perm/sec)   p_kst 3.089494e-04   p_cons 5.290261e-01   p_joint 3.089494e-04

Joint ci ratio: 1.386581e-01	ci left: 2.882147e-04	ci right 3.315244e-04	k: 798	n:2580000
Cons ci ratio: 2.302660e-03	ci left: 5.284236e-01	ci right 5.296422e-01	k: 1364905	n:2580000
KS ci ratio: 1.386581e-01	ci left: 2.882147e-04	ci right 3.315244e-04	k: 798	n:2580000
SPG11   2580000 perm   3203 sec   (806 perm/sec)   p_kst 3.093023e-04   p_cons 5.290329e-01   p_joint 3.093023e-04

Joint ci ratio: 1.382263e-01	ci left: 2.889656e-04	ci right 3.322417e-04	k: 803	n:2590000
Cons ci ratio: 2.298254e-03	ci left: 5.284154e-01	ci right 5.296316e-01	k: 1370171	n:2590000
KS ci ratio: 1.382263e-01	ci left: 2.889656e-04	ci right 3.322417e-04	k: 803	n:2590000
SPG11   2590000 perm   3223 sec   (803 perm/sec)   p_kst 3.100386e-04   p_cons 5.290236e-01   p_joint 3.100386e-04

Joint ci ratio: 1.379691e-01	ci left: 2.889682e-04	ci right 3.321575e-04	k: 806	n:2600000
Cons ci ratio: 2.293988e-03	ci left: 5.283823e-01	ci right 5.295961e-01	k: 1375372	n:2600000
KS ci ratio: 1.379691e-01	ci left: 2.889682e-04	ci right 3.321575e-04	k: 806	n:2600000
SPG11   2600000 perm   3244 sec   (801 perm/sec)   p_kst 3.100000e-04   p_cons 5.289892e-01   p_joint 3.100000e-04

Joint ci ratio: 1.378837e-01	ci left: 2.882309e-04	ci right 3.312813e-04	k: 807	n:2610000
Cons ci ratio: 2.289665e-03	ci left: 5.283670e-01	ci right 5.295785e-01	k: 1380619	n:2610000
KS ci ratio: 1.378837e-01	ci left: 2.882309e-04	ci right 3.312813e-04	k: 807	n:2610000
SPG11   2610000 perm   3265 sec   (799 perm/sec)   p_kst 3.091954e-04   p_cons 5.289728e-01   p_joint 3.091954e-04

Joint ci ratio: 1.376285e-01	ci left: 2.882364e-04	ci right 3.312013e-04	k: 810	n:2620000
Cons ci ratio: 2.285487e-03	ci left: 5.283255e-01	ci right 5.295347e-01	k: 1385797	n:2620000
KS ci ratio: 1.376285e-01	ci left: 2.882364e-04	ci right 3.312013e-04	k: 810	n:2620000
SPG11   2620000 perm   3285 sec   (797 perm/sec)   p_kst 3.091603e-04   p_cons 5.289302e-01   p_joint 3.091603e-04

Joint ci ratio: 1.373746e-01	ci left: 2.882419e-04	ci right 3.311219e-04	k: 813	n:2630000
Cons ci ratio: 2.281061e-03	ci left: 5.283433e-01	ci right 5.295502e-01	k: 1391130	n:2630000
KS ci ratio: 1.373746e-01	ci left: 2.882419e-04	ci right 3.311219e-04	k: 813	n:2630000
SPG11   2630000 perm   3306 sec   (795 perm/sec)   p_kst 3.091255e-04   p_cons 5.289468e-01   p_joint 3.091255e-04

Joint ci ratio: 1.373747e-01	ci left: 2.871500e-04	ci right 3.298677e-04	k: 813	n:2640000
Cons ci ratio: 2.276760e-03	ci left: 5.283393e-01	ci right 5.295440e-01	k: 1396406	n:2640000
KS ci ratio: 1.373747e-01	ci left: 2.871500e-04	ci right 3.298677e-04	k: 813	n:2640000
SPG11   2640000 perm   3328 sec   (793 perm/sec)   p_kst 3.079545e-04   p_cons 5.289417e-01   p_joint 3.079545e-04

Joint ci ratio: 1.372063e-01	ci left: 2.867952e-04	ci right 3.294035e-04	k: 815	n:2650000
Cons ci ratio: 2.272456e-03	ci left: 5.283414e-01	ci right 5.295438e-01	k: 1401698	n:2650000
KS ci ratio: 1.372063e-01	ci left: 2.867952e-04	ci right 3.294035e-04	k: 815	n:2650000
SPG11   2650000 perm   3349 sec   (791 perm/sec)   p_kst 3.075472e-04   p_cons 5.289426e-01   p_joint 3.075472e-04

Joint ci ratio: 1.366214e-01	ci left: 2.882585e-04	ci right 3.308868e-04	k: 822	n:2660000
Cons ci ratio: 2.268241e-03	ci left: 5.283292e-01	ci right 5.295293e-01	k: 1406952	n:2660000
KS ci ratio: 1.366214e-01	ci left: 2.882585e-04	ci right 3.308868e-04	k: 822	n:2660000
SPG11   2660000 perm   3370 sec   (789 perm/sec)   p_kst 3.090226e-04   p_cons 5.289293e-01   p_joint 3.090226e-04

Joint ci ratio: 1.365386e-01	ci left: 2.875406e-04	ci right 3.300348e-04	k: 823	n:2670000
Cons ci ratio: 2.264007e-03	ci left: 5.283265e-01	ci right 5.295244e-01	k: 1412231	n:2670000
KS ci ratio: 1.365386e-01	ci left: 2.875406e-04	ci right 3.300348e-04	k: 823	n:2670000
SPG11   2670000 perm   3391 sec   (787 perm/sec)   p_kst 3.082397e-04   p_cons 5.289255e-01   p_joint 3.082397e-04

Joint ci ratio: 1.360441e-01	ci left: 2.886302e-04	ci right 3.311185e-04	k: 829	n:2680000
Cons ci ratio: 2.259773e-03	ci left: 5.283290e-01	ci right 5.295246e-01	k: 1417524	n:2680000
KS ci ratio: 1.360441e-01	ci left: 2.886302e-04	ci right 3.311185e-04	k: 829	n:2680000
SPG11   2680000 perm   3413 sec   (785 perm/sec)   p_kst 3.093284e-04   p_cons 5.289269e-01   p_joint 3.093284e-04

Joint ci ratio: 1.353930e-01	ci left: 2.904302e-04	ci right 3.329624e-04	k: 837	n:2690000
Cons ci ratio: 2.255578e-03	ci left: 5.283282e-01	ci right 5.295216e-01	k: 1422808	n:2690000
KS ci ratio: 1.353930e-01	ci left: 2.904302e-04	ci right 3.329624e-04	k: 837	n:2690000
SPG11   2690000 perm   3434 sec   (783 perm/sec)   p_kst 3.111524e-04   p_cons 5.289249e-01   p_joint 3.111524e-04

Joint ci ratio: 1.352318e-01	ci left: 2.900702e-04	ci right 3.324950e-04	k: 839	n:2700000
Cons ci ratio: 2.251528e-03	ci left: 5.283003e-01	ci right 5.294915e-01	k: 1428019	n:2700000
KS ci ratio: 1.352318e-01	ci left: 2.900702e-04	ci right 3.324950e-04	k: 839	n:2700000
SPG11   2700000 perm   3456 sec   (781 perm/sec)   p_kst 3.107407e-04   p_cons 5.288959e-01   p_joint 3.107407e-04

Joint ci ratio: 1.349109e-01	ci left: 2.904260e-04	ci right 3.327939e-04	k: 843	n:2710000
Cons ci ratio: 2.247401e-03	ci left: 5.282944e-01	ci right 5.294834e-01	k: 1433289	n:2710000
KS ci ratio: 1.349109e-01	ci left: 2.904260e-04	ci right 3.327939e-04	k: 843	n:2710000
SPG11   2710000 perm   3477 sec   (779 perm/sec)   p_kst 3.110701e-04   p_cons 5.288889e-01   p_joint 3.110701e-04

Joint ci ratio: 1.348311e-01	ci left: 2.897135e-04	ci right 3.319505e-04	k: 844	n:2720000
Cons ci ratio: 2.243162e-03	ci left: 5.283187e-01	ci right 5.295055e-01	k: 1438641	n:2720000
KS ci ratio: 1.348311e-01	ci left: 2.897135e-04	ci right 3.319505e-04	k: 844	n:2720000
SPG11   2720000 perm   3499 sec   (777 perm/sec)   p_kst 3.102941e-04   p_cons 5.289121e-01   p_joint 3.102941e-04

Joint ci ratio: 1.347515e-01	ci left: 2.890062e-04	ci right 3.311132e-04	k: 845	n:2730000
Cons ci ratio: 2.239116e-03	ci left: 5.283051e-01	ci right 5.294897e-01	k: 1443890	n:2730000
KS ci ratio: 1.347515e-01	ci left: 2.890062e-04	ci right 3.311132e-04	k: 845	n:2730000
SPG11   2730000 perm   3520 sec   (775 perm/sec)   p_kst 3.095238e-04   p_cons 5.288974e-01   p_joint 3.095238e-04

Joint ci ratio: 1.341973e-01	ci left: 2.904203e-04	ci right 3.325454e-04	k: 852	n:2740000
Cons ci ratio: 2.235032e-03	ci left: 5.283047e-01	ci right 5.294872e-01	k: 1449175	n:2740000
KS ci ratio: 1.341973e-01	ci left: 2.904203e-04	ci right 3.325454e-04	k: 852	n:2740000
SPG11   2740000 perm   3542 sec   (774 perm/sec)   p_kst 3.109489e-04   p_cons 5.288960e-01   p_joint 3.109489e-04

Joint ci ratio: 1.338838e-01	ci left: 2.907700e-04	ci right 3.328394e-04	k: 856	n:2750000
Cons ci ratio: 2.231004e-03	ci left: 5.282971e-01	ci right 5.294774e-01	k: 1454440	n:2750000
KS ci ratio: 1.338838e-01	ci left: 2.907700e-04	ci right 3.328394e-04	k: 856	n:2750000
SPG11   2750000 perm   3564 sec   (772 perm/sec)   p_kst 3.112727e-04   p_cons 5.288873e-01   p_joint 3.112727e-04

Joint ci ratio: 1.338838e-01	ci left: 2.897164e-04	ci right 3.316335e-04	k: 856	n:2760000
Cons ci ratio: 2.226903e-03	ci left: 5.283105e-01	ci right 5.294887e-01	k: 1459763	n:2760000
KS ci ratio: 1.338838e-01	ci left: 2.897164e-04	ci right 3.316335e-04	k: 856	n:2760000
SPG11   2760000 perm   3586 sec   (770 perm/sec)   p_kst 3.101449e-04   p_cons 5.288996e-01   p_joint 3.101449e-04

Joint ci ratio: 1.337279e-01	ci left: 2.893684e-04	ci right 3.311824e-04	k: 858	n:2770000
Cons ci ratio: 2.222925e-03	ci left: 5.283015e-01	ci right 5.294775e-01	k: 1465024	n:2770000
KS ci ratio: 1.337279e-01	ci left: 2.893684e-04	ci right 3.311824e-04	k: 858	n:2770000
SPG11   2770000 perm   3608 sec   (768 perm/sec)   p_kst 3.097473e-04   p_cons 5.288895e-01   p_joint 3.097473e-04

Joint ci ratio: 1.334950e-01	ci left: 2.893706e-04	ci right 3.311063e-04	k: 861	n:2780000
Cons ci ratio: 2.218968e-03	ci left: 5.282925e-01	ci right 5.294664e-01	k: 1470285	n:2780000
KS ci ratio: 1.334950e-01	ci left: 2.893706e-04	ci right 3.311063e-04	k: 861	n:2780000
SPG11   2780000 perm   3630 sec   (766 perm/sec)   p_kst 3.097122e-04   p_cons 5.288795e-01   p_joint 3.097122e-04

Joint ci ratio: 1.334951e-01	ci left: 2.883334e-04	ci right 3.299196e-04	k: 861	n:2790000
Cons ci ratio: 2.214918e-03	ci left: 5.283094e-01	ci right 5.294812e-01	k: 1475618	n:2790000
KS ci ratio: 1.334951e-01	ci left: 2.883334e-04	ci right 3.299196e-04	k: 861	n:2790000
SPG11   2790000 perm   3653 sec   (764 perm/sec)   p_kst 3.086022e-04   p_cons 5.288953e-01   p_joint 3.086022e-04

Joint ci ratio: 1.331095e-01	ci left: 2.890298e-04	ci right 3.305865e-04	k: 866	n:2800000
Cons ci ratio: 2.211005e-03	ci left: 5.283001e-01	ci right 5.294698e-01	k: 1480878	n:2800000
KS ci ratio: 1.331095e-01	ci left: 2.890298e-04	ci right 3.305865e-04	k: 866	n:2800000
SPG11   2800000 perm   3675 sec   (762 perm/sec)   p_kst 3.092857e-04   p_cons 5.288850e-01   p_joint 3.092857e-04

Joint ci ratio: 1.329563e-01	ci left: 2.886893e-04	ci right 3.301455e-04	k: 868	n:2810000
Cons ci ratio: 2.207161e-03	ci left: 5.282799e-01	ci right 5.294475e-01	k: 1486107	n:2810000
KS ci ratio: 1.329563e-01	ci left: 2.886893e-04	ci right 3.301455e-04	k: 868	n:2810000
SPG11   2810000 perm   3698 sec   (760 perm/sec)   p_kst 3.088968e-04   p_cons 5.288637e-01   p_joint 3.088968e-04

Joint ci ratio: 1.329564e-01	ci left: 2.876655e-04	ci right 3.289748e-04	k: 868	n:2820000
Cons ci ratio: 2.203195e-03	ci left: 5.282920e-01	ci right 5.294576e-01	k: 1491427	n:2820000
KS ci ratio: 1.329564e-01	ci left: 2.876655e-04	ci right 3.289748e-04	k: 868	n:2820000
SPG11   2820000 perm   3720 sec   (758 perm/sec)   p_kst 3.078014e-04   p_cons 5.288748e-01   p_joint 3.078014e-04

Joint ci ratio: 1.327275e-01	ci left: 2.876739e-04	ci right 3.289076e-04	k: 871	n:2830000
Cons ci ratio: 2.199212e-03	ci left: 5.283129e-01	ci right 5.294764e-01	k: 1496772	n:2830000
KS ci ratio: 1.327275e-01	ci left: 2.876739e-04	ci right 3.289076e-04	k: 871	n:2830000
SPG11   2830000 perm   3743 sec   (756 perm/sec)   p_kst 3.077739e-04   p_cons 5.288947e-01   p_joint 3.077739e-04

Joint ci ratio: 1.323485e-01	ci left: 2.883631e-04	ci right 3.295684e-04	k: 876	n:2840000
Cons ci ratio: 2.195380e-03	ci left: 5.283041e-01	ci right 5.294655e-01	k: 1502033	n:2840000
KS ci ratio: 1.323485e-01	ci left: 2.883631e-04	ci right 3.295684e-04	k: 876	n:2840000
SPG11   2840000 perm   3765 sec   (754 perm/sec)   p_kst 3.084507e-04   p_cons 5.288849e-01   p_joint 3.084507e-04

Joint ci ratio: 1.320477e-01	ci left: 2.887084e-04	ci right 3.298619e-04	k: 880	n:2850000
Cons ci ratio: 2.191640e-03	ci left: 5.282789e-01	ci right 5.294383e-01	k: 1507247	n:2850000
KS ci ratio: 1.320477e-01	ci left: 2.887084e-04	ci right 3.298619e-04	k: 880	n:2850000
SPG11   2850000 perm   3787 sec   (753 perm/sec)   p_kst 3.087719e-04   p_cons 5.288586e-01   p_joint 3.087719e-04

Joint ci ratio: 1.318235e-01	ci left: 2.887133e-04	ci right 3.297921e-04	k: 883	n:2860000
Cons ci ratio: 2.187828e-03	ci left: 5.282748e-01	ci right 5.294322e-01	k: 1512521	n:2860000
KS ci ratio: 1.318235e-01	ci left: 2.887133e-04	ci right 3.297921e-04	k: 883	n:2860000
SPG11   2860000 perm   3810 sec   (751 perm/sec)   p_kst 3.087413e-04   p_cons 5.288535e-01   p_joint 3.087413e-04

Joint ci ratio: 1.316004e-01	ci left: 2.887182e-04	ci right 3.297227e-04	k: 886	n:2870000
Cons ci ratio: 2.183907e-03	ci left: 5.283000e-01	ci right 5.294553e-01	k: 1517879	n:2870000
KS ci ratio: 1.316004e-01	ci left: 2.887182e-04	ci right 3.297227e-04	k: 886	n:2870000
SPG11   2870000 perm   3833 sec   (749 perm/sec)   p_kst 3.087108e-04   p_cons 5.288777e-01   p_joint 3.087108e-04

Joint ci ratio: 1.314523e-01	ci left: 2.883873e-04	ci right 3.292951e-04	k: 888	n:2880000
Cons ci ratio: 2.179914e-03	ci left: 5.283462e-01	ci right 5.294996e-01	k: 1523298	n:2880000
KS ci ratio: 1.314523e-01	ci left: 2.883873e-04	ci right 3.292951e-04	k: 888	n:2880000
SPG11   2880000 perm   3856 sec   (747 perm/sec)   p_kst 3.083333e-04   p_cons 5.289229e-01   p_joint 3.083333e-04

Joint ci ratio: 1.309377e-01	ci left: 2.897321e-04	ci right 3.306572e-04	k: 895	n:2890000
Cons ci ratio: 2.176058e-03	ci left: 5.283658e-01	ci right 5.295172e-01	k: 1528641	n:2890000
KS ci ratio: 1.309377e-01	ci left: 2.897321e-04	ci right 3.306572e-04	k: 895	n:2890000
SPG11   2890000 perm   3879 sec   (745 perm/sec)   p_kst 3.096886e-04   p_cons 5.289415e-01   p_joint 3.096886e-04

Joint ci ratio: 1.306464e-01	ci left: 2.900672e-04	ci right 3.309415e-04	k: 899	n:2900000
Cons ci ratio: 2.172283e-03	ci left: 5.283715e-01	ci right 5.295209e-01	k: 1533944	n:2900000
KS ci ratio: 1.306464e-01	ci left: 2.900672e-04	ci right 3.309415e-04	k: 899	n:2900000
SPG11   2900000 perm   3901 sec   (743 perm/sec)   p_kst 3.100000e-04   p_cons 5.289462e-01   p_joint 3.100000e-04

Joint ci ratio: 1.304292e-01	ci left: 2.900676e-04	ci right 3.308688e-04	k: 902	n:2910000
Cons ci ratio: 2.168614e-03	ci left: 5.283572e-01	ci right 5.295046e-01	k: 1539189	n:2910000
KS ci ratio: 1.304292e-01	ci left: 2.900676e-04	ci right 3.308688e-04	k: 902	n:2910000
SPG11   2910000 perm   3924 sec   (742 perm/sec)   p_kst 3.099656e-04   p_cons 5.289309e-01   p_joint 3.099656e-04

Joint ci ratio: 1.301412e-01	ci left: 2.903995e-04	ci right 3.311501e-04	k: 906	n:2920000
Cons ci ratio: 2.164889e-03	ci left: 5.283601e-01	ci right 5.295055e-01	k: 1544484	n:2920000
KS ci ratio: 1.301412e-01	ci left: 2.903995e-04	ci right 3.311501e-04	k: 906	n:2920000
SPG11   2920000 perm   3947 sec   (740 perm/sec)   p_kst 3.102740e-04   p_cons 5.289329e-01   p_joint 3.102740e-04

Joint ci ratio: 1.301413e-01	ci left: 2.894083e-04	ci right 3.300199e-04	k: 906	n:2930000
Cons ci ratio: 2.161257e-03	ci left: 5.283460e-01	ci right 5.294894e-01	k: 1549729	n:2930000
KS ci ratio: 1.301413e-01	ci left: 2.894083e-04	ci right 3.300199e-04	k: 906	n:2930000
SPG11   2930000 perm   3970 sec   (738 perm/sec)   p_kst 3.092150e-04   p_cons 5.289177e-01   p_joint 3.092150e-04

Joint ci ratio: 1.299981e-01	ci left: 2.890821e-04	ci right 3.295998e-04	k: 908	n:2940000
Cons ci ratio: 2.157438e-03	ci left: 5.283792e-01	ci right 5.295207e-01	k: 1555113	n:2940000
KS ci ratio: 1.299981e-01	ci left: 2.890821e-04	ci right 3.295998e-04	k: 908	n:2940000
SPG11   2940000 perm   3994 sec   (736 perm/sec)   p_kst 3.088435e-04   p_cons 5.289500e-01   p_joint 3.088435e-04

Joint ci ratio: 1.296420e-01	ci left: 2.897420e-04	ci right 3.302325e-04	k: 913	n:2950000
Cons ci ratio: 2.153795e-03	ci left: 5.283763e-01	ci right 5.295159e-01	k: 1560391	n:2950000
KS ci ratio: 1.296420e-01	ci left: 2.897420e-04	ci right 3.302325e-04	k: 913	n:2950000
SPG11   2950000 perm   4017 sec   (734 perm/sec)   p_kst 3.094915e-04   p_cons 5.289461e-01   p_joint 3.094915e-04

Joint ci ratio: 1.295004e-01	ci left: 2.894170e-04	ci right 3.298144e-04	k: 915	n:2960000
Cons ci ratio: 2.150035e-03	ci left: 5.284048e-01	ci right 5.295424e-01	k: 1565762	n:2960000
KS ci ratio: 1.295004e-01	ci left: 2.894170e-04	ci right 3.298144e-04	k: 915	n:2960000
SPG11   2960000 perm   4040 sec   (733 perm/sec)   p_kst 3.091216e-04   p_cons 5.289736e-01   p_joint 3.091216e-04

Joint ci ratio: 1.291483e-01	ci left: 2.900715e-04	ci right 3.304418e-04	k: 920	n:2970000
Cons ci ratio: 2.146396e-03	ci left: 5.284096e-01	ci right 5.295453e-01	k: 1571063	n:2970000
KS ci ratio: 1.291483e-01	ci left: 2.900715e-04	ci right 3.304418e-04	k: 920	n:2970000
SPG11   2970000 perm   4063 sec   (731 perm/sec)   p_kst 3.097643e-04   p_cons 5.289774e-01   p_joint 3.097643e-04

Joint ci ratio: 1.290084e-01	ci left: 2.897476e-04	ci right 3.300258e-04	k: 922	n:2980000
Cons ci ratio: 2.142787e-03	ci left: 5.284116e-01	ci right 5.295454e-01	k: 1576356	n:2980000
KS ci ratio: 1.290084e-01	ci left: 2.897476e-04	ci right 3.300258e-04	k: 922	n:2980000
SPG11   2980000 perm   4088 sec   (729 perm/sec)   p_kst 3.093960e-04   p_cons 5.289785e-01   p_joint 3.093960e-04

Joint ci ratio: 1.288688e-01	ci left: 2.894259e-04	ci right 3.296125e-04	k: 924	n:2990000
Cons ci ratio: 2.139102e-03	ci left: 5.284357e-01	ci right 5.295676e-01	k: 1581715	n:2990000
KS ci ratio: 1.288688e-01	ci left: 2.894259e-04	ci right 3.296125e-04	k: 924	n:2990000
SPG11   2990000 perm   4111 sec   (727 perm/sec)   p_kst 3.090301e-04   p_cons 5.290017e-01   p_joint 3.090301e-04

Joint ci ratio: 1.288689e-01	ci left: 2.884611e-04	ci right 3.285138e-04	k: 924	n:3000000
Cons ci ratio: 2.135516e-03	ci left: 5.284406e-01	ci right 5.295706e-01	k: 1587017	n:3000000
KS ci ratio: 1.288689e-01	ci left: 2.884611e-04	ci right 3.285138e-04	k: 924	n:3000000
SPG11   3000000 perm   4135 sec   (726 perm/sec)   p_kst 3.080000e-04   p_cons 5.290057e-01   p_joint 3.080000e-04

Joint ci ratio: 1.286604e-01	ci left: 2.884673e-04	ci right 3.284511e-04	k: 927	n:3010000
Cons ci ratio: 2.132103e-03	ci left: 5.284097e-01	ci right 5.295378e-01	k: 1592211	n:3010000
KS ci ratio: 1.286604e-01	ci left: 2.884673e-04	ci right 3.284511e-04	k: 927	n:3010000
SPG11   3010000 perm   4159 sec   (724 perm/sec)   p_kst 3.079734e-04   p_cons 5.289738e-01   p_joint 3.079734e-04

Joint ci ratio: 1.285220e-01	ci left: 2.881531e-04	ci right 3.280471e-04	k: 929	n:3020000
Cons ci ratio: 2.128601e-03	ci left: 5.284034e-01	ci right 5.295297e-01	k: 1597479	n:3020000
KS ci ratio: 1.285220e-01	ci left: 2.881531e-04	ci right 3.280471e-04	k: 929	n:3020000
SPG11   3020000 perm   4182 sec   (722 perm/sec)   p_kst 3.076159e-04   p_cons 5.289666e-01   p_joint 3.076159e-04

Joint ci ratio: 1.282465e-01	ci left: 2.884798e-04	ci right 3.283269e-04	k: 933	n:3030000
Cons ci ratio: 2.125131e-03	ci left: 5.283935e-01	ci right 5.295180e-01	k: 1602736	n:3030000
KS ci ratio: 1.282465e-01	ci left: 2.884798e-04	ci right 3.283269e-04	k: 933	n:3030000
SPG11   3030000 perm   4206 sec   (720 perm/sec)   p_kst 3.079208e-04   p_cons 5.289558e-01   p_joint 3.079208e-04

Joint ci ratio: 1.281095e-01	ci left: 2.881677e-04	ci right 3.279259e-04	k: 935	n:3040000
Cons ci ratio: 2.121678e-03	ci left: 5.283838e-01	ci right 5.295063e-01	k: 1607993	n:3040000
KS ci ratio: 1.281095e-01	ci left: 2.881677e-04	ci right 3.279259e-04	k: 935	n:3040000
SPG11   3040000 perm   4231 sec   (718 perm/sec)   p_kst 3.075658e-04   p_cons 5.289451e-01   p_joint 3.075658e-04

Joint ci ratio: 1.279728e-01	ci left: 2.878576e-04	ci right 3.275274e-04	k: 937	n:3050000
Cons ci ratio: 2.118216e-03	ci left: 5.283803e-01	ci right 5.295010e-01	k: 1613269	n:3050000
KS ci ratio: 1.279728e-01	ci left: 2.878576e-04	ci right 3.275274e-04	k: 937	n:3050000
SPG11   3050000 perm   4256 sec   (717 perm/sec)   p_kst 3.072131e-04   p_cons 5.289407e-01   p_joint 3.072131e-04

Joint ci ratio: 1.276331e-01	ci left: 2.884986e-04	ci right 3.281433e-04	k: 942	n:3060000
Cons ci ratio: 2.114855e-03	ci left: 5.283569e-01	ci right 5.294758e-01	k: 1618484	n:3060000
KS ci ratio: 1.276331e-01	ci left: 2.884986e-04	ci right 3.281433e-04	k: 942	n:3060000
SPG11   3060000 perm   4280 sec   (715 perm/sec)   p_kst 3.078431e-04   p_cons 5.289163e-01   p_joint 3.078431e-04

Joint ci ratio: 1.274980e-01	ci left: 2.881896e-04	ci right 3.277467e-04	k: 944	n:3070000
Cons ci ratio: 2.111564e-03	ci left: 5.283209e-01	ci right 5.294380e-01	k: 1623660	n:3070000
KS ci ratio: 1.274980e-01	ci left: 2.881896e-04	ci right 3.277467e-04	k: 944	n:3070000
SPG11   3070000 perm   4304 sec   (713 perm/sec)   p_kst 3.074919e-04   p_cons 5.288795e-01   p_joint 3.074919e-04

Joint ci ratio: 1.272961e-01	ci left: 2.881969e-04	ci right 3.276876e-04	k: 947	n:3080000
Cons ci ratio: 2.108017e-03	ci left: 5.283495e-01	ci right 5.294647e-01	k: 1629034	n:3080000
KS ci ratio: 1.272961e-01	ci left: 2.881969e-04	ci right 3.276876e-04	k: 947	n:3080000
SPG11   3080000 perm   4329 sec   (712 perm/sec)   p_kst 3.074675e-04   p_cons 5.289071e-01   p_joint 3.074675e-04

Joint ci ratio: 1.270283e-01	ci left: 2.885175e-04	ci right 3.279628e-04	k: 951	n:3090000
Cons ci ratio: 2.104730e-03	ci left: 5.283203e-01	ci right 5.294337e-01	k: 1634230	n:3090000
KS ci ratio: 1.270283e-01	ci left: 2.885175e-04	ci right 3.279628e-04	k: 951	n:3090000
SPG11   3090000 perm   4353 sec   (710 perm/sec)   p_kst 3.077670e-04   p_cons 5.288770e-01   p_joint 3.077670e-04

Joint ci ratio: 1.268951e-01	ci left: 2.882115e-04	ci right 3.275705e-04	k: 953	n:3100000
Cons ci ratio: 2.101154e-03	ci left: 5.283635e-01	ci right 5.294751e-01	k: 1639650	n:3100000
KS ci ratio: 1.268951e-01	ci left: 2.882115e-04	ci right 3.275705e-04	k: 953	n:3100000
SPG11   3100000 perm   4378 sec   (708 perm/sec)   p_kst 3.074194e-04   p_cons 5.289194e-01   p_joint 3.074194e-04

Joint ci ratio: 1.267624e-01	ci left: 2.879075e-04	ci right 3.271807e-04	k: 955	n:3110000
Cons ci ratio: 2.097820e-03	ci left: 5.283534e-01	ci right 5.294633e-01	k: 1644905	n:3110000
KS ci ratio: 1.267624e-01	ci left: 2.879075e-04	ci right 3.271807e-04	k: 955	n:3110000
SPG11   3110000 perm   4402 sec   (706 perm/sec)   p_kst 3.070740e-04   p_cons 5.289084e-01   p_joint 3.070740e-04

Joint ci ratio: 1.266300e-01	ci left: 2.876054e-04	ci right 3.267934e-04	k: 957	n:3120000
Cons ci ratio: 2.094593e-03	ci left: 5.283216e-01	ci right 5.294297e-01	k: 1650092	n:3120000
KS ci ratio: 1.266300e-01	ci left: 2.876054e-04	ci right 3.267934e-04	k: 957	n:3120000
SPG11   3120000 perm   4427 sec   (705 perm/sec)   p_kst 3.067308e-04   p_cons 5.288756e-01   p_joint 3.067308e-04

Joint ci ratio: 1.264322e-01	ci left: 2.876146e-04	ci right 3.267381e-04	k: 960	n:3130000
Cons ci ratio: 2.091301e-03	ci left: 5.283088e-01	ci right 5.294151e-01	k: 1655338	n:3130000
KS ci ratio: 1.264322e-01	ci left: 2.876146e-04	ci right 3.267381e-04	k: 960	n:3130000
SPG11   3130000 perm   4451 sec   (703 perm/sec)   p_kst 3.067093e-04   p_cons 5.288620e-01   p_joint 3.067093e-04

Joint ci ratio: 1.260393e-01	ci left: 2.885492e-04	ci right 3.276686e-04	k: 966	n:3140000
Cons ci ratio: 2.087968e-03	ci left: 5.283098e-01	ci right 5.294143e-01	k: 1660627	n:3140000
KS ci ratio: 1.260393e-01	ci left: 2.885492e-04	ci right 3.276686e-04	k: 966	n:3140000
SPG11   3140000 perm   4476 sec   (702 perm/sec)   p_kst 3.076433e-04   p_cons 5.288621e-01   p_joint 3.076433e-04

Joint ci ratio: 1.259092e-01	ci left: 2.882480e-04	ci right 3.272833e-04	k: 968	n:3150000
Cons ci ratio: 2.084644e-03	ci left: 5.283124e-01	ci right 5.294152e-01	k: 1665921	n:3150000
KS ci ratio: 1.259092e-01	ci left: 2.882480e-04	ci right 3.272833e-04	k: 968	n:3150000
SPG11   3150000 perm   4501 sec   (700 perm/sec)   p_kst 3.073016e-04   p_cons 5.288638e-01   p_joint 3.073016e-04

Joint ci ratio: 1.257147e-01	ci left: 2.882554e-04	ci right 3.272269e-04	k: 971	n:3160000
Cons ci ratio: 2.081369e-03	ci left: 5.283070e-01	ci right 5.294081e-01	k: 1671190	n:3160000
KS ci ratio: 1.257147e-01	ci left: 2.882554e-04	ci right 3.272269e-04	k: 971	n:3160000
SPG11   3160000 perm   4525 sec   (698 perm/sec)   p_kst 3.072785e-04   p_cons 5.288576e-01   p_joint 3.072785e-04

Joint ci ratio: 1.255211e-01	ci left: 2.882627e-04	ci right 3.271707e-04	k: 974	n:3170000
Cons ci ratio: 2.078008e-03	ci left: 5.283260e-01	ci right 5.294253e-01	k: 1676536	n:3170000
KS ci ratio: 1.255211e-01	ci left: 2.882627e-04	ci right 3.271707e-04	k: 974	n:3170000
SPG11   3170000 perm   4550 sec   (697 perm/sec)   p_kst 3.072555e-04   p_cons 5.288757e-01   p_joint 3.072555e-04

Joint ci ratio: 1.253285e-01	ci left: 2.882700e-04	ci right 3.271148e-04	k: 977	n:3180000
Cons ci ratio: 2.074738e-03	ci left: 5.283270e-01	ci right 5.294245e-01	k: 1681825	n:3180000
KS ci ratio: 1.253285e-01	ci left: 2.882700e-04	ci right 3.271148e-04	k: 977	n:3180000
SPG11   3180000 perm   4575 sec   (695 perm/sec)   p_kst 3.072327e-04   p_cons 5.288758e-01   p_joint 3.072327e-04

Joint ci ratio: 1.252006e-01	ci left: 2.879736e-04	ci right 3.267360e-04	k: 979	n:3190000
Cons ci ratio: 2.071487e-03	ci left: 5.283270e-01	ci right 5.294228e-01	k: 1687111	n:3190000
KS ci ratio: 1.252006e-01	ci left: 2.879736e-04	ci right 3.267360e-04	k: 979	n:3190000
SPG11   3190000 perm   4599 sec   (694 perm/sec)   p_kst 3.068966e-04   p_cons 5.288749e-01   p_joint 3.068966e-04

Joint ci ratio: 1.250730e-01	ci left: 2.876791e-04	ci right 3.263595e-04	k: 981	n:3200000
Cons ci ratio: 2.068298e-03	ci left: 5.283157e-01	ci right 5.294099e-01	k: 1692361	n:3200000
KS ci ratio: 1.250730e-01	ci left: 2.876791e-04	ci right 3.263595e-04	k: 981	n:3200000
SPG11   3200000 perm   4624 sec   (692 perm/sec)   p_kst 3.065625e-04   p_cons 5.288628e-01   p_joint 3.065625e-04

Joint ci ratio: 1.247558e-01	ci left: 2.882919e-04	ci right 3.269491e-04	k: 986	n:3210000
Cons ci ratio: 2.065111e-03	ci left: 5.283077e-01	ci right 5.294001e-01	k: 1697621	n:3210000
KS ci ratio: 1.247558e-01	ci left: 2.882919e-04	ci right 3.269491e-04	k: 986	n:3210000
SPG11   3210000 perm   4649 sec   (690 perm/sec)   p_kst 3.071651e-04   p_cons 5.288539e-01   p_joint 3.071651e-04

Joint ci ratio: 1.245666e-01	ci left: 2.882992e-04	ci right 3.268944e-04	k: 989	n:3220000
Cons ci ratio: 2.061946e-03	ci left: 5.282978e-01	ci right 5.293885e-01	k: 1702875	n:3220000
KS ci ratio: 1.245666e-01	ci left: 2.882992e-04	ci right 3.268944e-04	k: 989	n:3220000
SPG11   3220000 perm   4674 sec   (689 perm/sec)   p_kst 3.071429e-04   p_cons 5.288432e-01   p_joint 3.071429e-04

Joint ci ratio: 1.241908e-01	ci left: 2.892064e-04	ci right 3.277977e-04	k: 995	n:3230000
Cons ci ratio: 2.058775e-03	ci left: 5.282929e-01	ci right 5.293820e-01	k: 1708145	n:3230000
KS ci ratio: 1.241908e-01	ci left: 2.892064e-04	ci right 3.277977e-04	k: 995	n:3230000
SPG11   3230000 perm   4699 sec   (687 perm/sec)   p_kst 3.080495e-04   p_cons 5.288375e-01   p_joint 3.080495e-04

Joint ci ratio: 1.240042e-01	ci left: 2.892110e-04	ci right 3.277406e-04	k: 998	n:3240000
Cons ci ratio: 2.055671e-03	ci left: 5.282754e-01	ci right 5.293628e-01	k: 1713374	n:3240000
KS ci ratio: 1.240042e-01	ci left: 2.892110e-04	ci right 3.277406e-04	k: 998	n:3240000
SPG11   3240000 perm   4724 sec   (686 perm/sec)   p_kst 3.080247e-04   p_cons 5.288191e-01   p_joint 3.080247e-04

Joint ci ratio: 1.238184e-01	ci left: 2.892156e-04	ci right 3.276839e-04	k: 1001	n:3250000
Cons ci ratio: 2.052419e-03	ci left: 5.282974e-01	ci right 5.293831e-01	k: 1718731	n:3250000
KS ci ratio: 1.238184e-01	ci left: 2.892156e-04	ci right 3.276839e-04	k: 1001	n:3250000
SPG11   3250000 perm   4749 sec   (684 perm/sec)   p_kst 3.080000e-04   p_cons 5.288403e-01   p_joint 3.080000e-04

Joint ci ratio: 1.235106e-01	ci left: 2.898147e-04	ci right 3.282599e-04	k: 1006	n:3260000
Cons ci ratio: 2.049298e-03	ci left: 5.282911e-01	ci right 5.293751e-01	k: 1723996	n:3260000
KS ci ratio: 1.235106e-01	ci left: 2.898147e-04	ci right 3.282599e-04	k: 1006	n:3260000
SPG11   3260000 perm   4775 sec   (683 perm/sec)   p_kst 3.085890e-04   p_cons 5.288331e-01   p_joint 3.085890e-04

Joint ci ratio: 1.232660e-01	ci left: 2.901140e-04	ci right 3.285170e-04	k: 1010	n:3270000
Cons ci ratio: 2.046274e-03	ci left: 5.282646e-01	ci right 5.293470e-01	k: 1729195	n:3270000
KS ci ratio: 1.232660e-01	ci left: 2.901140e-04	ci right 3.285170e-04	k: 1010	n:3270000
SPG11   3270000 perm   4800 sec   (681 perm/sec)   p_kst 3.088685e-04   p_cons 5.288058e-01   p_joint 3.088685e-04

Joint ci ratio: 1.228414e-01	ci left: 2.912979e-04	ci right 3.297152e-04	k: 1017	n:3280000
Cons ci ratio: 2.043028e-03	ci left: 5.282959e-01	ci right 5.293766e-01	k: 1734583	n:3280000
KS ci ratio: 1.228414e-01	ci left: 2.912979e-04	ci right 3.297152e-04	k: 1017	n:3280000
SPG11   3280000 perm   4826 sec   (680 perm/sec)   p_kst 3.100610e-04   p_cons 5.288363e-01   p_joint 3.100610e-04

Joint ci ratio: 1.227811e-01	ci left: 2.907071e-04	ci right 3.290263e-04	k: 1018	n:3290000
Cons ci ratio: 2.039927e-03	ci left: 5.282951e-01	ci right 5.293742e-01	k: 1739866	n:3290000
KS ci ratio: 1.227811e-01	ci left: 2.907071e-04	ci right 3.290263e-04	k: 1018	n:3290000
SPG11   3290000 perm   4851 sec   (678 perm/sec)   p_kst 3.094225e-04   p_cons 5.288347e-01   p_joint 3.094225e-04

Joint ci ratio: 1.225408e-01	ci left: 2.910011e-04	ci right 3.292786e-04	k: 1022	n:3300000
Cons ci ratio: 2.036808e-03	ci left: 5.283022e-01	ci right 5.293796e-01	k: 1745175	n:3300000
KS ci ratio: 1.225408e-01	ci left: 2.910011e-04	ci right 3.292786e-04	k: 1022	n:3300000
SPG11   3300000 perm   4877 sec   (677 perm/sec)   p_kst 3.096970e-04   p_cons 5.288409e-01   p_joint 3.096970e-04

Joint ci ratio: 1.222424e-01	ci left: 2.915863e-04	ci right 3.298406e-04	k: 1027	n:3310000
Cons ci ratio: 2.033734e-03	ci left: 5.283020e-01	ci right 5.293778e-01	k: 1750460	n:3310000
KS ci ratio: 1.222424e-01	ci left: 2.915863e-04	ci right 3.298406e-04	k: 1027	n:3310000
SPG11   3310000 perm   4902 sec   (675 perm/sec)   p_kst 3.102719e-04   p_cons 5.288399e-01   p_joint 3.102719e-04

Joint ci ratio: 1.221831e-01	ci left: 2.910000e-04	ci right 3.291575e-04	k: 1028	n:3320000
Cons ci ratio: 2.030628e-03	ci left: 5.283126e-01	ci right 5.293868e-01	k: 1755781	n:3320000
KS ci ratio: 1.221831e-01	ci left: 2.910000e-04	ci right 3.291575e-04	k: 1028	n:3320000
SPG11   3320000 perm   4929 sec   (674 perm/sec)   p_kst 3.096386e-04   p_cons 5.288497e-01   p_joint 3.096386e-04

Joint ci ratio: 1.220053e-01	ci left: 2.909995e-04	ci right 3.290974e-04	k: 1031	n:3330000
Cons ci ratio: 2.027525e-03	ci left: 5.283262e-01	ci right 5.293987e-01	k: 1761112	n:3330000
KS ci ratio: 1.220053e-01	ci left: 2.909995e-04	ci right 3.290974e-04	k: 1031	n:3330000
SPG11   3330000 perm   4955 sec   (672 perm/sec)   p_kst 3.096096e-04   p_cons 5.288625e-01   p_joint 3.096096e-04

Joint ci ratio: 1.218873e-01	ci left: 2.907088e-04	ci right 3.287292e-04	k: 1033	n:3340000
Cons ci ratio: 2.024406e-03	ci left: 5.283471e-01	ci right 5.294181e-01	k: 1766468	n:3340000
KS ci ratio: 1.218873e-01	ci left: 2.907088e-04	ci right 3.287292e-04	k: 1033	n:3340000
SPG11   3340000 perm   4980 sec   (671 perm/sec)   p_kst 3.092814e-04   p_cons 5.288826e-01   p_joint 3.092814e-04

Joint ci ratio: 1.216522e-01	ci left: 2.909987e-04	ci right 3.289783e-04	k: 1037	n:3350000
Cons ci ratio: 2.021397e-03	ci left: 5.283441e-01	ci right 5.294135e-01	k: 1771744	n:3350000
KS ci ratio: 1.216522e-01	ci left: 2.909987e-04	ci right 3.289783e-04	k: 1037	n:3350000
SPG11   3350000 perm   5007 sec   (669 perm/sec)   p_kst 3.095522e-04   p_cons 5.288788e-01   p_joint 3.095522e-04

Joint ci ratio: 1.215937e-01	ci left: 2.904212e-04	ci right 3.283058e-04	k: 1038	n:3360000
Cons ci ratio: 2.018385e-03	ci left: 5.283456e-01	ci right 5.294133e-01	k: 1777035	n:3360000
KS ci ratio: 1.215937e-01	ci left: 2.904212e-04	ci right 3.283058e-04	k: 1038	n:3360000
SPG11   3360000 perm   5033 sec   (668 perm/sec)   p_kst 3.089286e-04   p_cons 5.288795e-01   p_joint 3.089286e-04

Joint ci ratio: 1.214185e-01	ci left: 2.904226e-04	ci right 3.282489e-04	k: 1041	n:3370000
Cons ci ratio: 2.015392e-03	ci left: 5.283452e-01	ci right 5.294114e-01	k: 1782320	n:3370000
KS ci ratio: 1.214185e-01	ci left: 2.904226e-04	ci right 3.282489e-04	k: 1041	n:3370000
SPG11   3370000 perm   5059 sec   (666 perm/sec)   p_kst 3.089021e-04   p_cons 5.288783e-01   p_joint 3.089021e-04

Joint ci ratio: 1.213022e-01	ci left: 2.901371e-04	ci right 3.278874e-04	k: 1043	n:3380000
Cons ci ratio: 2.012442e-03	ci left: 5.283378e-01	ci right 5.294024e-01	k: 1787581	n:3380000
KS ci ratio: 1.213022e-01	ci left: 2.901371e-04	ci right 3.278874e-04	k: 1043	n:3380000
SPG11   3380000 perm   5086 sec   (665 perm/sec)   p_kst 3.085799e-04   p_cons 5.288701e-01   p_joint 3.085799e-04

Joint ci ratio: 1.211283e-01	ci left: 2.901393e-04	ci right 3.278320e-04	k: 1046	n:3390000
Cons ci ratio: 2.009456e-03	ci left: 5.283425e-01	ci right 5.294055e-01	k: 1792883	n:3390000
KS ci ratio: 1.211283e-01	ci left: 2.901393e-04	ci right 3.278320e-04	k: 1046	n:3390000
SPG11   3390000 perm   5113 sec   (663 perm/sec)   p_kst 3.085546e-04   p_cons 5.288740e-01   p_joint 3.085546e-04

Joint ci ratio: 1.209551e-01	ci left: 2.901416e-04	ci right 3.277768e-04	k: 1049	n:3400000
Cons ci ratio: 2.006460e-03	ci left: 5.283528e-01	ci right 5.294142e-01	k: 1798204	n:3400000
KS ci ratio: 1.209551e-01	ci left: 2.901416e-04	ci right 3.277768e-04	k: 1049	n:3400000
SPG11   3400000 perm   5139 sec   (662 perm/sec)   p_kst 3.085294e-04   p_cons 5.288835e-01   p_joint 3.085294e-04

Joint ci ratio: 1.207827e-01	ci left: 2.901439e-04	ci right 3.277219e-04	k: 1052	n:3410000
Cons ci ratio: 2.003528e-03	ci left: 5.283507e-01	ci right 5.294106e-01	k: 1803483	n:3410000
KS ci ratio: 1.207827e-01	ci left: 2.901439e-04	ci right 3.277219e-04	k: 1052	n:3410000
SPG11   3410000 perm   5165 sec   (660 perm/sec)   p_kst 3.085044e-04   p_cons 5.288806e-01   p_joint 3.085044e-04

Joint ci ratio: 1.206110e-01	ci left: 2.901463e-04	ci right 3.276673e-04	k: 1055	n:3420000
Cons ci ratio: 2.000665e-03	ci left: 5.283342e-01	ci right 5.293926e-01	k: 1808713	n:3420000
KS ci ratio: 1.206110e-01	ci left: 2.901463e-04	ci right 3.276673e-04	k: 1055	n:3420000
SPG11   3420000 perm   5192 sec   (659 perm/sec)   p_kst 3.084795e-04   p_cons 5.288635e-01   p_joint 3.084795e-04

Joint ci ratio: 1.203832e-01	ci left: 2.904314e-04	ci right 3.279134e-04	k: 1059	n:3430000
Cons ci ratio: 1.997790e-03	ci left: 5.283243e-01	ci right 5.293811e-01	k: 1813965	n:3430000
KS ci ratio: 1.203832e-01	ci left: 2.904314e-04	ci right 3.279134e-04	k: 1059	n:3430000
SPG11   3430000 perm   5220 sec   (657 perm/sec)   p_kst 3.087464e-04   p_cons 5.288528e-01   p_joint 3.087464e-04

Joint ci ratio: 1.202698e-01	ci left: 2.901510e-04	ci right 3.275590e-04	k: 1061	n:3440000
Cons ci ratio: 1.994772e-03	ci left: 5.283532e-01	ci right 5.294084e-01	k: 1819350	n:3440000
KS ci ratio: 1.202698e-01	ci left: 2.901510e-04	ci right 3.275590e-04	k: 1061	n:3440000
SPG11   3440000 perm   5247 sec   (656 perm/sec)   p_kst 3.084302e-04   p_cons 5.288808e-01   p_joint 3.084302e-04

Joint ci ratio: 1.201568e-01	ci left: 2.898723e-04	ci right 3.272067e-04	k: 1063	n:3450000
Cons ci ratio: 1.991944e-03	ci left: 5.283375e-01	ci right 5.293912e-01	k: 1824582	n:3450000
KS ci ratio: 1.201568e-01	ci left: 2.898723e-04	ci right 3.272067e-04	k: 1063	n:3450000
SPG11   3450000 perm   5274 sec   (654 perm/sec)   p_kst 3.081159e-04   p_cons 5.288643e-01   p_joint 3.081159e-04

Joint ci ratio: 1.201568e-01	ci left: 2.890345e-04	ci right 3.262610e-04	k: 1063	n:3460000
Cons ci ratio: 1.989094e-03	ci left: 5.283305e-01	ci right 5.293827e-01	k: 1829844	n:3460000
KS ci ratio: 1.201568e-01	ci left: 2.890345e-04	ci right 3.262610e-04	k: 1063	n:3460000
SPG11   3460000 perm   5301 sec   (653 perm/sec)   p_kst 3.072254e-04   p_cons 5.288566e-01   p_joint 3.072254e-04

Joint ci ratio: 1.200441e-01	ci left: 2.887606e-04	ci right 3.259145e-04	k: 1065	n:3470000
Cons ci ratio: 1.986203e-03	ci left: 5.283372e-01	ci right 5.293879e-01	k: 1835153	n:3470000
KS ci ratio: 1.200441e-01	ci left: 2.887606e-04	ci right 3.259145e-04	k: 1065	n:3470000
SPG11   3470000 perm   5328 sec   (651 perm/sec)   p_kst 3.069164e-04   p_cons 5.288625e-01   p_joint 3.069164e-04

Joint ci ratio: 1.198755e-01	ci left: 2.887670e-04	ci right 3.258659e-04	k: 1068	n:3480000
Cons ci ratio: 1.983347e-03	ci left: 5.283380e-01	ci right 5.293872e-01	k: 1840442	n:3480000
KS ci ratio: 1.198755e-01	ci left: 2.887670e-04	ci right 3.258659e-04	k: 1068	n:3480000
SPG11   3480000 perm   5356 sec   (650 perm/sec)   p_kst 3.068966e-04   p_cons 5.288626e-01   p_joint 3.068966e-04

Joint ci ratio: 1.198195e-01	ci left: 2.882175e-04	ci right 3.252273e-04	k: 1069	n:3490000
Cons ci ratio: 1.980368e-03	ci left: 5.283727e-01	ci right 5.294204e-01	k: 1845849	n:3490000
KS ci ratio: 1.198195e-01	ci left: 2.882175e-04	ci right 3.252273e-04	k: 1069	n:3490000
SPG11   3490000 perm   5383 sec   (648 perm/sec)   p_kst 3.063037e-04   p_cons 5.288966e-01   p_joint 3.063037e-04

Joint ci ratio: 1.434100e-01	ci left: 1.981217e-04	ci right 2.290008e-04	k: 746	n:3500000
Cons ci ratio: 1.977670e-03	ci left: 5.283400e-01	ci right 5.293862e-01	k: 1851021	n:3500000
KS ci ratio: 1.197077e-01	ci left: 2.879484e-04	ci right 3.248866e-04	k: 1071	n:3500000
SPG11   3500000 perm   5409 sec   (647 perm/sec)   p_kst 3.060000e-04   p_cons 5.288631e-01   p_joint 2.131429e-04

Joint ci ratio: 1.431228e-01	ci left: 1.983813e-04	ci right 2.292337e-04	k: 749	n:3510000
Cons ci ratio: 1.974847e-03	ci left: 5.283417e-01	ci right 5.293864e-01	k: 1856313	n:3510000
KS ci ratio: 1.195406e-01	ci left: 2.879571e-04	ci right 3.248413e-04	k: 1074	n:3510000
SPG11   3510000 perm   5437 sec   (646 perm/sec)   p_kst 3.059829e-04   p_cons 5.288641e-01   p_joint 2.133903e-04

Joint ci ratio: 1.570376e-01	ci left: 1.630899e-04	ci right 1.911523e-04	k: 622	n:3520000
Cons ci ratio: 1.972046e-03	ci left: 5.283409e-01	ci right 5.293841e-01	k: 1861596	n:3520000
KS ci ratio: 1.194295e-01	ci left: 2.876903e-04	ci right 3.245036e-04	k: 1076	n:3520000
SPG11   3520000 perm   5464 sec   (644 perm/sec)   p_kst 3.056818e-04   p_cons 5.288625e-01   p_joint 1.767045e-04

Joint ci ratio: 1.570376e-01	ci left: 1.626279e-04	ci right 1.906107e-04	k: 622	n:3530000
Cons ci ratio: 1.969268e-03	ci left: 5.283372e-01	ci right 5.293789e-01	k: 1866869	n:3530000
KS ci ratio: 1.193742e-01	ci left: 2.871501e-04	ci right 3.238760e-04	k: 1077	n:3530000
SPG11   3530000 perm   5491 sec   (643 perm/sec)   p_kst 3.050992e-04   p_cons 5.288581e-01   p_joint 1.762040e-04

Joint ci ratio: 1.565358e-01	ci left: 1.632541e-04	ci right 1.912465e-04	k: 626	n:3540000
Cons ci ratio: 1.966472e-03	ci left: 5.283411e-01	ci right 5.293814e-01	k: 1872169	n:3540000
KS ci ratio: 1.190433e-01	ci left: 2.879833e-04	ci right 3.247066e-04	k: 1083	n:3540000
SPG11   3540000 perm   5519 sec   (641 perm/sec)   p_kst 3.059322e-04   p_cons 5.288613e-01   p_joint 1.768362e-04

Joint ci ratio: 1.561627e-01	ci left: 1.636062e-04	ci right 1.915859e-04	k: 629	n:3550000
Cons ci ratio: 1.963634e-03	ci left: 5.283586e-01	ci right 5.293974e-01	k: 1877517	n:3550000
KS ci ratio: 1.188242e-01	ci left: 2.882653e-04	ci right 3.249522e-04	k: 1087	n:3550000
SPG11   3550000 perm   5547 sec   (640 perm/sec)   p_kst 3.061972e-04   p_cons 5.288780e-01   p_joint 1.771831e-04

Joint ci ratio: 1.561627e-01	ci left: 1.631467e-04	ci right 1.910478e-04	k: 629	n:3560000
Cons ci ratio: 1.960835e-03	ci left: 5.283695e-01	ci right 5.294068e-01	k: 1882842	n:3560000
KS ci ratio: 1.187697e-01	ci left: 2.877282e-04	ci right 3.243286e-04	k: 1088	n:3560000
SPG11   3560000 perm   5575 sec   (639 perm/sec)   p_kst 3.056180e-04   p_cons 5.288882e-01   p_joint 1.766854e-04

Joint ci ratio: 1.557922e-01	ci left: 1.634972e-04	ci right 1.913857e-04	k: 632	n:3570000
Cons ci ratio: 1.958058e-03	ci left: 5.283776e-01	ci right 5.294134e-01	k: 1888157	n:3570000
KS ci ratio: 1.186064e-01	ci left: 2.877376e-04	ci right 3.242854e-04	k: 1091	n:3570000
SPG11   3570000 perm   5603 sec   (637 perm/sec)   p_kst 3.056022e-04   p_cons 5.288955e-01   p_joint 1.770308e-04

Joint ci ratio: 1.557922e-01	ci left: 1.630405e-04	ci right 1.908511e-04	k: 632	n:3580000
Cons ci ratio: 1.955230e-03	ci left: 5.284015e-01	ci right 5.294359e-01	k: 1893529	n:3580000
KS ci ratio: 1.184980e-01	ci left: 2.874759e-04	ci right 3.239548e-04	k: 1093	n:3580000
SPG11   3580000 perm   5632 sec   (636 perm/sec)   p_kst 3.053073e-04   p_cons 5.289187e-01   p_joint 1.765363e-04

Joint ci ratio: 1.181743e-01	ci left: 2.882970e-04	ci right 3.247732e-04	k: 1099	n:3590000
Cons ci ratio: 1.952555e-03	ci left: 5.283893e-01	ci right 5.294223e-01	k: 1898772	n:3590000
KS ci ratio: 1.181743e-01	ci left: 2.882970e-04	ci right 3.247732e-04	k: 1099	n:3590000
SPG11   3590000 perm   5660 sec   (634 perm/sec)   p_kst 3.061281e-04   p_cons 5.289058e-01   p_joint 3.061281e-04

Joint ci ratio: 1.181744e-01	ci left: 2.874962e-04	ci right 3.238710e-04	k: 1099	n:3600000
Cons ci ratio: 1.949839e-03	ci left: 5.283906e-01	ci right 5.294221e-01	k: 1904063	n:3600000
KS ci ratio: 1.181744e-01	ci left: 2.874962e-04	ci right 3.238710e-04	k: 1099	n:3600000
SPG11   3600000 perm   5688 sec   (633 perm/sec)   p_kst 3.052778e-04   p_cons 5.289064e-01   p_joint 3.052778e-04

Joint ci ratio: 1.177469e-01	ci left: 2.888505e-04	ci right 3.252553e-04	k: 1107	n:3610000
Cons ci ratio: 1.947141e-03	ci left: 5.283902e-01	ci right 5.294203e-01	k: 1909348	n:3610000
KS ci ratio: 1.177469e-01	ci left: 2.888505e-04	ci right 3.252553e-04	k: 1107	n:3610000
SPG11   3610000 perm   5717 sec   (631 perm/sec)   p_kst 3.066482e-04   p_cons 5.289053e-01   p_joint 3.066482e-04

Joint ci ratio: 1.175878e-01	ci left: 2.888569e-04	ci right 3.252099e-04	k: 1110	n:3620000
Cons ci ratio: 1.944457e-03	ci left: 5.283892e-01	ci right 5.294179e-01	k: 1914631	n:3620000
KS ci ratio: 1.175878e-01	ci left: 2.888569e-04	ci right 3.252099e-04	k: 1110	n:3620000
SPG11   3620000 perm   5745 sec   (630 perm/sec)   p_kst 3.066298e-04   p_cons 5.289036e-01   p_joint 3.066298e-04

Joint ci ratio: 1.173241e-01	ci left: 2.893981e-04	ci right 3.257319e-04	k: 1115	n:3630000
Cons ci ratio: 1.941771e-03	ci left: 5.283913e-01	ci right 5.294186e-01	k: 1919925	n:3630000
KS ci ratio: 1.173241e-01	ci left: 2.893981e-04	ci right 3.257319e-04	k: 1115	n:3630000
SPG11   3630000 perm   5774 sec   (629 perm/sec)   p_kst 3.071625e-04   p_cons 5.289050e-01   p_joint 3.071625e-04

Joint ci ratio: 1.171667e-01	ci left: 2.894030e-04	ci right 3.256853e-04	k: 1118	n:3640000
Cons ci ratio: 1.939054e-03	ci left: 5.284044e-01	ci right 5.294302e-01	k: 1925259	n:3640000
KS ci ratio: 1.171667e-01	ci left: 2.894030e-04	ci right 3.256853e-04	k: 1118	n:3640000
SPG11   3640000 perm   5803 sec   (627 perm/sec)   p_kst 3.071429e-04   p_cons 5.289173e-01   p_joint 3.071429e-04

Joint ci ratio: 1.170100e-01	ci left: 2.894080e-04	ci right 3.256390e-04	k: 1121	n:3650000
Cons ci ratio: 1.936382e-03	ci left: 5.284086e-01	ci right 5.294330e-01	k: 1930561	n:3650000
KS ci ratio: 1.170100e-01	ci left: 2.894080e-04	ci right 3.256390e-04	k: 1121	n:3650000
SPG11   3650000 perm   5832 sec   (626 perm/sec)   p_kst 3.071233e-04   p_cons 5.289208e-01   p_joint 3.071233e-04

Joint ci ratio: 1.168538e-01	ci left: 2.894130e-04	ci right 3.255929e-04	k: 1124	n:3660000
Cons ci ratio: 1.933754e-03	ci left: 5.284043e-01	ci right 5.294273e-01	k: 1935832	n:3660000
KS ci ratio: 1.168538e-01	ci left: 2.894130e-04	ci right 3.255929e-04	k: 1124	n:3660000
SPG11   3660000 perm   5862 sec   (624 perm/sec)   p_kst 3.071038e-04   p_cons 5.289158e-01   p_joint 3.071038e-04

Joint ci ratio: 1.168020e-01	ci left: 2.888889e-04	ci right 3.249862e-04	k: 1125	n:3670000
Cons ci ratio: 1.931074e-03	ci left: 5.284164e-01	ci right 5.294381e-01	k: 1941163	n:3670000
KS ci ratio: 1.168020e-01	ci left: 2.888889e-04	ci right 3.249862e-04	k: 1125	n:3670000
SPG11   3670000 perm   5890 sec   (623 perm/sec)   p_kst 3.065395e-04   p_cons 5.289272e-01   p_joint 3.065395e-04

Joint ci ratio: 1.166984e-01	ci left: 2.886315e-04	ci right 3.246624e-04	k: 1127	n:3680000
Cons ci ratio: 1.928387e-03	ci left: 5.284331e-01	ci right 5.294533e-01	k: 1946511	n:3680000
KS ci ratio: 1.166984e-01	ci left: 2.886315e-04	ci right 3.246624e-04	k: 1127	n:3680000
SPG11   3680000 perm   5919 sec   (622 perm/sec)   p_kst 3.062500e-04   p_cons 5.289432e-01   p_joint 3.062500e-04

Joint ci ratio: 1.166467e-01	ci left: 2.881124e-04	ci right 3.240615e-04	k: 1128	n:3690000
Cons ci ratio: 1.925903e-03	ci left: 5.283998e-01	ci right 5.294186e-01	k: 1951675	n:3690000
KS ci ratio: 1.166467e-01	ci left: 2.881124e-04	ci right 3.240615e-04	k: 1128	n:3690000
SPG11   3690000 perm   5948 sec   (620 perm/sec)   p_kst 3.056911e-04   p_cons 5.289092e-01   p_joint 3.056911e-04

Joint ci ratio: 1.535055e-01	ci left: 1.626891e-04	ci right 1.899950e-04	k: 651	n:3700000
Cons ci ratio: 1.923382e-03	ci left: 5.283788e-01	ci right 5.293963e-01	k: 1956884	n:3700000
KS ci ratio: 1.164406e-01	ci left: 2.883833e-04	ci right 3.242982e-04	k: 1132	n:3700000
SPG11   3700000 perm   5977 sec   (619 perm/sec)   p_kst 3.059459e-04   p_cons 5.288876e-01   p_joint 1.759459e-04

Joint ci ratio: 1.533879e-01	ci left: 1.625098e-04	ci right 1.897628e-04	k: 652	n:3710000
Cons ci ratio: 1.920809e-03	ci left: 5.283741e-01	ci right 5.293903e-01	k: 1962153	n:3710000
KS ci ratio: 1.163893e-01	ci left: 2.878676e-04	ci right 3.237015e-04	k: 1133	n:3710000
SPG11   3710000 perm   6006 sec   (618 perm/sec)   p_kst 3.053908e-04   p_cons 5.288822e-01   p_joint 1.757412e-04

Joint ci ratio: 1.532706e-01	ci left: 1.623315e-04	ci right 1.895318e-04	k: 653	n:3720000
Cons ci ratio: 1.918242e-03	ci left: 5.283706e-01	ci right 5.293853e-01	k: 1967426	n:3720000
KS ci ratio: 1.163381e-01	ci left: 2.873548e-04	ci right 3.231080e-04	k: 1134	n:3720000
SPG11   3720000 perm   6034 sec   (616 perm/sec)   p_kst 3.048387e-04   p_cons 5.288780e-01   p_joint 1.755376e-04

Joint ci ratio: 1.526880e-01	ci left: 1.631854e-04	ci right 1.904154e-04	k: 658	n:3730000
Cons ci ratio: 1.915752e-03	ci left: 5.283496e-01	ci right 5.293630e-01	k: 1972634	n:3730000
KS ci ratio: 1.159809e-01	ci left: 2.884065e-04	ci right 3.241729e-04	k: 1141	n:3730000
SPG11   3730000 perm   6064 sec   (615 perm/sec)   p_kst 3.058981e-04   p_cons 5.288563e-01   p_joint 1.764075e-04

Joint ci ratio: 1.158795e-01	ci left: 2.881547e-04	ci right 3.238564e-04	k: 1143	n:3740000
Cons ci ratio: 1.913163e-03	ci left: 5.283571e-01	ci right 5.293691e-01	k: 1977948	n:3740000
KS ci ratio: 1.158795e-01	ci left: 2.881547e-04	ci right 3.238564e-04	k: 1143	n:3740000
SPG11   3740000 perm   6094 sec   (614 perm/sec)   p_kst 3.056150e-04   p_cons 5.288631e-01   p_joint 3.056150e-04

Joint ci ratio: 1.157783e-01	ci left: 2.879041e-04	ci right 3.235416e-04	k: 1145	n:3750000
Cons ci ratio: 1.910577e-03	ci left: 5.283666e-01	ci right 5.293773e-01	k: 1983270	n:3750000
KS ci ratio: 1.157783e-01	ci left: 2.879041e-04	ci right 3.235416e-04	k: 1145	n:3750000
SPG11   3750000 perm   6123 sec   (612 perm/sec)   p_kst 3.053333e-04   p_cons 5.288720e-01   p_joint 3.053333e-04

Joint ci ratio: 1.156271e-01	ci left: 2.879132e-04	ci right 3.235020e-04	k: 1148	n:3760000
Cons ci ratio: 1.908121e-03	ci left: 5.283445e-01	ci right 5.293539e-01	k: 1988473	n:3760000
KS ci ratio: 1.156271e-01	ci left: 2.879132e-04	ci right 3.235020e-04	k: 1148	n:3760000
SPG11   3760000 perm   6153 sec   (611 perm/sec)   p_kst 3.053191e-04   p_cons 5.288492e-01   p_joint 3.053191e-04

Joint ci ratio: 1.155768e-01	ci left: 2.874071e-04	ci right 3.229169e-04	k: 1149	n:3770000
Cons ci ratio: 1.905510e-03	ci left: 5.283660e-01	ci right 5.293740e-01	k: 1993840	n:3770000
KS ci ratio: 1.155768e-01	ci left: 2.874071e-04	ci right 3.229169e-04	k: 1149	n:3770000
SPG11   3770000 perm   6182 sec   (610 perm/sec)   p_kst 3.047745e-04   p_cons 5.288700e-01   p_joint 3.047745e-04

Joint ci ratio: 1.155267e-01	ci left: 2.869037e-04	ci right 3.223348e-04	k: 1150	n:3780000
Cons ci ratio: 1.902967e-03	ci left: 5.283720e-01	ci right 5.293787e-01	k: 1999149	n:3780000
KS ci ratio: 1.155267e-01	ci left: 2.869037e-04	ci right 3.223348e-04	k: 1150	n:3780000
SPG11   3780000 perm   6212 sec   (609 perm/sec)   p_kst 3.042328e-04   p_cons 5.288754e-01   p_joint 3.042328e-04

Joint ci ratio: 1.154765e-01	ci left: 2.864029e-04	ci right 3.217558e-04	k: 1151	n:3790000
Cons ci ratio: 1.900455e-03	ci left: 5.283725e-01	ci right 5.293779e-01	k: 2004437	n:3790000
KS ci ratio: 1.154765e-01	ci left: 2.864029e-04	ci right 3.217558e-04	k: 1151	n:3790000
SPG11   3790000 perm   6241 sec   (607 perm/sec)   p_kst 3.036939e-04   p_cons 5.288752e-01   p_joint 3.036939e-04

Joint ci ratio: 1.382331e-01	ci left: 1.969522e-04	ci right 2.264498e-04	k: 803	n:3800000
Cons ci ratio: 1.898001e-03	ci left: 5.283606e-01	ci right 5.293646e-01	k: 2009678	n:3800000
KS ci ratio: 1.154265e-01	ci left: 2.859047e-04	ci right 3.211798e-04	k: 1152	n:3800000
SPG11   3800000 perm   6271 sec   (606 perm/sec)   p_kst 3.031579e-04   p_cons 5.288626e-01   p_joint 2.113158e-04

Joint ci ratio: 1.382331e-01	ci left: 1.964353e-04	ci right 2.258554e-04	k: 803	n:3810000
Cons ci ratio: 1.895618e-03	ci left: 5.283325e-01	ci right 5.293352e-01	k: 2014857	n:3810000
KS ci ratio: 1.153265e-01	ci left: 2.856641e-04	ci right 3.208769e-04	k: 1154	n:3810000
SPG11   3810000 perm   6300 sec   (605 perm/sec)   p_kst 3.028871e-04   p_cons 5.288339e-01   p_joint 2.107612e-04

Joint ci ratio: 1.382332e-01	ci left: 1.959210e-04	ci right 2.252642e-04	k: 803	n:3820000
Cons ci ratio: 1.893136e-03	ci left: 5.283330e-01	ci right 5.293344e-01	k: 2020145	n:3820000
KS ci ratio: 1.152767e-01	ci left: 2.851705e-04	ci right 3.203062e-04	k: 1155	n:3820000
SPG11   3820000 perm   6329 sec   (604 perm/sec)   p_kst 3.023560e-04   p_cons 5.288338e-01   p_joint 2.102094e-04

Joint ci ratio: 1.381473e-01	ci left: 1.956616e-04	ci right 2.249461e-04	k: 804	n:3830000
Cons ci ratio: 1.890705e-03	ci left: 5.283224e-01	ci right 5.293225e-01	k: 2025390	n:3830000
KS ci ratio: 1.151771e-01	ci left: 2.849331e-04	ci right 3.200072e-04	k: 1157	n:3830000
SPG11   3830000 perm   6359 sec   (602 perm/sec)   p_kst 3.020888e-04   p_cons 5.288225e-01   p_joint 2.099217e-04

Joint ci ratio: 1.378906e-01	ci left: 1.959063e-04	ci right 2.251685e-04	k: 807	n:3840000
Cons ci ratio: 1.888281e-03	ci left: 5.283128e-01	ci right 5.293116e-01	k: 2030639	n:3840000
KS ci ratio: 1.150282e-01	ci left: 2.849498e-04	ci right 3.199775e-04	k: 1160	n:3840000
SPG11   3840000 perm   6388 sec   (601 perm/sec)   p_kst 3.020833e-04   p_cons 5.288122e-01   p_joint 2.101563e-04

Joint ci ratio: 1.375505e-01	ci left: 1.964006e-04	ci right 2.256584e-04	k: 811	n:3850000
Cons ci ratio: 1.885888e-03	ci left: 5.282973e-01	ci right 5.292948e-01	k: 2035865	n:3850000
KS ci ratio: 1.147813e-01	ci left: 2.854711e-04	ci right 3.204824e-04	k: 1165	n:3850000
SPG11   3850000 perm   6417 sec   (600 perm/sec)   p_kst 3.025974e-04   p_cons 5.287961e-01   p_joint 2.106494e-04

Joint ci ratio: 1.372971e-01	ci left: 1.966423e-04	ci right 2.258777e-04	k: 814	n:3860000
Cons ci ratio: 1.883432e-03	ci left: 5.283011e-01	ci right 5.292973e-01	k: 2041165	n:3860000
KS ci ratio: 1.146339e-01	ci left: 2.854864e-04	ci right 3.204517e-04	k: 1168	n:3860000
SPG11   3860000 perm   6447 sec   (599 perm/sec)   p_kst 3.025907e-04   p_cons 5.287992e-01   p_joint 2.108808e-04

Joint ci ratio: 1.368778e-01	ci left: 1.973819e-04	ci right 2.266303e-04	k: 819	n:3870000
Cons ci ratio: 1.880956e-03	ci left: 5.283126e-01	ci right 5.293075e-01	k: 2046495	n:3870000
KS ci ratio: 1.141950e-01	ci left: 2.870078e-04	ci right 3.220157e-04	k: 1177	n:3870000
SPG11   3870000 perm   6477 sec   (597 perm/sec)   p_kst 3.041344e-04   p_cons 5.288101e-01   p_joint 2.116279e-04

Joint ci ratio: 1.368779e-01	ci left: 1.968731e-04	ci right 2.260462e-04	k: 819	n:3880000
Cons ci ratio: 1.878616e-03	ci left: 5.282905e-01	ci right 5.292842e-01	k: 2051695	n:3880000
KS ci ratio: 1.141951e-01	ci left: 2.862681e-04	ci right 3.211858e-04	k: 1177	n:3880000
SPG11   3880000 perm   6507 sec   (596 perm/sec)   p_kst 3.033505e-04   p_cons 5.287874e-01   p_joint 2.110825e-04

Joint ci ratio: 1.367945e-01	ci left: 1.966153e-04	ci right 2.257310e-04	k: 820	n:3890000
Cons ci ratio: 1.876200e-03	ci left: 5.282910e-01	ci right 5.292833e-01	k: 2056982	n:3890000
KS ci ratio: 1.140983e-01	ci left: 2.860316e-04	ci right 3.208889e-04	k: 1179	n:3890000
SPG11   3890000 perm   6537 sec   (595 perm/sec)   p_kst 3.030848e-04   p_cons 5.287871e-01   p_joint 2.107969e-04

Joint ci ratio: 1.367113e-01	ci left: 1.963588e-04	ci right 2.254174e-04	k: 821	n:3900000
Cons ci ratio: 1.873785e-03	ci left: 5.282939e-01	ci right 5.292850e-01	k: 2062279	n:3900000
KS ci ratio: 1.140017e-01	ci left: 2.857964e-04	ci right 3.205936e-04	k: 1181	n:3900000
SPG11   3900000 perm   6568 sec   (594 perm/sec)   p_kst 3.028205e-04   p_cons 5.287895e-01   p_joint 2.105128e-04

Joint ci ratio: 1.363798e-01	ci left: 1.968447e-04	ci right 2.258988e-04	k: 825	n:3910000
Cons ci ratio: 1.871404e-03	ci left: 5.282900e-01	ci right 5.292798e-01	k: 2067549	n:3910000
KS ci ratio: 1.137613e-01	ci left: 2.863078e-04	ci right 3.210888e-04	k: 1186	n:3910000
SPG11   3910000 perm   6598 sec   (593 perm/sec)   p_kst 3.033248e-04   p_cons 5.287849e-01   p_joint 2.109974e-04

Joint ci ratio: 1.361328e-01	ci left: 1.970818e-04	ci right 2.261139e-04	k: 828	n:3920000
Cons ci ratio: 1.869049e-03	ci left: 5.282817e-01	ci right 5.292703e-01	k: 2072802	n:3920000
KS ci ratio: 1.134749e-01	ci left: 2.870646e-04	ci right 3.218438e-04	k: 1192	n:3920000
SPG11   3920000 perm   6628 sec   (591 perm/sec)   p_kst 3.040816e-04   p_cons 5.287760e-01   p_joint 2.112245e-04

Joint ci ratio: 1.358871e-01	ci left: 1.973177e-04	ci right 2.263279e-04	k: 831	n:3930000
Cons ci ratio: 1.866713e-03	ci left: 5.282707e-01	ci right 5.292580e-01	k: 2078044	n:3930000
KS ci ratio: 1.132378e-01	ci left: 2.875703e-04	ci right 3.223332e-04	k: 1197	n:3930000
SPG11   3930000 perm   6658 sec   (590 perm/sec)   p_kst 3.045802e-04   p_cons 5.287644e-01   p_joint 2.114504e-04

Joint ci ratio: 1.357241e-01	ci left: 1.973072e-04	ci right 2.262783e-04	k: 833	n:3940000
Cons ci ratio: 1.864349e-03	ci left: 5.282697e-01	ci right 5.292557e-01	k: 2083325	n:3940000
KS ci ratio: 1.130492e-01	ci left: 2.878269e-04	ci right 3.225590e-04	k: 1201	n:3940000
SPG11   3940000 perm   6688 sec   (589 perm/sec)   p_kst 3.048223e-04   p_cons 5.287627e-01   p_joint 2.114213e-04

Joint ci ratio: 1.354806e-01	ci left: 1.975414e-04	ci right 2.264907e-04	k: 836	n:3950000
Cons ci ratio: 1.861986e-03	ci left: 5.282706e-01	ci right 5.292554e-01	k: 2088614	n:3950000
KS ci ratio: 1.128148e-01	ci left: 2.883283e-04	ci right 3.230440e-04	k: 1206	n:3950000
SPG11   3950000 perm   6718 sec   (588 perm/sec)   p_kst 3.053165e-04   p_cons 5.287630e-01   p_joint 2.116456e-04

Joint ci ratio: 1.353998e-01	ci left: 1.972866e-04	ci right 2.261798e-04	k: 837	n:3960000
Cons ci ratio: 1.859705e-03	ci left: 5.282521e-01	ci right 5.292357e-01	k: 2093826	n:3960000
KS ci ratio: 1.127681e-01	ci left: 2.878456e-04	ci right 3.224879e-04	k: 1207	n:3960000
SPG11   3960000 perm   6749 sec   (587 perm/sec)   p_kst 3.047980e-04   p_cons 5.287439e-01   p_joint 2.113636e-04

Joint ci ratio: 1.125819e-01	ci left: 2.880997e-04	ci right 3.227115e-04	k: 1211	n:3970000
Cons ci ratio: 1.857355e-03	ci left: 5.282544e-01	ci right 5.292367e-01	k: 2099120	n:3970000
KS ci ratio: 1.125819e-01	ci left: 2.880997e-04	ci right 3.227115e-04	k: 1211	n:3970000
SPG11   3970000 perm   6779 sec   (586 perm/sec)   p_kst 3.050378e-04   p_cons 5.287456e-01   p_joint 3.050378e-04

Joint ci ratio: 1.123965e-01	ci left: 2.883526e-04	ci right 3.229339e-04	k: 1215	n:3980000
Cons ci ratio: 1.854970e-03	ci left: 5.282685e-01	ci right 5.292496e-01	k: 2104461	n:3980000
KS ci ratio: 1.123965e-01	ci left: 2.883526e-04	ci right 3.229339e-04	k: 1215	n:3980000
SPG11   3980000 perm   6810 sec   (584 perm/sec)   p_kst 3.052764e-04   p_cons 5.287590e-01   p_joint 3.052764e-04

Joint ci ratio: 1.123042e-01	ci left: 2.881171e-04	ci right 3.226399e-04	k: 1217	n:3990000
Cons ci ratio: 1.852617e-03	ci left: 5.282765e-01	ci right 5.292563e-01	k: 2109778	n:3990000
KS ci ratio: 1.123042e-01	ci left: 2.881171e-04	ci right 3.226399e-04	k: 1217	n:3990000
SPG11   3990000 perm   6840 sec   (583 perm/sec)   p_kst 3.050125e-04   p_cons 5.287664e-01   p_joint 3.050125e-04

Joint ci ratio: 1.119828e-01	ci left: 2.890977e-04	ci right 3.236324e-04	k: 1224	n:4000000
Cons ci ratio: 1.850244e-03	ci left: 5.282922e-01	ci right 5.292708e-01	k: 2115126	n:4000000
KS ci ratio: 1.119828e-01	ci left: 2.890977e-04	ci right 3.236324e-04	k: 1224	n:4000000
SPG11   4000000 perm   6871 sec   (582 perm/sec)   p_kst 3.060000e-04   p_cons 5.287815e-01   p_joint 3.060000e-04

Joint ci ratio: 1.118460e-01	ci left: 2.891040e-04	ci right 3.235944e-04	k: 1227	n:4010000
Cons ci ratio: 1.847881e-03	ci left: 5.283075e-01	ci right 5.292849e-01	k: 2120473	n:4010000
KS ci ratio: 1.118460e-01	ci left: 2.891040e-04	ci right 3.235944e-04	k: 1227	n:4010000
SPG11   4010000 perm   6902 sec   (581 perm/sec)   p_kst 3.059850e-04   p_cons 5.287963e-01   p_joint 3.059850e-04

Joint ci ratio: 1.116189e-01	ci left: 2.895938e-04	ci right 3.240679e-04	k: 1232	n:4020000
Cons ci ratio: 1.845600e-03	ci left: 5.283029e-01	ci right 5.292791e-01	k: 2125740	n:4020000
KS ci ratio: 1.116189e-01	ci left: 2.895938e-04	ci right 3.240679e-04	k: 1232	n:4020000
SPG11   4020000 perm   6932 sec   (580 perm/sec)   p_kst 3.064677e-04   p_cons 5.287910e-01   p_joint 3.064677e-04

Joint ci ratio: 1.114834e-01	ci left: 2.895989e-04	ci right 3.240290e-04	k: 1235	n:4030000
Cons ci ratio: 1.843317e-03	ci left: 5.283013e-01	ci right 5.292763e-01	k: 2131019	n:4030000
KS ci ratio: 1.114834e-01	ci left: 2.895989e-04	ci right 3.240290e-04	k: 1235	n:4030000
SPG11   4030000 perm   6963 sec   (579 perm/sec)   p_kst 3.064516e-04   p_cons 5.287888e-01   p_joint 3.064516e-04

Joint ci ratio: 1.113483e-01	ci left: 2.896039e-04	ci right 3.239902e-04	k: 1238	n:4040000
Cons ci ratio: 1.840914e-03	ci left: 5.283346e-01	ci right 5.293084e-01	k: 2136439	n:4040000
KS ci ratio: 1.113483e-01	ci left: 2.896039e-04	ci right 3.239902e-04	k: 1238	n:4040000
SPG11   4040000 perm   6994 sec   (578 perm/sec)   p_kst 3.064356e-04   p_cons 5.288215e-01   p_joint 3.064356e-04

Joint ci ratio: 1.113035e-01	ci left: 2.891289e-04	ci right 3.234440e-04	k: 1239	n:4050000
Cons ci ratio: 1.838618e-03	ci left: 5.283411e-01	ci right 5.293137e-01	k: 2141751	n:4050000
KS ci ratio: 1.113035e-01	ci left: 2.891289e-04	ci right 3.234440e-04	k: 1239	n:4050000
SPG11   4050000 perm   7025 sec   (576 perm/sec)   p_kst 3.059259e-04   p_cons 5.288274e-01   p_joint 3.059259e-04

Joint ci ratio: 1.111691e-01	ci left: 2.891351e-04	ci right 3.234068e-04	k: 1242	n:4060000
Cons ci ratio: 1.836345e-03	ci left: 5.283436e-01	ci right 5.293150e-01	k: 2147047	n:4060000
KS ci ratio: 1.111691e-01	ci left: 2.891351e-04	ci right 3.234068e-04	k: 1242	n:4060000
SPG11   4060000 perm   7057 sec   (575 perm/sec)   p_kst 3.059113e-04   p_cons 5.288293e-01   p_joint 3.059113e-04

Joint ci ratio: 1.109017e-01	ci left: 2.898580e-04	ci right 3.241273e-04	k: 1248	n:4070000
Cons ci ratio: 1.834078e-03	ci left: 5.283468e-01	ci right 5.293170e-01	k: 2152346	n:4070000
KS ci ratio: 1.109017e-01	ci left: 2.898580e-04	ci right 3.241273e-04	k: 1248	n:4070000
SPG11   4070000 perm   7088 sec   (574 perm/sec)   p_kst 3.066339e-04   p_cons 5.288319e-01   p_joint 3.066339e-04

Joint ci ratio: 1.108130e-01	ci left: 2.896241e-04	ci right 3.238367e-04	k: 1250	n:4080000
Cons ci ratio: 1.831842e-03	ci left: 5.283439e-01	ci right 5.293129e-01	k: 2157620	n:4080000
KS ci ratio: 1.108130e-01	ci left: 2.896241e-04	ci right 3.238367e-04	k: 1250	n:4080000
SPG11   4080000 perm   7119 sec   (573 perm/sec)   p_kst 3.063725e-04   p_cons 5.288284e-01   p_joint 3.063725e-04

Joint ci ratio: 1.106804e-01	ci left: 2.896292e-04	ci right 3.237987e-04	k: 1253	n:4090000
Cons ci ratio: 1.829582e-03	ci left: 5.283498e-01	ci right 5.293176e-01	k: 2162930	n:4090000
KS ci ratio: 1.106804e-01	ci left: 2.896292e-04	ci right 3.237987e-04	k: 1253	n:4090000
SPG11   4090000 perm   7151 sec   (572 perm/sec)   p_kst 3.063570e-04   p_cons 5.288337e-01   p_joint 3.063570e-04

Joint ci ratio: 1.105043e-01	ci left: 2.898714e-04	ci right 3.240115e-04	k: 1257	n:4100000
Cons ci ratio: 1.827352e-03	ci left: 5.283496e-01	ci right 5.293162e-01	k: 2168215	n:4100000
KS ci ratio: 1.105043e-01	ci left: 2.898714e-04	ci right 3.240115e-04	k: 1257	n:4100000
SPG11   4100000 perm   7182 sec   (571 perm/sec)   p_kst 3.065854e-04   p_cons 5.288329e-01   p_joint 3.065854e-04

Joint ci ratio: 1.103727e-01	ci left: 2.898759e-04	ci right 3.239733e-04	k: 1260	n:4110000
Cons ci ratio: 1.825079e-03	ci left: 5.283635e-01	ci right 5.293289e-01	k: 2173558	n:4110000
KS ci ratio: 1.103727e-01	ci left: 2.898759e-04	ci right 3.239733e-04	k: 1260	n:4110000
SPG11   4110000 perm   7214 sec   (570 perm/sec)   p_kst 3.065693e-04   p_cons 5.288462e-01   p_joint 3.065693e-04

Joint ci ratio: 1.101981e-01	ci left: 2.901164e-04	ci right 3.241846e-04	k: 1264	n:4120000
Cons ci ratio: 1.822921e-03	ci left: 5.283482e-01	ci right 5.293124e-01	k: 2178781	n:4120000
KS ci ratio: 1.101981e-01	ci left: 2.901164e-04	ci right 3.241846e-04	k: 1264	n:4120000
SPG11   4120000 perm   7245 sec   (569 perm/sec)   p_kst 3.067961e-04   p_cons 5.288303e-01   p_joint 3.067961e-04

Joint ci ratio: 1.101111e-01	ci left: 2.898849e-04	ci right 3.238972e-04	k: 1266	n:4130000
Cons ci ratio: 1.820730e-03	ci left: 5.283441e-01	ci right 5.293072e-01	k: 2184050	n:4130000
KS ci ratio: 1.101111e-01	ci left: 2.898849e-04	ci right 3.238972e-04	k: 1266	n:4130000
SPG11   4130000 perm   7277 sec   (568 perm/sec)   p_kst 3.065375e-04   p_cons 5.288257e-01   p_joint 3.065375e-04

Joint ci ratio: 1.101111e-01	ci left: 2.891847e-04	ci right 3.231149e-04	k: 1266	n:4140000
Cons ci ratio: 1.818607e-03	ci left: 5.283234e-01	ci right 5.292853e-01	k: 2189250	n:4140000
KS ci ratio: 1.101111e-01	ci left: 2.891847e-04	ci right 3.231149e-04	k: 1266	n:4140000
SPG11   4140000 perm   7308 sec   (566 perm/sec)   p_kst 3.057971e-04   p_cons 5.288043e-01   p_joint 3.057971e-04

Joint ci ratio: 1.100243e-01	ci left: 2.889565e-04	ci right 3.228315e-04	k: 1268	n:4150000
Cons ci ratio: 1.816359e-03	ci left: 5.283394e-01	ci right 5.293001e-01	k: 2194602	n:4150000
KS ci ratio: 1.100243e-01	ci left: 2.889565e-04	ci right 3.228315e-04	k: 1268	n:4150000
SPG11   4150000 perm   7340 sec   (565 perm/sec)   p_kst 3.055422e-04   p_cons 5.288198e-01   p_joint 3.055422e-04

Joint ci ratio: 1.098082e-01	ci left: 2.894308e-04	ci right 3.232904e-04	k: 1273	n:4160000
Cons ci ratio: 1.814257e-03	ci left: 5.283173e-01	ci right 5.292769e-01	k: 2199796	n:4160000
KS ci ratio: 1.098082e-01	ci left: 2.894308e-04	ci right 3.232904e-04	k: 1273	n:4160000
SPG11   4160000 perm   7372 sec   (564 perm/sec)   p_kst 3.060096e-04   p_cons 5.287971e-01   p_joint 3.060096e-04

Joint ci ratio: 1.097652e-01	ci left: 2.889699e-04	ci right 3.227615e-04	k: 1274	n:4170000
Cons ci ratio: 1.812050e-03	ci left: 5.283260e-01	ci right 5.292845e-01	k: 2205118	n:4170000
KS ci ratio: 1.097652e-01	ci left: 2.889699e-04	ci right 3.227615e-04	k: 1274	n:4170000
SPG11   4170000 perm   7407 sec   (563 perm/sec)   p_kst 3.055156e-04   p_cons 5.288053e-01   p_joint 3.055156e-04

Joint ci ratio: 1.096792e-01	ci left: 2.887439e-04	ci right 3.224809e-04	k: 1276	n:4180000
Cons ci ratio: 1.809893e-03	ci left: 5.283235e-01	ci right 5.292808e-01	k: 2210393	n:4180000
KS ci ratio: 1.096792e-01	ci left: 2.887439e-04	ci right 3.224809e-04	k: 1276	n:4180000
SPG11   4180000 perm   7439 sec   (562 perm/sec)   p_kst 3.052632e-04   p_cons 5.288022e-01   p_joint 3.052632e-04

Joint ci ratio: 1.094224e-01	ci left: 2.894475e-04	ci right 3.231825e-04	k: 1282	n:4190000
Cons ci ratio: 1.807799e-03	ci left: 5.283054e-01	ci right 5.292616e-01	k: 2215603	n:4190000
KS ci ratio: 1.094224e-01	ci left: 2.894475e-04	ci right 3.231825e-04	k: 1282	n:4190000
SPG11   4190000 perm   7471 sec   (561 perm/sec)   p_kst 3.059666e-04   p_cons 5.287835e-01   p_joint 3.059666e-04

Joint ci ratio: 1.094224e-01	ci left: 2.887584e-04	ci right 3.224130e-04	k: 1282	n:4200000
Cons ci ratio: 1.805545e-03	ci left: 5.283339e-01	ci right 5.292889e-01	k: 2221008	n:4200000
KS ci ratio: 1.094224e-01	ci left: 2.887584e-04	ci right 3.224130e-04	k: 1282	n:4200000
SPG11   4200000 perm   7506 sec   (560 perm/sec)   p_kst 3.052381e-04   p_cons 5.288114e-01   p_joint 3.052381e-04

Joint ci ratio: 1.091674e-01	ci left: 2.894587e-04	ci right 3.231113e-04	k: 1288	n:4210000
Cons ci ratio: 1.803338e-03	ci left: 5.283513e-01	ci right 5.293052e-01	k: 2226367	n:4210000
KS ci ratio: 1.091674e-01	ci left: 2.894587e-04	ci right 3.231113e-04	k: 1288	n:4210000
SPG11   4210000 perm   7538 sec   (558 perm/sec)   p_kst 3.059382e-04   p_cons 5.288283e-01   p_joint 3.059382e-04

Joint ci ratio: 1.090828e-01	ci left: 2.892338e-04	ci right 3.228325e-04	k: 1290	n:4220000
Cons ci ratio: 1.801207e-03	ci left: 5.283499e-01	ci right 5.293027e-01	k: 2231647	n:4220000
KS ci ratio: 1.090828e-01	ci left: 2.892338e-04	ci right 3.228325e-04	k: 1290	n:4220000
SPG11   4220000 perm   7572 sec   (557 perm/sec)   p_kst 3.056872e-04   p_cons 5.288263e-01   p_joint 3.056872e-04

Joint ci ratio: 1.089985e-01	ci left: 2.890099e-04	ci right 3.225550e-04	k: 1292	n:4230000
Cons ci ratio: 1.799076e-03	ci left: 5.283506e-01	ci right 5.293023e-01	k: 2236936	n:4230000
KS ci ratio: 1.089985e-01	ci left: 2.890099e-04	ci right 3.225550e-04	k: 1292	n:4230000
SPG11   4230000 perm   7604 sec   (556 perm/sec)   p_kst 3.054374e-04   p_cons 5.288265e-01   p_joint 3.054374e-04

Joint ci ratio: 1.087883e-01	ci left: 2.894754e-04	ci right 3.230056e-04	k: 1297	n:4240000
Cons ci ratio: 1.796993e-03	ci left: 5.283403e-01	ci right 5.292908e-01	k: 2242178	n:4240000
KS ci ratio: 1.087883e-01	ci left: 2.894754e-04	ci right 3.230056e-04	k: 1297	n:4240000
SPG11   4240000 perm   7638 sec   (555 perm/sec)   p_kst 3.058962e-04   p_cons 5.288156e-01   p_joint 3.058962e-04

Joint ci ratio: 1.087046e-01	ci left: 2.892521e-04	ci right 3.227290e-04	k: 1299	n:4250000
Cons ci ratio: 1.794899e-03	ci left: 5.283349e-01	ci right 5.292843e-01	k: 2247441	n:4250000
KS ci ratio: 1.087046e-01	ci left: 2.892521e-04	ci right 3.227290e-04	k: 1299	n:4250000
SPG11   4250000 perm   7671 sec   (554 perm/sec)   p_kst 3.056471e-04   p_cons 5.288096e-01   p_joint 3.056471e-04

Joint ci ratio: 1.085377e-01	ci left: 2.894866e-04	ci right 3.229359e-04	k: 1303	n:4260000
Cons ci ratio: 1.792739e-03	ci left: 5.283500e-01	ci right 5.292983e-01	k: 2252791	n:4260000
KS ci ratio: 1.085377e-01	ci left: 2.894866e-04	ci right 3.229359e-04	k: 1303	n:4260000
SPG11   4260000 perm   7705 sec   (553 perm/sec)   p_kst 3.058685e-04   p_cons 5.288242e-01   p_joint 3.058685e-04

Joint ci ratio: 1.084546e-01	ci left: 2.892643e-04	ci right 3.226607e-04	k: 1305	n:4270000
Cons ci ratio: 1.790674e-03	ci left: 5.283407e-01	ci right 5.292878e-01	k: 2258037	n:4270000
KS ci ratio: 1.084546e-01	ci left: 2.892643e-04	ci right 3.226607e-04	k: 1305	n:4270000
SPG11   4270000 perm   7739 sec   (552 perm/sec)   p_kst 3.056206e-04   p_cons 5.288143e-01   p_joint 3.056206e-04

Joint ci ratio: 1.083717e-01	ci left: 2.890431e-04	ci right 3.223867e-04	k: 1307	n:4280000
Cons ci ratio: 1.788555e-03	ci left: 5.283485e-01	ci right 5.292945e-01	k: 2263356	n:4280000
KS ci ratio: 1.083717e-01	ci left: 2.890431e-04	ci right 3.223867e-04	k: 1307	n:4280000
SPG11   4280000 perm   7771 sec   (551 perm/sec)   p_kst 3.053738e-04   p_cons 5.288215e-01   p_joint 3.053738e-04

Joint ci ratio: 1.083717e-01	ci left: 2.883693e-04	ci right 3.216353e-04	k: 1307	n:4290000
Cons ci ratio: 1.786460e-03	ci left: 5.283515e-01	ci right 5.292965e-01	k: 2268655	n:4290000
KS ci ratio: 1.083717e-01	ci left: 2.883693e-04	ci right 3.216353e-04	k: 1307	n:4290000
SPG11   4290000 perm   7805 sec   (550 perm/sec)   p_kst 3.046620e-04   p_cons 5.288240e-01   p_joint 3.046620e-04

Joint ci ratio: 1.083303e-01	ci left: 2.879249e-04	ci right 3.211261e-04	k: 1308	n:4300000
Cons ci ratio: 1.784375e-03	ci left: 5.283539e-01	ci right 5.292977e-01	k: 2273951	n:4300000
KS ci ratio: 1.083303e-01	ci left: 2.879249e-04	ci right 3.211261e-04	k: 1308	n:4300000
SPG11   4300000 perm   7838 sec   (549 perm/sec)   p_kst 3.041860e-04   p_cons 5.288258e-01   p_joint 3.041860e-04

Joint ci ratio: 1.081652e-01	ci left: 2.881598e-04	ci right 3.213342e-04	k: 1312	n:4310000
Cons ci ratio: 1.782387e-03	ci left: 5.283312e-01	ci right 5.292739e-01	k: 2279139	n:4310000
KS ci ratio: 1.081652e-01	ci left: 2.881598e-04	ci right 3.213342e-04	k: 1312	n:4310000
SPG11   4310000 perm   7872 sec   (547 perm/sec)   p_kst 3.044084e-04   p_cons 5.288026e-01   p_joint 3.044084e-04

Joint ci ratio: 1.081652e-01	ci left: 2.874928e-04	ci right 3.205904e-04	k: 1312	n:4320000
Cons ci ratio: 1.780385e-03	ci left: 5.283143e-01	ci right 5.292560e-01	k: 2284352	n:4320000
KS ci ratio: 1.081652e-01	ci left: 2.874928e-04	ci right 3.205904e-04	k: 1312	n:4320000
SPG11   4320000 perm   7906 sec   (546 perm/sec)   p_kst 3.037037e-04   p_cons 5.287852e-01   p_joint 3.037037e-04

Joint ci ratio: 1.081241e-01	ci left: 2.870535e-04	ci right 3.200872e-04	k: 1313	n:4330000
Cons ci ratio: 1.778342e-03	ci left: 5.283110e-01	ci right 5.292516e-01	k: 2289623	n:4330000
KS ci ratio: 1.081241e-01	ci left: 2.870535e-04	ci right 3.200872e-04	k: 1313	n:4330000
SPG11   4330000 perm   7940 sec   (545 perm/sec)   p_kst 3.032333e-04   p_cons 5.287813e-01   p_joint 3.032333e-04

Joint ci ratio: 1.080830e-01	ci left: 2.866163e-04	ci right 3.195863e-04	k: 1314	n:4340000
Cons ci ratio: 1.776331e-03	ci left: 5.283005e-01	ci right 5.292400e-01	k: 2294863	n:4340000
KS ci ratio: 1.080830e-01	ci left: 2.866163e-04	ci right 3.195863e-04	k: 1314	n:4340000
SPG11   4340000 perm   7975 sec   (544 perm/sec)   p_kst 3.027650e-04   p_cons 5.287703e-01   p_joint 3.027650e-04

Joint ci ratio: 1.077964e-01	ci left: 2.875232e-04	ci right 3.205043e-04	k: 1321	n:4350000
Cons ci ratio: 1.774313e-03	ci left: 5.282940e-01	ci right 5.292324e-01	k: 2300120	n:4350000
KS ci ratio: 1.077964e-01	ci left: 2.875232e-04	ci right 3.205043e-04	k: 1321	n:4350000
SPG11   4350000 perm   8008 sec   (543 perm/sec)   p_kst 3.036782e-04   p_cons 5.287632e-01   p_joint 3.036782e-04

Joint ci ratio: 1.075121e-01	ci left: 2.884260e-04	ci right 3.214179e-04	k: 1328	n:4360000
Cons ci ratio: 1.772319e-03	ci left: 5.282829e-01	ci right 5.292203e-01	k: 2305357	n:4360000
KS ci ratio: 1.075121e-01	ci left: 2.884260e-04	ci right 3.214179e-04	k: 1328	n:4360000
SPG11   4360000 perm   8043 sec   (542 perm/sec)   p_kst 3.045872e-04   p_cons 5.287516e-01   p_joint 3.045872e-04

Joint ci ratio: 1.073104e-01	ci left: 2.888794e-04	ci right 3.218573e-04	k: 1333	n:4370000
Cons ci ratio: 1.770243e-03	ci left: 5.282966e-01	ci right 5.292329e-01	k: 2310702	n:4370000
KS ci ratio: 1.073104e-01	ci left: 2.888794e-04	ci right 3.218573e-04	k: 1333	n:4370000
SPG11   4370000 perm   8077 sec   (541 perm/sec)   p_kst 3.050343e-04   p_cons 5.287648e-01   p_joint 3.050343e-04

Joint ci ratio: 1.072702e-01	ci left: 2.884421e-04	ci right 3.213569e-04	k: 1334	n:4380000
Cons ci ratio: 1.768115e-03	ci left: 5.283269e-01	ci right 5.292621e-01	k: 2316120	n:4380000
KS ci ratio: 1.072702e-01	ci left: 2.884421e-04	ci right 3.213569e-04	k: 1334	n:4380000
SPG11   4380000 perm   8111 sec   (540 perm/sec)   p_kst 3.045662e-04   p_cons 5.287945e-01   p_joint 3.045662e-04

Joint ci ratio: 1.072301e-01	ci left: 2.880067e-04	ci right 3.208587e-04	k: 1335	n:4390000
Cons ci ratio: 1.766028e-03	ci left: 5.283480e-01	ci right 5.292821e-01	k: 2321498	n:4390000
KS ci ratio: 1.072301e-01	ci left: 2.880067e-04	ci right 3.208587e-04	k: 1335	n:4390000
SPG11   4390000 perm   8146 sec   (539 perm/sec)   p_kst 3.041002e-04   p_cons 5.288150e-01   p_joint 3.041002e-04

Joint ci ratio: 1.071900e-01	ci left: 2.875733e-04	ci right 3.203629e-04	k: 1336	n:4400000
Cons ci ratio: 1.764049e-03	ci left: 5.283403e-01	ci right 5.292733e-01	k: 2326750	n:4400000
KS ci ratio: 1.071900e-01	ci left: 2.875733e-04	ci right 3.203629e-04	k: 1336	n:4400000
SPG11   4400000 perm   8181 sec   (538 perm/sec)   p_kst 3.036364e-04   p_cons 5.288068e-01   p_joint 3.036364e-04

Joint ci ratio: 1.071900e-01	ci left: 2.869212e-04	ci right 3.196364e-04	k: 1336	n:4410000
Cons ci ratio: 1.762015e-03	ci left: 5.283501e-01	ci right 5.292821e-01	k: 2332079	n:4410000
KS ci ratio: 1.071900e-01	ci left: 2.869212e-04	ci right 3.196364e-04	k: 1336	n:4410000
SPG11   4410000 perm   8215 sec   (537 perm/sec)   p_kst 3.029478e-04   p_cons 5.288161e-01   p_joint 3.029478e-04

Joint ci ratio: 1.070301e-01	ci left: 2.871528e-04	ci right 3.198425e-04	k: 1340	n:4420000
Cons ci ratio: 1.760045e-03	ci left: 5.283436e-01	ci right 5.292745e-01	k: 2337336	n:4420000
KS ci ratio: 1.070301e-01	ci left: 2.871528e-04	ci right 3.198425e-04	k: 1340	n:4420000
SPG11   4420000 perm   8251 sec   (536 perm/sec)   p_kst 3.031674e-04   p_cons 5.288090e-01   p_joint 3.031674e-04

Joint ci ratio: 1.069503e-01	ci left: 2.869440e-04	ci right 3.195841e-04	k: 1342	n:4430000
Cons ci ratio: 1.758075e-03	ci left: 5.283391e-01	ci right 5.292690e-01	k: 2342602	n:4430000
KS ci ratio: 1.069503e-01	ci left: 2.869440e-04	ci right 3.195841e-04	k: 1342	n:4430000
SPG11   4430000 perm   8286 sec   (535 perm/sec)   p_kst 3.029345e-04   p_cons 5.288041e-01   p_joint 3.029345e-04

Joint ci ratio: 1.067914e-01	ci left: 2.871745e-04	ci right 3.197892e-04	k: 1346	n:4440000
Cons ci ratio: 1.756086e-03	ci left: 5.283421e-01	ci right 5.292709e-01	k: 2347901	n:4440000
KS ci ratio: 1.067914e-01	ci left: 2.871745e-04	ci right 3.197892e-04	k: 1346	n:4440000
SPG11   4440000 perm   8320 sec   (534 perm/sec)   p_kst 3.031532e-04   p_cons 5.288065e-01   p_joint 3.031532e-04

Joint ci ratio: 1.067122e-01	ci left: 2.869666e-04	ci right 3.195320e-04	k: 1348	n:4450000
Cons ci ratio: 1.754131e-03	ci left: 5.283370e-01	ci right 5.292648e-01	k: 2353164	n:4450000
KS ci ratio: 1.067122e-01	ci left: 2.869666e-04	ci right 3.195320e-04	k: 1348	n:4450000
SPG11   4450000 perm   8354 sec   (533 perm/sec)   p_kst 3.029213e-04   p_cons 5.288009e-01   p_joint 3.029213e-04

Joint ci ratio: 1.065544e-01	ci left: 2.871962e-04	ci right 3.197364e-04	k: 1352	n:4460000
Cons ci ratio: 1.752162e-03	ci left: 5.283380e-01	ci right 5.292647e-01	k: 2358454	n:4460000
KS ci ratio: 1.065544e-01	ci left: 2.871962e-04	ci right 3.197364e-04	k: 1352	n:4460000
SPG11   4460000 perm   8389 sec   (532 perm/sec)   p_kst 3.031390e-04   p_cons 5.288013e-01   p_joint 3.031390e-04

Joint ci ratio: 1.065150e-01	ci left: 2.867714e-04	ci right 3.192508e-04	k: 1353	n:4470000
Cons ci ratio: 1.750158e-03	ci left: 5.283508e-01	ci right 5.292765e-01	k: 2363797	n:4470000
KS ci ratio: 1.065150e-01	ci left: 2.867714e-04	ci right 3.192508e-04	k: 1353	n:4470000
SPG11   4470000 perm   8425 sec   (531 perm/sec)   p_kst 3.026846e-04   p_cons 5.288136e-01   p_joint 3.026846e-04

Joint ci ratio: 1.062798e-01	ci left: 2.874349e-04	ci right 3.199131e-04	k: 1359	n:4480000
Cons ci ratio: 1.748154e-03	ci left: 5.283653e-01	ci right 5.292900e-01	k: 2369148	n:4480000
KS ci ratio: 1.062798e-01	ci left: 2.874349e-04	ci right 3.199131e-04	k: 1359	n:4480000
SPG11   4480000 perm   8461 sec   (529 perm/sec)   p_kst 3.033482e-04   p_cons 5.288277e-01   p_joint 3.033482e-04

Joint ci ratio: 1.060849e-01	ci left: 2.878788e-04	ci right 3.203437e-04	k: 1364	n:4490000
Cons ci ratio: 1.746187e-03	ci left: 5.283713e-01	ci right 5.292950e-01	k: 2374461	n:4490000
KS ci ratio: 1.060849e-01	ci left: 2.878788e-04	ci right 3.203437e-04	k: 1364	n:4490000
SPG11   4490000 perm   8497 sec   (528 perm/sec)   p_kst 3.037862e-04   p_cons 5.288332e-01   p_joint 3.037862e-04

Joint ci ratio: 1.060073e-01	ci left: 2.876717e-04	ci right 3.200880e-04	k: 1366	n:4500000
Cons ci ratio: 1.744271e-03	ci left: 5.283647e-01	ci right 5.292873e-01	k: 2379717	n:4500000
KS ci ratio: 1.060073e-01	ci left: 2.876717e-04	ci right 3.200880e-04	k: 1366	n:4500000
SPG11   4500000 perm   8531 sec   (527 perm/sec)   p_kst 3.035556e-04   p_cons 5.288260e-01   p_joint 3.035556e-04

Joint ci ratio: 1.058525e-01	ci left: 2.878973e-04	ci right 3.202887e-04	k: 1370	n:4510000
Cons ci ratio: 1.742360e-03	ci left: 5.283583e-01	ci right 5.292798e-01	k: 2384974	n:4510000
KS ci ratio: 1.058525e-01	ci left: 2.878973e-04	ci right 3.202887e-04	k: 1370	n:4510000
SPG11   4510000 perm   8565 sec   (527 perm/sec)   p_kst 3.037694e-04   p_cons 5.288191e-01   p_joint 3.037694e-04

Joint ci ratio: 1.057369e-01	ci left: 2.879065e-04	ci right 3.202614e-04	k: 1373	n:4520000
Cons ci ratio: 1.740515e-03	ci left: 5.283348e-01	ci right 5.292554e-01	k: 2390154	n:4520000
KS ci ratio: 1.057369e-01	ci left: 2.879065e-04	ci right 3.202614e-04	k: 1373	n:4520000
SPG11   4520000 perm   8601 sec   (526 perm/sec)   p_kst 3.037611e-04   p_cons 5.287951e-01   p_joint 3.037611e-04

Joint ci ratio: 1.055833e-01	ci left: 2.881306e-04	ci right 3.204607e-04	k: 1377	n:4530000
Cons ci ratio: 1.738592e-03	ci left: 5.283358e-01	ci right 5.292553e-01	k: 2395444	n:4530000
KS ci ratio: 1.055833e-01	ci left: 2.881306e-04	ci right 3.204607e-04	k: 1377	n:4530000
SPG11   4530000 perm   8636 sec   (525 perm/sec)   p_kst 3.039735e-04   p_cons 5.287956e-01   p_joint 3.039735e-04

Joint ci ratio: 1.055068e-01	ci left: 2.879249e-04	ci right 3.202070e-04	k: 1379	n:4540000
Cons ci ratio: 1.736676e-03	ci left: 5.283363e-01	ci right 5.292549e-01	k: 2400732	n:4540000
KS ci ratio: 1.055068e-01	ci left: 2.879249e-04	ci right 3.202070e-04	k: 1379	n:4540000
SPG11   4540000 perm   8672 sec   (523 perm/sec)   p_kst 3.037445e-04   p_cons 5.287956e-01   p_joint 3.037445e-04

Joint ci ratio: 1.053542e-01	ci left: 2.881480e-04	ci right 3.204056e-04	k: 1383	n:4550000
Cons ci ratio: 1.734689e-03	ci left: 5.283590e-01	ci right 5.292766e-01	k: 2406121	n:4550000
KS ci ratio: 1.053542e-01	ci left: 2.881480e-04	ci right 3.204056e-04	k: 1383	n:4550000
SPG11   4550000 perm   8709 sec   (522 perm/sec)   p_kst 3.039560e-04   p_cons 5.288178e-01   p_joint 3.039560e-04

Joint ci ratio: 1.052402e-01	ci left: 2.881567e-04	ci right 3.203781e-04	k: 1386	n:4560000
Cons ci ratio: 1.732774e-03	ci left: 5.283630e-01	ci right 5.292795e-01	k: 2411425	n:4560000
KS ci ratio: 1.052402e-01	ci left: 2.881567e-04	ci right 3.203781e-04	k: 1386	n:4560000
SPG11   4560000 perm   8745 sec   (521 perm/sec)   p_kst 3.039474e-04   p_cons 5.288213e-01   p_joint 3.039474e-04

Joint ci ratio: 1.051266e-01	ci left: 2.881653e-04	ci right 3.203508e-04	k: 1389	n:4570000
Cons ci ratio: 1.730824e-03	ci left: 5.283788e-01	ci right 5.292943e-01	k: 2416783	n:4570000
KS ci ratio: 1.051266e-01	ci left: 2.881653e-04	ci right 3.203508e-04	k: 1389	n:4570000
SPG11   4570000 perm   8781 sec   (520 perm/sec)   p_kst 3.039387e-04   p_cons 5.288365e-01   p_joint 3.039387e-04

Joint ci ratio: 1.050133e-01	ci left: 2.881739e-04	ci right 3.203236e-04	k: 1392	n:4580000
Cons ci ratio: 1.728844e-03	ci left: 5.284049e-01	ci right 5.293195e-01	k: 2422189	n:4580000
KS ci ratio: 1.050133e-01	ci left: 2.881739e-04	ci right 3.203236e-04	k: 1392	n:4580000
SPG11   4580000 perm   8817 sec   (519 perm/sec)   p_kst 3.039301e-04   p_cons 5.288622e-01   p_joint 3.039301e-04

Joint ci ratio: 1.048253e-01	ci left: 2.886069e-04	ci right 3.207436e-04	k: 1397	n:4590000
Cons ci ratio: 1.726965e-03	ci left: 5.284040e-01	ci right 5.293175e-01	k: 2427471	n:4590000
KS ci ratio: 1.048253e-01	ci left: 2.886069e-04	ci right 3.207436e-04	k: 1397	n:4590000
SPG11   4590000 perm   8855 sec   (518 perm/sec)   p_kst 3.043573e-04   p_cons 5.288608e-01   p_joint 3.043573e-04

Joint ci ratio: 1.046757e-01	ci left: 2.888262e-04	ci right 3.209387e-04	k: 1401	n:4600000
Cons ci ratio: 1.725094e-03	ci left: 5.284024e-01	ci right 5.293149e-01	k: 2432750	n:4600000
KS ci ratio: 1.046757e-01	ci left: 2.888262e-04	ci right 3.209387e-04	k: 1401	n:4600000
SPG11   4600000 perm   8892 sec   (517 perm/sec)   p_kst 3.045652e-04   p_cons 5.288587e-01   p_joint 3.045652e-04

Joint ci ratio: 1.044895e-01	ci left: 2.892559e-04	ci right 3.213555e-04	k: 1406	n:4610000
Cons ci ratio: 1.723220e-03	ci left: 5.284034e-01	ci right 5.293150e-01	k: 2438041	n:4610000
KS ci ratio: 1.044895e-01	ci left: 2.892559e-04	ci right 3.213555e-04	k: 1406	n:4610000
SPG11   4610000 perm   8929 sec   (516 perm/sec)   p_kst 3.049892e-04   p_cons 5.288592e-01   p_joint 3.049892e-04

Joint ci ratio: 1.044153e-01	ci left: 2.890514e-04	ci right 3.211041e-04	k: 1408	n:4620000
Cons ci ratio: 1.721287e-03	ci left: 5.284233e-01	ci right 5.293338e-01	k: 2443419	n:4620000
KS ci ratio: 1.044153e-01	ci left: 2.890514e-04	ci right 3.211041e-04	k: 1408	n:4620000
SPG11   4620000 perm   8966 sec   (515 perm/sec)   p_kst 3.047619e-04   p_cons 5.288786e-01   p_joint 3.047619e-04

Joint ci ratio: 1.043044e-01	ci left: 2.890582e-04	ci right 3.210754e-04	k: 1411	n:4630000
Cons ci ratio: 1.719398e-03	ci left: 5.284322e-01	ci right 5.293418e-01	k: 2448747	n:4630000
KS ci ratio: 1.043044e-01	ci left: 2.890582e-04	ci right 3.210754e-04	k: 1411	n:4630000
SPG11   4630000 perm   9003 sec   (514 perm/sec)   p_kst 3.047516e-04   p_cons 5.288870e-01   p_joint 3.047516e-04

Joint ci ratio: 1.041201e-01	ci left: 2.894847e-04	ci right 3.214891e-04	k: 1416	n:4640000
Cons ci ratio: 1.717495e-03	ci left: 5.284472e-01	ci right 5.293558e-01	k: 2454103	n:4640000
KS ci ratio: 1.041201e-01	ci left: 2.894847e-04	ci right 3.214891e-04	k: 1416	n:4640000
SPG11   4640000 perm   9040 sec   (513 perm/sec)   p_kst 3.051724e-04   p_cons 5.289015e-01   p_joint 3.051724e-04

Joint ci ratio: 1.040101e-01	ci left: 2.894905e-04	ci right 3.214597e-04	k: 1419	n:4650000
Cons ci ratio: 1.715666e-03	ci left: 5.284421e-01	ci right 5.293497e-01	k: 2459366	n:4650000
KS ci ratio: 1.040101e-01	ci left: 2.894905e-04	ci right 3.214597e-04	k: 1419	n:4650000
SPG11   4650000 perm   9078 sec   (512 perm/sec)   p_kst 3.051613e-04   p_cons 5.288959e-01   p_joint 3.051613e-04

Joint ci ratio: 1.039004e-01	ci left: 2.894963e-04	ci right 3.214303e-04	k: 1422	n:4660000
Cons ci ratio: 1.713818e-03	ci left: 5.284443e-01	ci right 5.293509e-01	k: 2464663	n:4660000
KS ci ratio: 1.039004e-01	ci left: 2.894963e-04	ci right 3.214303e-04	k: 1422	n:4660000
SPG11   4660000 perm   9115 sec   (511 perm/sec)   p_kst 3.051502e-04   p_cons 5.288976e-01   p_joint 3.051502e-04

Joint ci ratio: 1.037547e-01	ci left: 2.897107e-04	ci right 3.216208e-04	k: 1426	n:4670000
Cons ci ratio: 1.712001e-03	ci left: 5.284394e-01	ci right 5.293451e-01	k: 2469927	n:4670000
KS ci ratio: 1.037547e-01	ci left: 2.897107e-04	ci right 3.216208e-04	k: 1426	n:4670000
SPG11   4670000 perm   9152 sec   (510 perm/sec)   p_kst 3.053533e-04   p_cons 5.288923e-01   p_joint 3.053533e-04

Joint ci ratio: 1.036458e-01	ci left: 2.897161e-04	ci right 3.215912e-04	k: 1429	n:4680000
Cons ci ratio: 1.710194e-03	ci left: 5.284333e-01	ci right 5.293380e-01	k: 2475185	n:4680000
KS ci ratio: 1.036458e-01	ci left: 2.897161e-04	ci right 3.215912e-04	k: 1429	n:4680000
SPG11   4680000 perm   9190 sec   (509 perm/sec)   p_kst 3.053419e-04   p_cons 5.288857e-01   p_joint 3.053419e-04

Joint ci ratio: 1.033930e-01	ci left: 2.905523e-04	ci right 3.224367e-04	k: 1436	n:4690000
Cons ci ratio: 1.708321e-03	ci left: 5.284479e-01	ci right 5.293516e-01	k: 2480540	n:4690000
KS ci ratio: 1.033930e-01	ci left: 2.905523e-04	ci right 3.224367e-04	k: 1436	n:4690000
SPG11   4690000 perm   9228 sec   (508 perm/sec)   p_kst 3.061834e-04   p_cons 5.288998e-01   p_joint 3.061834e-04

Joint ci ratio: 1.031778e-01	ci left: 2.911777e-04	ci right 3.230602e-04	k: 1442	n:4700000
Cons ci ratio: 1.706540e-03	ci left: 5.284375e-01	ci right 5.293403e-01	k: 2485778	n:4700000
KS ci ratio: 1.031778e-01	ci left: 2.911777e-04	ci right 3.230602e-04	k: 1442	n:4700000
SPG11   4700000 perm   9266 sec   (507 perm/sec)   p_kst 3.068085e-04   p_cons 5.288889e-01   p_joint 3.068085e-04

Joint ci ratio: 1.030351e-01	ci left: 2.913868e-04	ci right 3.232455e-04	k: 1446	n:4710000
Cons ci ratio: 1.704707e-03	ci left: 5.284440e-01	ci right 5.293458e-01	k: 2491095	n:4710000
KS ci ratio: 1.030351e-01	ci left: 2.913868e-04	ci right 3.232455e-04	k: 1446	n:4710000
SPG11   4710000 perm   9304 sec   (506 perm/sec)   p_kst 3.070064e-04   p_cons 5.288949e-01   p_joint 3.070064e-04

Joint ci ratio: 1.028575e-01	ci left: 2.918015e-04	ci right 3.236472e-04	k: 1451	n:4720000
Cons ci ratio: 1.702900e-03	ci left: 5.284445e-01	ci right 5.293453e-01	k: 2496384	n:4720000
KS ci ratio: 1.028575e-01	ci left: 2.918015e-04	ci right 3.236472e-04	k: 1451	n:4720000
SPG11   4720000 perm   9342 sec   (505 perm/sec)   p_kst 3.074153e-04   p_cons 5.288949e-01   p_joint 3.074153e-04

Joint ci ratio: 1.027514e-01	ci left: 2.918026e-04	ci right 3.236135e-04	k: 1454	n:4730000
Cons ci ratio: 1.701152e-03	ci left: 5.284295e-01	ci right 5.293294e-01	k: 2501600	n:4730000
KS ci ratio: 1.027514e-01	ci left: 2.918026e-04	ci right 3.236135e-04	k: 1454	n:4730000
SPG11   4730000 perm   9380 sec   (504 perm/sec)   p_kst 3.073996e-04   p_cons 5.288795e-01   p_joint 3.073996e-04

Joint ci ratio: 1.025753e-01	ci left: 2.922147e-04	ci right 3.240127e-04	k: 1459	n:4740000
Cons ci ratio: 1.699350e-03	ci left: 5.284317e-01	ci right 5.293307e-01	k: 2506897	n:4740000
KS ci ratio: 1.025753e-01	ci left: 2.922147e-04	ci right 3.240127e-04	k: 1459	n:4740000
SPG11   4740000 perm   9418 sec   (503 perm/sec)   p_kst 3.078059e-04   p_cons 5.288812e-01   p_joint 3.078059e-04

Joint ci ratio: 1.024001e-01	ci left: 2.926252e-04	ci right 3.244102e-04	k: 1464	n:4750000
Cons ci ratio: 1.697532e-03	ci left: 5.284405e-01	ci right 5.293385e-01	k: 2512225	n:4750000
KS ci ratio: 1.024001e-01	ci left: 2.926252e-04	ci right 3.244102e-04	k: 1464	n:4750000
SPG11   4750000 perm   9456 sec   (502 perm/sec)   p_kst 3.082105e-04   p_cons 5.288895e-01   p_joint 3.082105e-04

Joint ci ratio: 1.020869e-01	ci left: 2.938528e-04	ci right 3.256677e-04	k: 1473	n:4760000
Cons ci ratio: 1.695753e-03	ci left: 5.284395e-01	ci right 5.293365e-01	k: 2517507	n:4760000
KS ci ratio: 1.020869e-01	ci left: 2.938528e-04	ci right 3.256677e-04	k: 1473	n:4760000
SPG11   4760000 perm   9495 sec   (501 perm/sec)   p_kst 3.094538e-04   p_cons 5.288880e-01   p_joint 3.094538e-04

Joint ci ratio: 1.020177e-01	ci left: 2.936454e-04	ci right 3.254150e-04	k: 1475	n:4770000
Cons ci ratio: 1.693983e-03	ci left: 5.284375e-01	ci right 5.293336e-01	k: 2522784	n:4770000
KS ci ratio: 1.020177e-01	ci left: 2.936454e-04	ci right 3.254150e-04	k: 1475	n:4770000
SPG11   4770000 perm   9533 sec   (500 perm/sec)   p_kst 3.092243e-04   p_cons 5.288855e-01   p_joint 3.092243e-04

Joint ci ratio: 1.019487e-01	ci left: 2.934388e-04	ci right 3.251633e-04	k: 1477	n:4780000
Cons ci ratio: 1.692229e-03	ci left: 5.284325e-01	ci right 5.293277e-01	k: 2528047	n:4780000
KS ci ratio: 1.019487e-01	ci left: 2.934388e-04	ci right 3.251633e-04	k: 1477	n:4780000
SPG11   4780000 perm   9572 sec   (499 perm/sec)   p_kst 3.089958e-04   p_cons 5.288801e-01   p_joint 3.089958e-04

Joint ci ratio: 1.018110e-01	ci left: 2.936400e-04	ci right 3.253408e-04	k: 1481	n:4790000
Cons ci ratio: 1.690443e-03	ci left: 5.284385e-01	ci right 5.293327e-01	k: 2533362	n:4790000
KS ci ratio: 1.018110e-01	ci left: 2.936400e-04	ci right 3.253408e-04	k: 1481	n:4790000
SPG11   4790000 perm   9610 sec   (498 perm/sec)   p_kst 3.091858e-04   p_cons 5.288856e-01   p_joint 3.091858e-04

Joint ci ratio: 1.017424e-01	ci left: 2.934343e-04	ci right 3.250902e-04	k: 1483	n:4800000
Cons ci ratio: 1.688692e-03	ci left: 5.284356e-01	ci right 5.293289e-01	k: 2538635	n:4800000
KS ci ratio: 1.017424e-01	ci left: 2.934343e-04	ci right 3.250902e-04	k: 1483	n:4800000
SPG11   4800000 perm   9649 sec   (497 perm/sec)   p_kst 3.089583e-04   p_cons 5.288823e-01   p_joint 3.089583e-04

Joint ci ratio: 1.016055e-01	ci left: 2.936347e-04	ci right 3.252671e-04	k: 1487	n:4810000
Cons ci ratio: 1.686971e-03	ci left: 5.284257e-01	ci right 5.293181e-01	k: 2543874	n:4810000
KS ci ratio: 1.016055e-01	ci left: 2.936347e-04	ci right 3.252671e-04	k: 1487	n:4810000
SPG11   4810000 perm   9687 sec   (497 perm/sec)   p_kst 3.091476e-04   p_cons 5.288719e-01   p_joint 3.091476e-04

Joint ci ratio: 1.015033e-01	ci left: 2.936321e-04	ci right 3.252305e-04	k: 1490	n:4820000
Cons ci ratio: 1.685256e-03	ci left: 5.284155e-01	ci right 5.293069e-01	k: 2549111	n:4820000
KS ci ratio: 1.015033e-01	ci left: 2.936321e-04	ci right 3.252305e-04	k: 1490	n:4820000
SPG11   4820000 perm   9726 sec   (496 perm/sec)   p_kst 3.091286e-04   p_cons 5.288612e-01   p_joint 3.091286e-04

Joint ci ratio: 1.013335e-01	ci left: 2.940331e-04	ci right 3.256186e-04	k: 1495	n:4830000
Cons ci ratio: 1.683525e-03	ci left: 5.284119e-01	ci right 5.293024e-01	k: 2554380	n:4830000
KS ci ratio: 1.013335e-01	ci left: 2.940331e-04	ci right 3.256186e-04	k: 1495	n:4830000
SPG11   4830000 perm   9764 sec   (495 perm/sec)   p_kst 3.095238e-04   p_cons 5.288571e-01   p_joint 3.095238e-04

Joint ci ratio: 1.012658e-01	ci left: 2.938284e-04	ci right 3.253695e-04	k: 1497	n:4840000
Cons ci ratio: 1.681786e-03	ci left: 5.284120e-01	ci right 5.293016e-01	k: 2559667	n:4840000
KS ci ratio: 1.012658e-01	ci left: 2.938284e-04	ci right 3.253695e-04	k: 1497	n:4840000
SPG11   4840000 perm   9803 sec   (494 perm/sec)   p_kst 3.092975e-04   p_cons 5.288568e-01   p_joint 3.092975e-04

Joint ci ratio: 1.011646e-01	ci left: 2.938254e-04	ci right 3.253329e-04	k: 1500	n:4850000
Cons ci ratio: 1.680076e-03	ci left: 5.284049e-01	ci right 5.292936e-01	k: 2564919	n:4850000
KS ci ratio: 1.011646e-01	ci left: 2.938254e-04	ci right 3.253329e-04	k: 1500	n:4850000
SPG11   4850000 perm   9841 sec   (493 perm/sec)   p_kst 3.092784e-04   p_cons 5.288493e-01   p_joint 3.092784e-04

Joint ci ratio: 1.010973e-01	ci left: 2.936220e-04	ci right 3.250854e-04	k: 1502	n:4860000
Cons ci ratio: 1.678300e-03	ci left: 5.284195e-01	ci right 5.293072e-01	k: 2570276	n:4860000
KS ci ratio: 1.010973e-01	ci left: 2.936220e-04	ci right 3.250854e-04	k: 1502	n:4860000
SPG11   4860000 perm   9880 sec   (492 perm/sec)   p_kst 3.090535e-04   p_cons 5.288634e-01   p_joint 3.090535e-04

Joint ci ratio: 1.008960e-01	ci left: 2.942200e-04	ci right 3.256810e-04	k: 1508	n:4870000
Cons ci ratio: 1.676539e-03	ci left: 5.284309e-01	ci right 5.293177e-01	k: 2575618	n:4870000
KS ci ratio: 1.008960e-01	ci left: 2.942200e-04	ci right 3.256810e-04	k: 1508	n:4870000
SPG11   4870000 perm   9918 sec   (491 perm/sec)   p_kst 3.096509e-04   p_cons 5.288743e-01   p_joint 3.096509e-04

Joint ci ratio: 1.008961e-01	ci left: 2.936170e-04	ci right 3.250136e-04	k: 1508	n:4880000
Cons ci ratio: 1.674823e-03	ci left: 5.284304e-01	ci right 5.293163e-01	k: 2580902	n:4880000
KS ci ratio: 1.008961e-01	ci left: 2.936170e-04	ci right 3.250136e-04	k: 1508	n:4880000
SPG11   4880000 perm   9957 sec   (490 perm/sec)   p_kst 3.090164e-04   p_cons 5.288734e-01   p_joint 3.090164e-04

Joint ci ratio: 1.007293e-01	ci left: 2.940133e-04	ci right 3.253972e-04	k: 1513	n:4890000
Cons ci ratio: 1.673143e-03	ci left: 5.284209e-01	ci right 5.293059e-01	k: 2586142	n:4890000
KS ci ratio: 1.007293e-01	ci left: 2.940133e-04	ci right 3.253972e-04	k: 1513	n:4890000
SPG11   4890000 perm   9996 sec   (489 perm/sec)   p_kst 3.094070e-04   p_cons 5.288634e-01   p_joint 3.094070e-04

Joint ci ratio: 1.005965e-01	ci left: 2.942091e-04	ci right 3.255700e-04	k: 1517	n:4900000
Cons ci ratio: 1.671432e-03	ci left: 5.284224e-01	ci right 5.293065e-01	k: 2591436	n:4900000
KS ci ratio: 1.005965e-01	ci left: 2.942091e-04	ci right 3.255700e-04	k: 1517	n:4900000
SPG11   4900000 perm   10036 sec   (488 perm/sec)   p_kst 3.095918e-04   p_cons 5.288645e-01   p_joint 3.095918e-04

Joint ci ratio: 1.004642e-01	ci left: 2.944041e-04	ci right 3.257421e-04	k: 1521	n:4910000
Cons ci ratio: 1.669763e-03	ci left: 5.284127e-01	ci right 5.292960e-01	k: 2596675	n:4910000
KS ci ratio: 1.004642e-01	ci left: 2.944041e-04	ci right 3.257421e-04	k: 1521	n:4910000
SPG11   4910000 perm   10075 sec   (487 perm/sec)   p_kst 3.097760e-04   p_cons 5.288544e-01   p_joint 3.097760e-04

Joint ci ratio: 1.004312e-01	ci left: 2.940038e-04	ci right 3.252884e-04	k: 1522	n:4920000
Cons ci ratio: 1.668057e-03	ci left: 5.284155e-01	ci right 5.292979e-01	k: 2601975	n:4920000
KS ci ratio: 1.004312e-01	ci left: 2.940038e-04	ci right 3.252884e-04	k: 1522	n:4920000
SPG11   4920000 perm   10114 sec   (486 perm/sec)   p_kst 3.093496e-04   p_cons 5.288567e-01   p_joint 3.093496e-04

Joint ci ratio: 1.003325e-01	ci left: 2.940007e-04	ci right 3.252523e-04	k: 1525	n:4930000
Cons ci ratio: 1.666344e-03	ci left: 5.284221e-01	ci right 5.293036e-01	k: 2607294	n:4930000
KS ci ratio: 1.003325e-01	ci left: 2.940007e-04	ci right 3.252523e-04	k: 1525	n:4930000
SPG11   4930000 perm   10154 sec   (486 perm/sec)   p_kst 3.093306e-04   p_cons 5.288629e-01   p_joint 3.093306e-04

Joint ci ratio: 1.002340e-01	ci left: 2.939976e-04	ci right 3.252165e-04	k: 1528	n:4940000
Cons ci ratio: 1.664724e-03	ci left: 5.284024e-01	ci right 5.292830e-01	k: 2612483	n:4940000
KS ci ratio: 1.002340e-01	ci left: 2.939976e-04	ci right 3.252165e-04	k: 1528	n:4940000
SPG11   4940000 perm   10193 sec   (485 perm/sec)   p_kst 3.093117e-04   p_cons 5.288427e-01   p_joint 3.093117e-04

Joint ci ratio: 1.001358e-01	ci left: 2.939946e-04	ci right 3.251807e-04	k: 1531	n:4950000
Cons ci ratio: 1.663073e-03	ci left: 5.283935e-01	ci right 5.292732e-01	k: 2617725	n:4950000
KS ci ratio: 1.001358e-01	ci left: 2.939946e-04	ci right 3.251807e-04	k: 1531	n:4950000
SPG11   4950000 perm   10233 sec   (484 perm/sec)   p_kst 3.092929e-04   p_cons 5.288333e-01   p_joint 3.092929e-04

Joint ci ratio: 1.000379e-01	ci left: 2.939915e-04	ci right 3.251451e-04	k: 1534	n:4960000
Cons ci ratio: 1.661426e-03	ci left: 5.283846e-01	ci right 5.292634e-01	k: 2622967	n:4960000
KS ci ratio: 1.000379e-01	ci left: 2.939915e-04	ci right 3.251451e-04	k: 1534	n:4960000
SPG11   4960000 perm   10273 sec   (483 perm/sec)   p_kst 3.092742e-04   p_cons 5.288240e-01   p_joint 3.092742e-04

Joint ci ratio: 9.997282e-02	ci left: 2.937923e-04	ci right 3.249033e-04	k: 1536	n:4970000
Cons ci ratio: 1.659746e-03	ci left: 5.283876e-01	ci right 5.292655e-01	k: 2628268	n:4970000
KS ci ratio: 9.997282e-02	ci left: 2.937923e-04	ci right 3.249033e-04	k: 1536	n:4970000
SPG11   4970000 perm   10312 sec   (482 perm/sec)   p_kst 3.090543e-04   p_cons 5.288266e-01   p_joint 3.090543e-04

Outputting figure to mutsig2_images.part000000000165/SPG11.2_7492_4970000_0.00030905_0.52883_0.00030905.png
                gene_name: SPG11
               theta_stop: 0.100 
                    nperm: 4970000 
                     p_ks: 0.00031 
        ci_ks_bounds_left: 0.00029 
       ci_ks_bounds_right: 0.00032 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.53 
     ci_cons_bounds_right: 0.53 
                  p_joint: 0.00031 
     ci_joint_bounds_left: 0.00029 
    ci_joint_bounds_right: 0.00032 

Current progress: 80 percent done.
SPHK2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.273416e-02	ci left: 8.986739e-01	ci right 9.102893e-01	k: 9046	n:10000
Cons ci ratio: 1.574622e-02	ci left: 8.541665e-01	ci right 8.678225e-01	k: 8611	n:10000
KS ci ratio: 4.310302e-02	ci left: 4.428093e-01	ci right 4.624183e-01	k: 4526	n:10000
SPHK2   10000 perm   2 sec   (6017 perm/sec)   p_kst 4.526000e-01   p_cons 8.611000e-01   p_joint 9.046000e-01

Outputting figure to mutsig2_images.part000000000165/SPHK2.2_1989_10000_0.4526_0.8611_0.9046.png
                gene_name: SPHK2
               theta_stop: 0.043 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.87 
                  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.165.3896/
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/181708/iteration1/scatter.0000000165
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 165 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1726>
Subject: Job 1120273: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1726>, 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/181708/iteration1/scatter.0000000166> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:47:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000166.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000166.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 166  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     90.58 sec.
    Max Memory :      1267 MB
    Max Swap   :      3956 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.165.3896/
-whichjob
166
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 166: processing genes 14929 - 15018
Calculating significance of each gene.
Using projection method.
14929	SPNS1	7.013876e-02
14930	SPNS2	1
14931	SPNS3	1
14932	SPO11	1
14933	SPOCD1	3.987667e-01
14934	SPOCK1	1
14935	SPOCK2	5.377180e-02
14936	SPOCK3	1
14937	SPON1	1
14938	SPON2	1
14939	SPOP	1
14940	SPOPL	1
14941	SPP1	1
14942	SPP2	1
14943	SPPL2A	1
14944	SPPL2B	1
14945	SPPL3	1
14946	SPR	1
14947	SPRED1	1.764563e-01
14948	SPRED2	1
14949	SPRED3	1
14950	SPRR1A	1
14951	SPRR1B	1
14952	SPRR2A	1
14953	SPRR2B	1
14954	SPRR2D	1
14955	SPRR2E	1
14956	SPRR2F	3.146721e-03
14957	SPRR2G	1
14958	SPRR3	1
14959	SPRR4	1
14960	SPRY1	1
14961	SPRY2	1
14962	SPRY3	1
14963	SPRY4	1
14964	SPRYD3	1.935137e-01
14965	SPRYD4	1
14966	SPRYD5	1
14967	SPSB1	1
14968	SPSB2	1
14969	SPSB3	1
14970	SPSB4	1
14971	SPTA1	8.008329e-03
14972	SPTAN1	7.606248e-01
14973	SPTB	6.668519e-01
14974	SPTBN1	1
14975	SPTBN2	1
14976	SPTBN4	5.172000e-01
14977	SPTBN5	1
14978	SPTLC1	1.096928e-01
14979	SPTLC2	1
14980	SPTLC3	1
14981	SPTY2D1	1
14982	SPZ1	1
14983	SQLE	1
14984	SQRDL	1
14985	SQSTM1	1
14986	SR140	1
14987	SRA1	1
14988	SRBD1	3.148926e-01
14989	SRC	1.151270e-01
14990	SRCAP	1
14991	SRCIN1	1
14992	SRCRB4D	1.453282e-01
14993	SRD5A1	1
14994	SRD5A2	1
14995	SRD5A3	1
14996	SREBF1	1.226344e-01
14997	SREBF2	1
14998	SRF	1
14999	SRFBP1	1
15000/18094 15000	SRGAP1	1
15001	SRGAP2	1
15002	SRGAP3	1
15003	SRGN	1
15004	SRI	1
15005	SRL	1
15006	SRM	1.075780e-01
15007	SRMS	1
15008	SRP14	1
15009	SRP19	1
15010	SRP54	1
15011	SRP68	1
15012	SRP72	1
15013	SRP9	1
15014	SRPK1	1
15015	SRPK2	1
15016	SRPK3	1
15017	SRPR	1.201509e-01
15018	SRPRB	3.458127e-03
Done

Running MutSig 2:
Scatter job 166: processing genes 14929 - 15018
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SPTA1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.605201e-02	ci left: 2.018551e-01	ci right 2.179143e-01	k: 2098	n:10000
Cons ci ratio: 8.088317e-02	ci left: 1.824506e-01	ci right 1.979303e-01	k: 1901	n:10000
KS ci ratio: 7.512432e-02	ci left: 2.058972e-01	ci right 2.220697e-01	k: 2139	n:10000
SPTA1   10000 perm   2 sec   (4073 perm/sec)   p_kst 2.139000e-01   p_cons 1.901000e-01   p_joint 2.098000e-01

Outputting figure to mutsig2_images.part000000000166/SPTA1.5_7468_10000_0.2139_0.1901_0.2098.png
                gene_name: SPTA1
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.18 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.22 

Current progress: 33 percent done.
SPRYD3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.017375e-02	ci left: 6.183401e-01	ci right 6.373854e-01	k: 6279	n:10000
Cons ci ratio: 7.564171e-02	ci left: 2.036295e-01	ci right 2.197388e-01	k: 2116	n:10000
KS ci ratio: 2.847290e-01	ci left: 1.594989e-02	ci right 2.133572e-02	k: 185	n:10000
SPRYD3   10000 perm   1 sec   (6764 perm/sec)   p_kst 1.850000e-02   p_cons 2.116000e-01   p_joint 6.279000e-01

Joint ci ratio: 4.221000e-02	ci left: 2.948957e-01	ci right 3.076621e-01	k: 6025	n:20000
Cons ci ratio: 5.281551e-02	ci left: 2.102144e-01	ci right 2.216683e-01	k: 4318	n:20000
KS ci ratio: 2.117242e-01	ci left: 1.506432e-02	ci right 1.867810e-02	k: 336	n:20000
SPRYD3   20000 perm   3 sec   (5900 perm/sec)   p_kst 1.680000e-02   p_cons 2.159000e-01   p_joint 3.012500e-01

Joint ci ratio: 1.898170e-02	ci left: 5.814369e-01	ci right 5.926129e-01	k: 17611	n:30000
Cons ci ratio: 4.330506e-02	ci left: 2.098663e-01	ci right 2.191891e-01	k: 6435	n:30000
KS ci ratio: 1.727866e-01	ci left: 1.540785e-02	ci right 1.835345e-02	k: 505	n:30000
SPRYD3   30000 perm   5 sec   (5591 perm/sec)   p_kst 1.683333e-02   p_cons 2.145000e-01   p_joint 5.870333e-01

Joint ci ratio: 2.165347e-02	ci left: 4.454406e-01	ci right 4.552166e-01	k: 18013	n:40000
Cons ci ratio: 3.753491e-02	ci left: 2.102126e-01	ci right 2.182789e-01	k: 8569	n:40000
KS ci ratio: 1.519060e-01	ci left: 1.512992e-02	ci right 1.764100e-02	k: 654	n:40000
SPRYD3   40000 perm   7 sec   (5393 perm/sec)   p_kst 1.635000e-02   p_cons 2.142250e-01   p_joint 4.503250e-01

Joint ci ratio: 3.419987e-02	ci left: 2.045090e-01	ci right 2.116449e-01	k: 10403	n:50000
Cons ci ratio: 3.359923e-02	ci left: 2.103721e-01	ci right 2.175812e-01	k: 10698	n:50000
KS ci ratio: 1.372172e-01	ci left: 1.495700e-02	ci right 1.717970e-02	k: 802	n:50000
SPRYD3   50000 perm   10 sec   (5238 perm/sec)   p_kst 1.604000e-02   p_cons 2.139600e-01   p_joint 2.080600e-01

Joint ci ratio: 2.717259e-02	ci left: 2.540213e-01	ci right 2.610355e-01	k: 15451	n:60000
Cons ci ratio: 3.059570e-02	ci left: 2.115194e-01	ci right 2.181082e-01	k: 12888	n:60000
KS ci ratio: 1.247104e-01	ci left: 1.518882e-02	ci right 1.722503e-02	k: 971	n:60000
SPRYD3   60000 perm   12 sec   (5103 perm/sec)   p_kst 1.618333e-02   p_cons 2.148000e-01   p_joint 2.575167e-01

Joint ci ratio: 2.886867e-02	ci left: 2.054672e-01	ci right 2.114999e-01	k: 14593	n:70000
Cons ci ratio: 2.837680e-02	ci left: 2.111655e-01	ci right 2.172582e-01	k: 14994	n:70000
KS ci ratio: 1.146402e-01	ci left: 1.548595e-02	ci right 1.738301e-02	k: 1149	n:70000
SPRYD3   70000 perm   14 sec   (4978 perm/sec)   p_kst 1.641429e-02   p_cons 2.142000e-01   p_joint 2.084714e-01

Joint ci ratio: 3.250387e-02	ci left: 1.513313e-01	ci right 1.563438e-01	k: 12306	n:80000
Cons ci ratio: 2.654816e-02	ci left: 2.113114e-01	ci right 2.170093e-01	k: 17132	n:80000
KS ci ratio: 1.073728e-01	ci left: 1.550688e-02	ci right 1.727845e-02	k: 1310	n:80000
SPRYD3   80000 perm   16 sec   (4864 perm/sec)   p_kst 1.637500e-02   p_cons 2.141500e-01   p_joint 1.538250e-01

Joint ci ratio: 3.060627e-02	ci left: 1.518020e-01	ci right 1.565314e-01	k: 13874	n:90000
Cons ci ratio: 2.505519e-02	ci left: 2.111362e-01	ci right 2.165045e-01	k: 19243	n:90000
KS ci ratio: 1.013675e-01	ci left: 1.551528e-02	ci right 1.718277e-02	k: 1470	n:90000
SPRYD3   90000 perm   19 sec   (4758 perm/sec)   p_kst 1.633333e-02   p_cons 2.138111e-01   p_joint 1.541556e-01

Joint ci ratio: 2.974459e-02	ci left: 1.457745e-01	ci right 1.501859e-01	k: 14797	n:100000
Cons ci ratio: 2.379296e-02	ci left: 2.109436e-01	ci right 2.160330e-01	k: 21348	n:100000
KS ci ratio: 9.602979e-02	ci left: 1.560233e-02	ci right 1.718590e-02	k: 1638	n:100000
SPRYD3   100000 perm   21 sec   (4664 perm/sec)   p_kst 1.638000e-02   p_cons 2.134800e-01   p_joint 1.479700e-01

Outputting figure to mutsig2_images.part000000000166/SPRYD3.2_1373_100000_0.01638_0.21348_0.14797.png
                gene_name: SPRYD3
               theta_stop: 0.096 
                    nperm: 100000 
                     p_ks: 0.016 
        ci_ks_bounds_left: 0.016 
       ci_ks_bounds_right: 0.017 
                   p_cons: 0.21 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.22 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.15 
    ci_joint_bounds_right: 0.15 

Current progress: 67 percent done.
SRPRB
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.641604e-02	ci left: 5.268671e-01	ci right 5.465115e-01	k: 5367	n:10000
Cons ci ratio: 4.005790e-02	ci left: 4.792569e-01	ci right 4.989495e-01	k: 4891	n:10000
KS ci ratio: 2.323517e-02	ci left: 7.312838e-01	ci right 7.485762e-01	k: 7400	n:10000
SRPRB   10000 perm   1 sec   (6741 perm/sec)   p_kst 7.400000e-01   p_cons 4.891000e-01   p_joint 5.367000e-01

Outputting figure to mutsig2_images.part000000000166/SRPRB.2_844_10000_0.74_0.4891_0.5367.png
                gene_name: SRPRB
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.75 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  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.165.3896/
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/181708/iteration1/scatter.0000000166
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 166 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1645>
Subject: Job 1120277: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1645>, 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/181708/iteration1/scatter.0000000167> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:50:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000167.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000167.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 167  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    322.84 sec.
    Max Memory :      1353 MB
    Max Swap   :      3846 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.165.3896/
-whichjob
167
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 167: processing genes 15019 - 15108
Calculating significance of each gene.
Using projection method.
15019	SRPX	4.584060e-02
15020	SRPX2	1
15021	SRR	4.936729e-02
15022	SRRD	1
15023	SRRM1	1.785882e-01
15024	SRRM2	1
15025	SRRM3	1
15026	SRRM4	1
15027	SRRT	3.445585e-01
15028	SRXN1	1
15029	SRY	1
15030	SS18	1
15031	SS18L1	1
15032	SS18L2	1
15033	SSB	5.207895e-02
15034	SSBP1	1
15035	SSBP2	1
15036	SSBP3	1
15037	SSBP4	1
15038	SSFA2	1
15039	SSH1	3.805606e-01
15040	SSH2	4.604847e-01
15041	SSH3	9.219539e-02
15042	SSNA1	1
15043	SSPN	1
15044	SSPO	1.357715e-01
15045	SSR1	1
15046	SSR2	1
15047	SSR3	1
15048	SSR4	1
15049	SSRP1	1
15050	SSSCA1	1
15051	SST	1
15052	SSTR1	1
15053	SSTR2	1
15054	SSTR3	1
15055	SSTR4	1
15056	SSTR5	1
15057	SSU72	1
15058	SSX1	1
15059	SSX2IP	2.076718e-01
15060	SSX3	1
15061	SSX5	1
15062	SSX7	1
15063	ST13	1
15064	ST14	1
15065	ST18	3.630257e-01
15066	ST20	7.699050e-03
15067	ST3GAL1	1
15068	ST3GAL2	1
15069	ST3GAL3	1
15070	ST3GAL4	1
15071	ST3GAL5	1
15072	ST3GAL6	1
15073	ST5	1
15074	ST6GAL1	1
15075	ST6GAL2	1.065993e-01
15076	ST6GALNAC1	1
15077	ST6GALNAC2	1
15078	ST6GALNAC3	1
15079	ST6GALNAC4	1
15080	ST6GALNAC5	1
15081	ST6GALNAC6	2.361848e-02
15082	ST7	1
15083	ST7L	1.723800e-01
15084	ST8SIA1	1
15085	ST8SIA2	3.688723e-02
15086	ST8SIA3	1
15087	ST8SIA4	1
15088	ST8SIA5	1
15089	ST8SIA6	1
15090	STAB1	5.308112e-02
15091	STAB2	1
15092	STAC	1
15093	STAC2	1
15094	STAC3	1
15095	STAG1	1
15096	STAG2	2.457493e-01
15097	STAG3	1
15098	STAG3L2	1
15099	STAG3L4	1
15100	STAM	1
15101	STAM2	1
15102	STAMBP	1
15103	STAMBPL1	1
15104	STAP1	1
15105	STAP2	1
15106	STAR	1
15107	STARD10	1
15108	STARD13	1
Done

Running MutSig 2:
Scatter job 167: processing genes 15019 - 15108
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SSPO
Processing conservation and coverage...
62% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.920119e-01	ci left: 1.511403e-02	ci right 2.037228e-02	k: 176	n:10000
Cons ci ratio: 3.621153e-02	ci left: 5.296705e-01	ci right 5.493065e-01	k: 5395	n:10000
KS ci ratio: 5.132010e-01	ci left: 4.319899e-03	ci right 7.378784e-03	k: 57	n:10000
SSPO   10000 perm   4 sec   (2751 perm/sec)   p_kst 5.700000e-03   p_cons 5.395000e-01   p_joint 1.760000e-02

Joint ci ratio: 1.767584e-01	ci left: 2.187547e-02	ci right 2.616445e-02	k: 479	n:20000
Cons ci ratio: 2.416459e-02	ci left: 5.612507e-01	ci right 5.750295e-01	k: 11363	n:20000
KS ci ratio: 3.693575e-01	ci left: 4.567803e-03	ci right 6.679840e-03	k: 111	n:20000
SSPO   20000 perm   9 sec   (2137 perm/sec)   p_kst 5.550000e-03   p_cons 5.681500e-01   p_joint 2.395000e-02

Joint ci ratio: 1.412388e-01	ci left: 2.326276e-02	ci right 2.683003e-02	k: 750	n:30000
Cons ci ratio: 2.024421e-02	ci left: 5.498552e-01	ci right 5.611340e-01	k: 16665	n:30000
KS ci ratio: 2.971666e-01	ci left: 4.910451e-03	ci right 6.654022e-03	k: 172	n:30000
SSPO   30000 perm   13 sec   (2232 perm/sec)   p_kst 5.733333e-03   p_cons 5.555000e-01   p_joint 2.500000e-02

Joint ci ratio: 1.357340e-01	ci left: 1.903706e-02	ci right 2.183317e-02	k: 816	n:40000
Cons ci ratio: 1.752420e-02	ci left: 5.508392e-01	ci right 5.606027e-01	k: 22229	n:40000
KS ci ratio: 2.555046e-01	ci left: 5.102800e-03	ci right 6.620287e-03	k: 233	n:40000
SSPO   40000 perm   18 sec   (2268 perm/sec)   p_kst 5.825000e-03   p_cons 5.557250e-01   p_joint 2.040000e-02

Joint ci ratio: 1.269922e-01	ci left: 1.751126e-02	ci right 1.990508e-02	k: 934	n:50000
Cons ci ratio: 1.561859e-02	ci left: 5.531132e-01	ci right 5.618401e-01	k: 27874	n:50000
KS ci ratio: 2.303197e-01	ci left: 5.096658e-03	ci right 6.441699e-03	k: 287	n:50000
SSPO   50000 perm   22 sec   (2301 perm/sec)   p_kst 5.740000e-03   p_cons 5.574800e-01   p_joint 1.868000e-02

Joint ci ratio: 1.070323e-01	ci left: 2.069507e-02	ci right 2.305150e-02	k: 1311	n:60000
Cons ci ratio: 1.426639e-02	ci left: 5.531978e-01	ci right 5.611633e-01	k: 33431	n:60000
KS ci ratio: 2.095221e-01	ci left: 5.192265e-03	ci right 6.422943e-03	k: 347	n:60000
SSPO   60000 perm   26 sec   (2290 perm/sec)   p_kst 5.783333e-03   p_cons 5.571833e-01   p_joint 2.185000e-02

Joint ci ratio: 1.065839e-01	ci left: 1.794581e-02	ci right 1.998005e-02	k: 1326	n:70000
Cons ci ratio: 1.319815e-02	ci left: 5.538683e-01	ci right 5.612412e-01	k: 39029	n:70000
KS ci ratio: 1.918526e-01	ci left: 5.359683e-03	ci right 6.510422e-03	k: 414	n:70000
SSPO   70000 perm   31 sec   (2271 perm/sec)   p_kst 5.914286e-03   p_cons 5.575571e-01   p_joint 1.894286e-02

Joint ci ratio: 1.059440e-01	ci left: 1.593289e-02	ci right 1.772740e-02	k: 1345	n:80000
Cons ci ratio: 1.234000e-02	ci left: 5.543377e-01	ci right 5.612331e-01	k: 44623	n:80000
KS ci ratio: 1.770896e-01	ci left: 5.548265e-03	ci right 6.638020e-03	k: 486	n:80000
SSPO   80000 perm   35 sec   (2282 perm/sec)   p_kst 6.075000e-03   p_cons 5.577875e-01   p_joint 1.681250e-02

Joint ci ratio: 8.750542e-02	ci left: 2.085584e-02	ci right 2.277516e-02	k: 1962	n:90000
Cons ci ratio: 1.165471e-02	ci left: 5.536695e-01	ci right 5.601713e-01	k: 50123	n:90000
KS ci ratio: 1.677141e-01	ci left: 5.527173e-03	ci right 6.549503e-03	k: 542	n:90000
SSPO   90000 perm   41 sec   (2208 perm/sec)   p_kst 6.022222e-03   p_cons 5.569222e-01   p_joint 2.180000e-02

Joint ci ratio: 8.400688e-02	ci left: 2.041403e-02	ci right 2.221389e-02	k: 2130	n:100000
Cons ci ratio: 1.104169e-02	ci left: 5.545050e-01	ci right 5.606716e-01	k: 55759	n:100000
KS ci ratio: 1.691806e-01	ci left: 4.888111e-03	ci right 5.800941e-03	k: 533	n:100000
SSPO   100000 perm   45 sec   (2211 perm/sec)   p_kst 5.330000e-03   p_cons 5.575900e-01   p_joint 2.130000e-02

Joint ci ratio: 8.431219e-02	ci left: 1.845952e-02	ci right 2.009324e-02	k: 2119	n:110000
Cons ci ratio: 1.052589e-02	ci left: 5.547408e-01	ci right 5.606198e-01	k: 61345	n:110000
KS ci ratio: 1.612247e-01	ci left: 4.914364e-03	ci right 5.784757e-03	k: 587	n:110000
SSPO   110000 perm   50 sec   (2192 perm/sec)   p_kst 5.336364e-03   p_cons 5.576818e-01   p_joint 1.926364e-02

Joint ci ratio: 8.138420e-02	ci left: 1.819419e-02	ci right 1.974585e-02	k: 2275	n:120000
Cons ci ratio: 1.007112e-02	ci left: 5.551929e-01	ci right 5.608209e-01	k: 66961	n:120000
KS ci ratio: 1.551477e-01	ci left: 4.880992e-03	ci right 5.709858e-03	k: 634	n:120000
SSPO   120000 perm   55 sec   (2192 perm/sec)   p_kst 5.283333e-03   p_cons 5.580083e-01   p_joint 1.895833e-02

Joint ci ratio: 8.375939e-02	ci left: 1.587475e-02	ci right 1.727002e-02	k: 2153	n:130000
Cons ci ratio: 9.681166e-03	ci left: 5.550413e-01	ci right 5.604485e-01	k: 72507	n:130000
KS ci ratio: 1.494895e-01	ci left: 4.868088e-03	ci right 5.661918e-03	k: 683	n:130000
SSPO   130000 perm   59 sec   (2189 perm/sec)   p_kst 5.253846e-03   p_cons 5.577462e-01   p_joint 1.656154e-02

Joint ci ratio: 8.223421e-02	ci left: 1.531421e-02	ci right 1.663452e-02	k: 2235	n:140000
Cons ci ratio: 9.327588e-03	ci left: 5.552151e-01	ci right 5.604253e-01	k: 78095	n:140000
KS ci ratio: 1.432345e-01	ci left: 4.940143e-03	ci right 5.709135e-03	k: 744	n:140000
SSPO   140000 perm   64 sec   (2184 perm/sec)   p_kst 5.314286e-03   p_cons 5.578214e-01   p_joint 1.596429e-02

Joint ci ratio: 7.280534e-02	ci left: 1.826924e-02	ci right 1.965610e-02	k: 2843	n:150000
Cons ci ratio: 9.007929e-03	ci left: 5.554890e-01	ci right 5.605221e-01	k: 83701	n:150000
KS ci ratio: 1.387465e-01	ci left: 4.925943e-03	ci right 5.666711e-03	k: 793	n:150000
SSPO   150000 perm   69 sec   (2177 perm/sec)   p_kst 5.286667e-03   p_cons 5.580067e-01   p_joint 1.895333e-02

Joint ci ratio: 7.212966e-02	ci left: 1.747081e-02	ci right 1.878423e-02	k: 2899	n:160000
Cons ci ratio: 8.726875e-03	ci left: 5.552873e-01	ci right 5.601606e-01	k: 89236	n:160000
KS ci ratio: 1.351397e-01	ci left: 4.877606e-03	ci right 5.590504e-03	k: 836	n:160000
SSPO   160000 perm   74 sec   (2169 perm/sec)   p_kst 5.225000e-03   p_cons 5.577250e-01   p_joint 1.811875e-02

Joint ci ratio: 6.756225e-02	ci left: 1.876119e-02	ci right 2.007880e-02	k: 3300	n:170000
Cons ci ratio: 8.465635e-03	ci left: 5.553999e-01	ci right 5.601275e-01	k: 94820	n:170000
KS ci ratio: 1.313510e-01	ci left: 4.869314e-03	ci right 5.559490e-03	k: 885	n:170000
SSPO   170000 perm   79 sec   (2153 perm/sec)   p_kst 5.205882e-03   p_cons 5.577647e-01   p_joint 1.941176e-02

Joint ci ratio: 5.855373e-02	ci left: 2.358261e-02	ci right 2.501055e-02	k: 4372	n:180000
Cons ci ratio: 8.227367e-03	ci left: 5.554519e-01	ci right 5.600462e-01	k: 100395	n:180000
KS ci ratio: 1.270470e-01	ci left: 4.926743e-03	ci right 5.600453e-03	k: 946	n:180000
SSPO   180000 perm   84 sec   (2144 perm/sec)   p_kst 5.255556e-03   p_cons 5.577500e-01   p_joint 2.428889e-02

Joint ci ratio: 6.102912e-02	ci left: 2.060362e-02	ci right 2.190578e-02	k: 4037	n:190000
Cons ci ratio: 8.014216e-03	ci left: 5.551263e-01	ci right 5.595983e-01	k: 105899	n:190000
KS ci ratio: 1.232631e-01	ci left: 4.968252e-03	ci right 5.625928e-03	k: 1005	n:190000
SSPO   190000 perm   90 sec   (2114 perm/sec)   p_kst 5.289474e-03   p_cons 5.573632e-01   p_joint 2.124737e-02

Joint ci ratio: 6.038653e-02	ci left: 2.001150e-02	ci right 2.126245e-02	k: 4126	n:200000
Cons ci ratio: 7.813085e-03	ci left: 5.550698e-01	ci right 5.594286e-01	k: 111450	n:200000
KS ci ratio: 1.201390e-01	ci left: 4.976774e-03	ci right 5.617693e-03	k: 1058	n:200000
SSPO   200000 perm   96 sec   (2082 perm/sec)   p_kst 5.290000e-03   p_cons 5.572500e-01   p_joint 2.063000e-02

Joint ci ratio: 5.225803e-02	ci left: 2.541287e-02	ci right 2.678120e-02	k: 5479	n:210000
Cons ci ratio: 7.622475e-03	ci left: 5.552725e-01	ci right 5.595259e-01	k: 117054	n:210000
KS ci ratio: 1.172411e-01	ci left: 4.984674e-03	ci right 5.610053e-03	k: 1111	n:210000
SSPO   210000 perm   101 sec   (2071 perm/sec)   p_kst 5.290476e-03   p_cons 5.574000e-01   p_joint 2.609048e-02

Joint ci ratio: 5.067245e-02	ci left: 2.581036e-02	ci right 2.715670e-02	k: 5825	n:220000
Cons ci ratio: 7.451410e-03	ci left: 5.550441e-01	ci right 5.591999e-01	k: 122567	n:220000
KS ci ratio: 1.137605e-01	ci left: 5.062686e-03	ci right 5.677730e-03	k: 1180	n:220000
SSPO   220000 perm   107 sec   (2060 perm/sec)   p_kst 5.363636e-03   p_cons 5.571227e-01   p_joint 2.647727e-02

Joint ci ratio: 4.988696e-02	ci left: 2.549089e-02	ci right 2.679935e-02	k: 6012	n:230000
Cons ci ratio: 7.289951e-03	ci left: 5.549322e-01	ci right 5.589968e-01	k: 128102	n:230000
KS ci ratio: 1.111551e-01	ci left: 5.079201e-03	ci right 5.681194e-03	k: 1236	n:230000
SSPO   230000 perm   113 sec   (2044 perm/sec)   p_kst 5.373913e-03   p_cons 5.569652e-01   p_joint 2.613913e-02

Joint ci ratio: 4.931252e-02	ci left: 2.502117e-02	ci right 2.629032e-02	k: 6156	n:240000
Cons ci ratio: 7.132225e-03	ci left: 5.552683e-01	ci right 5.592469e-01	k: 133742	n:240000
KS ci ratio: 1.089328e-01	ci left: 5.074218e-03	ci right 5.662825e-03	k: 1287	n:240000
SSPO   240000 perm   118 sec   (2026 perm/sec)   p_kst 5.362500e-03   p_cons 5.572583e-01   p_joint 2.565000e-02

Joint ci ratio: 5.497534e-02	ci left: 1.938375e-02	ci right 2.048342e-02	k: 4982	n:250000
Cons ci ratio: 7.171641e-03	ci left: 5.424773e-01	ci right 5.463857e-01	k: 136108	n:250000
KS ci ratio: 1.070399e-01	ci left: 5.050276e-03	ci right 5.625284e-03	k: 1333	n:250000
SSPO   250000 perm   124 sec   (2015 perm/sec)   p_kst 5.332000e-03   p_cons 5.444320e-01   p_joint 1.992800e-02

Joint ci ratio: 5.573694e-02	ci left: 1.814861e-02	ci right 1.919293e-02	k: 4853	n:260000
Cons ci ratio: 7.027159e-03	ci left: 5.428834e-01	ci right 5.467156e-01	k: 141648	n:260000
KS ci ratio: 1.048231e-01	ci left: 5.069459e-03	ci right 5.633961e-03	k: 1390	n:260000
SSPO   260000 perm   130 sec   (2004 perm/sec)   p_kst 5.346154e-03   p_cons 5.448000e-01   p_joint 1.866538e-02

Joint ci ratio: 5.239389e-02	ci left: 1.977868e-02	ci right 2.084647e-02	k: 5483	n:270000
Cons ci ratio: 6.899457e-03	ci left: 5.426562e-01	ci right 5.464169e-01	k: 147025	n:270000
KS ci ratio: 1.028099e-01	ci left: 5.080118e-03	ci right 5.634285e-03	k: 1445	n:270000
SSPO   270000 perm   135 sec   (1993 perm/sec)   p_kst 5.351852e-03   p_cons 5.445370e-01   p_joint 2.030741e-02

Joint ci ratio: 5.299783e-02	ci left: 1.865613e-02	ci right 1.967528e-02	k: 5365	n:280000
Cons ci ratio: 6.781251e-03	ci left: 5.422423e-01	ci right 5.459354e-01	k: 152345	n:280000
KS ci ratio: 1.008747e-01	ci left: 5.093592e-03	ci right 5.638152e-03	k: 1501	n:280000
SSPO   280000 perm   141 sec   (1981 perm/sec)   p_kst 5.360714e-03   p_cons 5.440893e-01   p_joint 1.916071e-02

Joint ci ratio: 4.930583e-02	ci left: 2.080483e-02	ci right 2.185994e-02	k: 6185	n:290000
Cons ci ratio: 6.661312e-03	ci left: 5.424231e-01	ci right 5.460518e-01	k: 157829	n:290000
KS ci ratio: 9.914085e-02	ci left: 5.096139e-03	ci right 5.631061e-03	k: 1554	n:290000
SSPO   290000 perm   147 sec   (1970 perm/sec)   p_kst 5.358621e-03   p_cons 5.442379e-01   p_joint 2.132759e-02

Outputting figure to mutsig2_images.part000000000167/SSPO.4_15875_290000_0.0053586_0.54424_0.021328.png
                gene_name: SSPO
               theta_stop: 0.099 
                    nperm: 290000 
                     p_ks: 0.0054 
        ci_ks_bounds_left: 0.0051 
       ci_ks_bounds_right: 0.0056 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.55 
                  p_joint: 0.021 
     ci_joint_bounds_left: 0.021 
    ci_joint_bounds_right: 0.022 

Current progress: 25 percent done.
STAB1
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: 1.458799e-02	ci left: 8.718340e-01	ci right 8.847448e-01	k: 8784	n:10000
KS ci ratio: 1.395289e-02	ci left: 8.812461e-01	ci right 8.937272e-01	k: 8876	n:10000
STAB1   10000 perm   2 sec   (4172 perm/sec)   p_kst 8.876000e-01   p_cons 8.784000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000167/STAB1.3_7989_10000_0.8876_0.8784_1.png
                gene_name: STAB1
               theta_stop: 0.015 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   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: 50 percent done.
SRRM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.895240e-01	ci left: 1.539246e-02	ci right 2.069361e-02	k: 179	n:10000
Cons ci ratio: 1.511704e-01	ci left: 5.821938e-02	ci right 6.783712e-02	k: 629	n:10000
KS ci ratio: 3.541838e-01	ci left: 9.958933e-03	ci right 1.433217e-02	k: 120	n:10000
SRRM1   10000 perm   2 sec   (5811 perm/sec)   p_kst 1.200000e-02   p_cons 6.290000e-02   p_joint 1.790000e-02

Joint ci ratio: 1.477441e-01	ci left: 3.148306e-02	ci right 3.655359e-02	k: 679	n:20000
Cons ci ratio: 1.077657e-01	ci left: 5.869667e-02	ci right 6.543134e-02	k: 1240	n:20000
KS ci ratio: 2.499297e-01	ci left: 1.063101e-02	ci right 1.371326e-02	k: 242	n:20000
SRRM1   20000 perm   4 sec   (5325 perm/sec)   p_kst 1.210000e-02   p_cons 6.200000e-02   p_joint 3.395000e-02

Joint ci ratio: 1.219389e-01	ci left: 3.126601e-02	ci right 3.535836e-02	k: 998	n:30000
Cons ci ratio: 8.733012e-02	ci left: 6.017846e-02	ci right 6.570655e-02	k: 1887	n:30000
KS ci ratio: 2.071094e-01	ci left: 1.057722e-02	ci right 1.305201e-02	k: 353	n:30000
SRRM1   30000 perm   6 sec   (5086 perm/sec)   p_kst 1.176667e-02   p_cons 6.290000e-02   p_joint 3.326667e-02

Joint ci ratio: 6.951086e-02	ci left: 7.108420e-02	ci right 7.622790e-02	k: 2945	n:40000
Cons ci ratio: 7.579653e-02	ci left: 6.029450e-02	ci right 6.506923e-02	k: 2506	n:40000
KS ci ratio: 1.774699e-01	ci left: 1.097988e-02	ci right 1.314182e-02	k: 481	n:40000
SRRM1   40000 perm   8 sec   (4794 perm/sec)   p_kst 1.202500e-02   p_cons 6.265000e-02   p_joint 7.362500e-02

Joint ci ratio: 6.118710e-02	ci left: 7.353415e-02	ci right 7.819524e-02	k: 3792	n:50000
Cons ci ratio: 6.795381e-02	ci left: 6.027563e-02	ci right 6.453535e-02	k: 3119	n:50000
KS ci ratio: 1.597437e-01	ci left: 1.094874e-02	ci right 1.286855e-02	k: 594	n:50000
SRRM1   50000 perm   11 sec   (4669 perm/sec)   p_kst 1.188000e-02   p_cons 6.238000e-02   p_joint 7.584000e-02

Joint ci ratio: 6.946440e-02	ci left: 4.864657e-02	ci right 5.216375e-02	k: 3023	n:60000
Cons ci ratio: 6.200665e-02	ci left: 6.051030e-02	ci right 6.439882e-02	k: 3746	n:60000
KS ci ratio: 1.458256e-01	ci left: 1.103162e-02	ci right 1.278274e-02	k: 713	n:60000
SRRM1   60000 perm   13 sec   (4596 perm/sec)   p_kst 1.188333e-02   p_cons 6.243333e-02   p_joint 5.038333e-02

Joint ci ratio: 7.742137e-02	ci left: 3.395912e-02	ci right 3.670814e-02	k: 2472	n:70000
Cons ci ratio: 5.746668e-02	ci left: 6.053462e-02	ci right 6.413034e-02	k: 4362	n:70000
KS ci ratio: 1.352552e-01	ci left: 1.105461e-02	ci right 1.267194e-02	k: 829	n:70000
SRRM1   70000 perm   15 sec   (4518 perm/sec)   p_kst 1.184286e-02   p_cons 6.231429e-02   p_joint 3.531429e-02

Joint ci ratio: 4.835470e-02	ci left: 7.407395e-02	ci right 7.775687e-02	k: 6072	n:80000
Cons ci ratio: 5.366507e-02	ci left: 6.084461e-02	ci right 6.421220e-02	k: 5001	n:80000
KS ci ratio: 1.267614e-01	ci left: 1.106321e-02	ci right 1.257250e-02	k: 944	n:80000
SRRM1   80000 perm   18 sec   (4445 perm/sec)   p_kst 1.180000e-02   p_cons 6.251250e-02   p_joint 7.590000e-02

Joint ci ratio: 4.381355e-02	ci left: 7.988545e-02	ci right 8.347490e-02	k: 7350	n:90000
Cons ci ratio: 5.059235e-02	ci left: 6.094908e-02	ci right 6.412363e-02	k: 5627	n:90000
KS ci ratio: 1.196901e-01	ci left: 1.107238e-02	ci right 1.249268e-02	k: 1059	n:90000
SRRM1   90000 perm   21 sec   (4373 perm/sec)   p_kst 1.176667e-02   p_cons 6.252222e-02   p_joint 8.166667e-02

Joint ci ratio: 4.162566e-02	ci left: 7.976186e-02	ci right 8.316246e-02	k: 8145	n:100000
Cons ci ratio: 4.790767e-02	ci left: 6.124473e-02	ci right 6.426069e-02	k: 6274	n:100000
KS ci ratio: 1.134398e-01	ci left: 1.113018e-02	ci right 1.247836e-02	k: 1179	n:100000
SRRM1   100000 perm   23 sec   (4302 perm/sec)   p_kst 1.179000e-02   p_cons 6.274000e-02   p_joint 8.145000e-02

Joint ci ratio: 3.669735e-02	ci left: 9.225456e-02	ci right 9.571234e-02	k: 10337	n:110000
Cons ci ratio: 4.580755e-02	ci left: 6.098660e-02	ci right 6.385470e-02	k: 6865	n:110000
KS ci ratio: 1.085421e-01	ci left: 1.108174e-02	ci right 1.236238e-02	k: 1288	n:110000
SRRM1   110000 perm   26 sec   (4232 perm/sec)   p_kst 1.170909e-02   p_cons 6.240909e-02   p_joint 9.397273e-02

Joint ci ratio: 3.810337e-02	ci left: 7.950359e-02	ci right 8.260002e-02	k: 9725	n:120000
Cons ci ratio: 4.392055e-02	ci left: 6.088117e-02	ci right 6.362337e-02	k: 7469	n:120000
KS ci ratio: 1.045695e-01	ci left: 1.096935e-02	ci right 1.218776e-02	k: 1388	n:120000
SRRM1   120000 perm   29 sec   (4168 perm/sec)   p_kst 1.156667e-02   p_cons 6.224167e-02   p_joint 8.104167e-02

Joint ci ratio: 3.668912e-02	ci left: 7.924016e-02	ci right 8.220934e-02	k: 10493	n:130000
Cons ci ratio: 4.221837e-02	ci left: 6.087781e-02	ci right 6.351099e-02	k: 8084	n:130000
KS ci ratio: 1.010720e-01	ci left: 1.085999e-02	ci right 1.202350e-02	k: 1486	n:130000
SRRM1   130000 perm   32 sec   (4107 perm/sec)   p_kst 1.143077e-02   p_cons 6.218462e-02   p_joint 8.071538e-02

Joint ci ratio: 3.530737e-02	ci left: 7.949092e-02	ci right 8.235503e-02	k: 11328	n:140000
Cons ci ratio: 4.080252e-02	ci left: 6.058664e-02	ci right 6.311726e-02	k: 8658	n:140000
KS ci ratio: 9.743805e-02	ci left: 1.087139e-02	ci right 1.199184e-02	k: 1599	n:140000
SRRM1   140000 perm   35 sec   (4050 perm/sec)   p_kst 1.142143e-02   p_cons 6.184286e-02   p_joint 8.091429e-02

Outputting figure to mutsig2_images.part000000000167/SRRM1.2_2783_140000_0.011421_0.061843_0.080914.png
                gene_name: SRRM1
               theta_stop: 0.097 
                    nperm: 140000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.011 
       ci_ks_bounds_right: 0.012 
                   p_cons: 0.062 
      ci_cons_bounds_left: 0.061 
     ci_cons_bounds_right: 0.063 
                  p_joint: 0.081 
     ci_joint_bounds_left: 0.079 
    ci_joint_bounds_right: 0.082 

Current progress: 75 percent done.
ST18
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.438733e-01	ci left: 6.410846e-02	ci right 7.414431e-02	k: 690	n:10000
Cons ci ratio: 1.799927e-02	ci left: 8.183233e-01	ci right 8.332864e-01	k: 8259	n:10000
KS ci ratio: 1.564030e-01	ci left: 5.446081e-02	ci right 6.379808e-02	k: 590	n:10000
ST18   10000 perm   2 sec   (5783 perm/sec)   p_kst 5.900000e-02   p_cons 8.259000e-01   p_joint 6.900000e-02

Joint ci ratio: 4.451602e-03	ci left: 9.726368e-01	ci right 9.770237e-01	k: 19498	n:20000
Cons ci ratio: 1.262282e-02	ci left: 8.229503e-01	ci right 8.334541e-01	k: 16565	n:20000
KS ci ratio: 1.090837e-01	ci left: 5.733236e-02	ci right 6.399608e-02	k: 1212	n:20000
ST18   20000 perm   4 sec   (5203 perm/sec)   p_kst 6.060000e-02   p_cons 8.282500e-01   p_joint 9.749000e-01

Joint ci ratio: 1.306580e-04	ci left: 9.998770e-01	ci right 1	k: 30000	n:30000
Cons ci ratio: 1.029125e-02	ci left: 8.243544e-01	ci right 8.329152e-01	k: 24860	n:30000
KS ci ratio: 8.838394e-02	ci left: 5.880731e-02	ci right 6.427798e-02	k: 1845	n:30000
ST18   30000 perm   6 sec   (4948 perm/sec)   p_kst 6.150000e-02   p_cons 8.286667e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000167/ST18.2_3224_30000_0.0615_0.82867_1.png
                gene_name: ST18
               theta_stop: 0.088 
                    nperm: 30000 
                     p_ks: 0.061 
        ci_ks_bounds_left: 0.059 
       ci_ks_bounds_right: 0.064 
                   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: 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.165.3896/
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/181708/iteration1/scatter.0000000167
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 167 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120280: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000168> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:46:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000168.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000168.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 168  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     62.75 sec.
    Max Memory :      1136 MB
    Max Swap   :      3986 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.165.3896/
-whichjob
168
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 168: processing genes 15109 - 15199
Calculating significance of each gene.
Using projection method.
15109	STARD3	1
15110	STARD3NL	1
15111	STARD4	1
15112	STARD5	1
15113	STARD6	1
15114	STARD7	1
15115	STARD8	2.651830e-01
15116	STAT1	2.282757e-01
15117	STAT2	1
15118	STAT3	1
15119	STAT4	1
15120	STAT5A	1
15121	STAT5B	1.000574e-01
15122	STAT6	1
15123	STATH	1
15124	STAU1	2.208948e-01
15125	STAU2	1
15126	STBD1	1
15127	STC1	1
15128	STC2	1
15129	STEAP1	1
15130	STEAP2	1
15131	STEAP3	1
15132	STEAP4	1
15133	STH	1
15134	STIL	2.492050e-01
15135	STIM1	1
15136	STIM2	1
15137	STIP1	1
15138	STK10	1.415891e-01
15139	STK11	1
15140	STK11IP	1
15141	STK16	1
15142	STK17A	1
15143	STK17B	1
15144	STK19	1
15145	STK24	1
15146	STK25	1
15147	STK3	1
15148	STK31	1
15149	STK32A	1
15150	STK32B	1
15151	STK32C	1
15152	STK33	1
15153	STK35	1
15154	STK36	1
15155	STK38	5.524235e-02
15156	STK38L	1
15157	STK39	1
15158	STK4	1
15159	STK40	1
15160	STMN1	1
15161	STMN2	1
15162	STMN3	1
15163	STMN4	1
15164	STOM	1.081584e-01
15165	STOML1	1
15166	STOML2	1
15167	STOML3	1
15168	STON1	1
15169	STON1-GTF2A1L	1
15170	STON2	1
15171	STOX1	1
15172	STOX2	1
15173	STRA13	1
15174	STRA6	1
15175	STRA8	1.184543e-02
15176	STRADA	1
15177	STRADB	1
15178	STRAP	1
15179	STRBP	1
15180	STRC	1
15181	STRN	1
15182	STRN3	1
15183	STRN4	1
15184	STS	1
15185	STT3A	1
15186	STT3B	1
15187	STUB1	8.820655e-02
15188	STX10	1
15189	STX11	1
15190	STX12	1
15191	STX16	1
15192	STX17	1
15193	STX18	1
15194	STX19	1
15195	STX1A	1
15196	STX1B	1
15197	STX2	1
15198	STX3	1
15199	STX4	1
Done

Running MutSig 2:
Scatter job 168: processing genes 15109 - 15199
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
STUB1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.281323e-02	ci left: 2.164518e-01	ci right 2.329089e-01	k: 2246	n:10000
Cons ci ratio: 1.515559e-01	ci left: 5.793006e-02	ci right 6.752661e-02	k: 626	n:10000
KS ci ratio: 1.941074e-02	ci left: 7.951683e-01	ci right 8.108548e-01	k: 8031	n:10000
STUB1   10000 perm   1 sec   (6867 perm/sec)   p_kst 8.031000e-01   p_cons 6.260000e-02   p_joint 2.246000e-01

Joint ci ratio: 3.133476e-02	ci left: 4.320566e-01	ci right 4.458611e-01	k: 8779	n:20000
Cons ci ratio: 1.091316e-01	ci left: 5.728364e-02	ci right 6.394481e-02	k: 1211	n:20000
KS ci ratio: 1.385089e-02	ci left: 7.945900e-01	ci right 8.057226e-01	k: 16004	n:20000
STUB1   20000 perm   5 sec   (3842 perm/sec)   p_kst 8.002000e-01   p_cons 6.055000e-02   p_joint 4.389500e-01

Joint ci ratio: 5.975088e-02	ci left: 1.217051e-01	ci right 1.292342e-01	k: 3763	n:30000
Cons ci ratio: 8.848614e-02	ci left: 5.867675e-02	ci right 6.414190e-02	k: 1841	n:30000
KS ci ratio: 1.123954e-02	ci left: 7.976130e-01	ci right 8.066618e-01	k: 24065	n:30000
STUB1   30000 perm   7 sec   (4231 perm/sec)   p_kst 8.021667e-01   p_cons 6.136667e-02   p_joint 1.254333e-01

Outputting figure to mutsig2_images.part000000000168/STUB1.2_940_30000_0.80217_0.061367_0.12543.png
                gene_name: STUB1
               theta_stop: 0.088 
                    nperm: 30000 
                     p_ks: 0.80 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.061 
      ci_cons_bounds_left: 0.059 
     ci_cons_bounds_right: 0.064 
                  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.165.3896/
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/181708/iteration1/scatter.0000000168
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 168 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1642>
Subject: Job 1120283: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, 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/181708/iteration1/scatter.0000000169> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:46:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000169.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000169.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 169  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    110.97 sec.
    Max Memory :       866 MB
    Max Swap   :      3773 MB

    Max Processes  :         7
    Max Threads    :        91

The output (if any) follows:

fh_MutSigRun
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/
-whichjob
169
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 169: processing genes 15200 - 15289
Calculating significance of each gene.
Using projection method.
15200	STX5	1
15201	STX6	1
15202	STX7	1
15203	STX8	1.211613e-01
15204	STXBP1	1
15205	STXBP2	1
15206	STXBP3	1.711439e-01
15207	STXBP4	1
15208	STXBP5	3.601878e-02
15209	STXBP5L	1.863585e-01
15210	STXBP6	1
15211	STYK1	1
15212	STYX	1
15213	STYXL1	1
15214	SUB1	1
15215	SUCLA2	1
15216	SUCLG1	1
15217	SUCLG2	1
15218	SUCNR1	1.085044e-01
15219	SUDS3	1
15220	SUFU	1
15221	SUGT1	1
15222	SULF1	1.680725e-01
15223	SULF2	3.251057e-01
15224	SULT1A1	1
15225	SULT1A2	1
15226	SULT1B1	1
15227	SULT1C2	1
15228	SULT1C3	1
15229	SULT1C4	1
15230	SULT1E1	1
15231	SULT2A1	1
15232	SULT2B1	1.696416e-02
15233	SULT4A1	1
15234	SULT6B1	1
15235	SUMF1	3.824302e-02
15236	SUMF2	1
15237	SUMO1	1
15238	SUMO2	1
15239	SUMO3	1
15240	SUMO4	1
15241	SUN1	1.593026e-01
15242	SUN2	1
15243	SUN3	1.130803e-01
15244	SUN5	1
15245	SUOX	1
15246	SUPT16H	2.586382e-01
15247	SUPT3H	1
15248	SUPT4H1	1
15249	SUPT5H	1
15250	SUPT6H	5.537486e-01
15251	SUPT7L	1.743478e-01
15252	SUPV3L1	1
15253	SURF1	1
15254	SURF2	1
15255	SURF4	1
15256	SURF6	1
15257	SUSD1	1
15258	SUSD2	1
15259	SUSD3	1
15260	SUSD4	1
15261	SUSD5	1.252377e-01
15262	SUV39H1	1
15263	SUV39H2	1
15264	SUV420H1	1.648465e-02
15265	SUV420H2	1
15266	SUZ12	1
15267	SV2A	1.619305e-01
15268	SV2B	1
15269	SV2C	7.090822e-02
15270	SVEP1	2.297830e-01
15271	SVIL	4.919622e-01
15272	SVIP	1
15273	SVOP	1
15274	SVOPL	1
15275	SWAP70	1
15276	SYAP1	1
15277	SYBU	2.808270e-01
15278	SYCE1	1
15279	SYCE2	3.405547e-02
15280	SYCN	1
15281	SYCP1	1
15282	SYCP2	2.170796e-01
15283	SYCP2L	2.230961e-01
15284	SYCP3	1
15285	SYDE1	1
15286	SYDE2	1
15287	SYF2	1
15288	SYK	1
15289	SYMPK	4.266660e-01
Done

Running MutSig 2:
Scatter job 169: processing genes 15200 - 15289
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: 4.391215e-02	ci left: 4.336308e-01	ci right 4.532021e-01	k: 4434	n:10000
Cons ci ratio: 1.721173e-02	ci left: 8.310374e-01	ci right 8.455650e-01	k: 8384	n:10000
KS ci ratio: 8.818083e-02	ci left: 1.576751e-01	ci right 1.723206e-01	k: 1649	n:10000
SVEP1   10000 perm   3 sec   (3560 perm/sec)   p_kst 1.649000e-01   p_cons 8.384000e-01   p_joint 4.434000e-01

Outputting figure to mutsig2_images.part000000000169/SVEP1.4_10908_10000_0.1649_0.8384_0.4434.png
                gene_name: SVEP1
               theta_stop: 0.088 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.85 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.45 

Current progress: 33 percent done.
STXBP5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.966806e-02	ci left: 7.909075e-01	ci right 8.067181e-01	k: 7989	n:10000
Cons ci ratio: 2.089156e-02	ci left: 7.705345e-01	ci right 7.869028e-01	k: 7788	n:10000
KS ci ratio: 3.082280e-02	ci left: 6.082933e-01	ci right 6.274380e-01	k: 6179	n:10000
STXBP5   10000 perm   2 sec   (5412 perm/sec)   p_kst 6.179000e-01   p_cons 7.788000e-01   p_joint 7.989000e-01

Outputting figure to mutsig2_images.part000000000169/STXBP5.2_3568_10000_0.6179_0.7788_0.7989.png
                gene_name: STXBP5
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.61 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.80 
     ci_joint_bounds_left: 0.79 
    ci_joint_bounds_right: 0.81 

Current progress: 67 percent done.
SUV420H1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.957012e-02	ci left: 7.925305e-01	ci right 8.082941e-01	k: 8005	n:10000
Cons ci ratio: 6.804040e-02	ci left: 2.406473e-01	ci right 2.576990e-01	k: 2491	n:10000
KS ci ratio: 4.420689e-02	ci left: 4.303394e-01	ci right 4.498955e-01	k: 4401	n:10000
SUV420H1   10000 perm   2 sec   (5871 perm/sec)   p_kst 4.401000e-01   p_cons 2.491000e-01   p_joint 8.005000e-01

Outputting figure to mutsig2_images.part000000000169/SUV420H1.2_2706_10000_0.4401_0.2491_0.8005.png
                gene_name: SUV420H1
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.80 
     ci_joint_bounds_left: 0.79 
    ci_joint_bounds_right: 0.81 

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.165.3896/
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/181708/iteration1/scatter.0000000169
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 169 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120287: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000170> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:48:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000170.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000170.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 170  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    173.82 sec.
    Max Memory :      1330 MB
    Max Swap   :      3936 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.165.3896/
-whichjob
170
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 170: processing genes 15290 - 15380
Calculating significance of each gene.
Using projection method.
15290	SYN1	1
15291	SYN2	2.957806e-02
15292	SYN3	1
15293	SYNC	1
15294	SYNCRIP	1
15295	SYNE1	9.455537e-01
15296	SYNE2	8.307277e-01
15297	SYNGAP1	2.544304e-01
15298	SYNGR1	1
15299	SYNGR2	1
15300	SYNGR3	1
15301	SYNGR4	1
15302	SYNJ1	1.976937e-01
15303	SYNJ2	5.289827e-01
15304	SYNJ2BP	1
15305	SYNM	2.661490e-01
15306	SYNPO	2.152835e-02
15307	SYNPO2	4.078710e-01
15308	SYNPO2L	1
15309	SYNPR	1
15310	SYNRG	2.909159e-01
15311	SYP	1
15312	SYPL1	1
15313	SYPL2	1
15314	SYS1	1
15315	SYT1	1
15316	SYT10	1.420384e-02
15317	SYT11	1
15318	SYT12	1.684407e-01
15319	SYT13	1
15320	SYT14	1
15321	SYT15	1
15322	SYT16	1
15323	SYT17	1
15324	SYT2	1
15325	SYT3	6.942484e-03
15326	SYT4	1
15327	SYT5	1
15328	SYT6	1
15329	SYT7	1.619799e-01
15330	SYT8	1
15331	SYT9	1
15332	SYTL1	1.621993e-01
15333	SYTL2	2.503460e-01
15334	SYTL3	1.518363e-01
15335	SYTL4	1
15336	SYTL5	2.693077e-01
15337	SYVN1	1
15338	T	2.098150e-01
15339	TAAR1	1
15340	TAAR2	1
15341	TAAR5	1
15342	TAAR6	1
15343	TAAR8	1
15344	TAAR9	1
15345	TAB1	1.837131e-01
15346	TAB2	1.235421e-01
15347	TAB3	1
15348	TAC1	7.704547e-03
15349	TAC3	1
15350	TAC4	1
15351	TACC1	1
15352	TACC2	1
15353	TACC3	3.601748e-03
15354	TACO1	1
15355	TACR1	1
15356	TACR2	1
15357	TACR3	1
15358	TACSTD2	1
15359	TADA1	1
15360	TADA2A	1
15361	TADA2B	1
15362	TADA3	1
15363	TAF1	1.775562e-01
15364	TAF10	1
15365	TAF11	1
15366	TAF12	1
15367	TAF13	1
15368	TAF15	1
15369	TAF1A	1
15370	TAF1B	1
15371	TAF1C	1
15372	TAF1D	1
15373	TAF1L	1
15374	TAF2	1
15375	TAF3	1
15376	TAF4	1
15377	TAF4B	1
15378	TAF5	5.266796e-02
15379	TAF5L	1
15380	TAF6	2.853029e-01
Done

Running MutSig 2:
Scatter job 170: processing genes 15290 - 15380
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
SYNE1
Processing conservation and coverage...
36% 73% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.399229e-02	ci left: 4.327331e-01	ci right 4.523004e-01	k: 4425	n:10000
Cons ci ratio: 1.397384e-02	ci left: 8.809390e-01	ci right 8.934345e-01	k: 8873	n:10000
KS ci ratio: 5.867464e-02	ci left: 2.994543e-01	ci right 3.176574e-01	k: 3085	n:10000
SYNE1   10000 perm   5 sec   (2078 perm/sec)   p_kst 3.085000e-01   p_cons 8.873000e-01   p_joint 4.425000e-01

Outputting figure to mutsig2_images.part000000000170/SYNE1.8_27068_10000_0.3085_0.8873_0.4425.png
                gene_name: SYNE1
               theta_stop: 0.059 
                    nperm: 10000 
                     p_ks: 0.31 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.32 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.45 

Current progress: 11 percent done.
SYNE2
Processing conservation and coverage...
47% 94% 
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: 3.510363e-02	ci left: 5.450946e-01	ci right 5.646734e-01	k: 5549	n:10000
KS ci ratio: 2.920119e-01	ci left: 1.511403e-02	ci right 2.037228e-02	k: 176	n:10000
SYNE2   10000 perm   4 sec   (2582 perm/sec)   p_kst 1.760000e-02   p_cons 5.549000e-01   p_joint 1.361000e-01

Joint ci ratio: 1.156184e-01	ci left: 5.119939e-02	ci right 5.753095e-02	k: 1086	n:20000
Cons ci ratio: 2.560971e-02	ci left: 5.325118e-01	ci right 5.463768e-01	k: 10789	n:20000
KS ci ratio: 2.101441e-01	ci left: 1.530131e-02	ci right 1.894102e-02	k: 341	n:20000
SYNE2   20000 perm   8 sec   (2399 perm/sec)   p_kst 1.705000e-02   p_cons 5.394500e-01   p_joint 5.430000e-02

Joint ci ratio: 8.182361e-02	ci left: 6.815148e-02	ci right 7.399858e-02	k: 2131	n:30000
Cons ci ratio: 2.085957e-02	ci left: 5.350071e-01	ci right 5.463184e-01	k: 16220	n:30000
KS ci ratio: 1.756326e-01	ci left: 1.489743e-02	ci right 1.779733e-02	k: 489	n:30000
SYNE2   30000 perm   13 sec   (2314 perm/sec)   p_kst 1.630000e-02   p_cons 5.406667e-01   p_joint 7.103333e-02

Joint ci ratio: 7.209315e-02	ci left: 6.633840e-02	ci right 7.132442e-02	k: 2752	n:40000
Cons ci ratio: 1.800217e-02	ci left: 5.375023e-01	ci right 5.472915e-01	k: 21696	n:40000
KS ci ratio: 1.553160e-01	ci left: 1.445643e-02	ci right 1.691461e-02	k: 626	n:40000
SYNE2   40000 perm   18 sec   (2278 perm/sec)   p_kst 1.565000e-02   p_cons 5.424000e-01   p_joint 6.880000e-02

Joint ci ratio: 6.434427e-02	ci left: 6.687229e-02	ci right 7.133790e-02	k: 3454	n:50000
Cons ci ratio: 1.609201e-02	ci left: 5.383210e-01	ci right 5.470740e-01	k: 27135	n:50000
KS ci ratio: 1.397137e-01	ci left: 1.441612e-02	ci right 1.660066e-02	k: 774	n:50000
SYNE2   50000 perm   22 sec   (2249 perm/sec)   p_kst 1.548000e-02   p_cons 5.427000e-01   p_joint 6.908000e-02

Joint ci ratio: 6.806549e-02	ci left: 5.059756e-02	ci right 5.417923e-02	k: 3142	n:60000
Cons ci ratio: 1.470134e-02	ci left: 5.383200e-01	ci right 5.463093e-01	k: 32539	n:60000
KS ci ratio: 1.298284e-01	ci left: 1.399417e-02	ci right 1.595315e-02	k: 897	n:60000
SYNE2   60000 perm   27 sec   (2221 perm/sec)   p_kst 1.495000e-02   p_cons 5.423167e-01   p_joint 5.236667e-02

Joint ci ratio: 6.539231e-02	ci left: 4.722961e-02	ci right 5.043650e-02	k: 3417	n:70000
Cons ci ratio: 1.360855e-02	ci left: 5.387005e-01	ci right 5.460960e-01	k: 37968	n:70000
KS ci ratio: 1.189176e-01	ci left: 1.437598e-02	ci right 1.620738e-02	k: 1069	n:70000
SYNE2   70000 perm   32 sec   (2197 perm/sec)   p_kst 1.527143e-02   p_cons 5.424000e-01   p_joint 4.881429e-02

Joint ci ratio: 5.910050e-02	ci left: 5.058240e-02	ci right 5.367518e-02	k: 4169	n:80000
Cons ci ratio: 1.271429e-02	ci left: 5.395403e-01	ci right 5.464566e-01	k: 43440	n:80000
KS ci ratio: 1.110925e-01	ci left: 1.447297e-02	ci right 1.618744e-02	k: 1225	n:80000
SYNE2   80000 perm   37 sec   (2176 perm/sec)   p_kst 1.531250e-02   p_cons 5.430000e-01   p_joint 5.211250e-02

Joint ci ratio: 5.480975e-02	ci left: 5.230190e-02	ci right 5.526028e-02	k: 4839	n:90000
Cons ci ratio: 1.199361e-02	ci left: 5.394718e-01	ci right 5.459921e-01	k: 48846	n:90000
KS ci ratio: 1.047487e-01	ci left: 1.451901e-02	ci right 1.613467e-02	k: 1378	n:90000
SYNE2   90000 perm   42 sec   (2155 perm/sec)   p_kst 1.531111e-02   p_cons 5.427333e-01   p_joint 5.376667e-02

Joint ci ratio: 5.125484e-02	ci left: 5.384188e-02	ci right 5.668398e-02	k: 5525	n:100000
Cons ci ratio: 1.135876e-02	ci left: 5.404866e-01	ci right 5.466709e-01	k: 54358	n:100000
KS ci ratio: 9.984504e-02	ci left: 1.442152e-02	ci right 1.594679e-02	k: 1517	n:100000
SYNE2   100000 perm   47 sec   (2133 perm/sec)   p_kst 1.517000e-02   p_cons 5.435800e-01   p_joint 5.525000e-02

Outputting figure to mutsig2_images.part000000000170/SYNE2.3_21229_100000_0.01517_0.54358_0.05525.png
                gene_name: SYNE2
               theta_stop: 0.100 
                    nperm: 100000 
                     p_ks: 0.015 
        ci_ks_bounds_left: 0.014 
       ci_ks_bounds_right: 0.016 
                   p_cons: 0.54 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.55 
                  p_joint: 0.055 
     ci_joint_bounds_left: 0.054 
    ci_joint_bounds_right: 0.057 

Current progress: 22 percent done.
TACC3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.331091e-01	ci left: 7.446484e-02	ci right 8.518145e-02	k: 797	n:10000
Cons ci ratio: 1.895761e-01	ci left: 3.710237e-02	ci right 4.496786e-02	k: 409	n:10000
KS ci ratio: 5.842809e-02	ci left: 3.012392e-01	ci right 3.194714e-01	k: 3103	n:10000
TACC3   10000 perm   2 sec   (5805 perm/sec)   p_kst 3.103000e-01   p_cons 4.090000e-02   p_joint 7.970000e-02

Joint ci ratio: 9.509900e-02	ci left: 7.456446e-02	ci right 8.205869e-02	k: 1565	n:20000
Cons ci ratio: 1.318881e-01	ci left: 3.950386e-02	ci right 4.513019e-02	k: 845	n:20000
KS ci ratio: 4.152340e-02	ci left: 3.018038e-01	ci right 3.146519e-01	k: 6164	n:20000
TACC3   20000 perm   4 sec   (5175 perm/sec)   p_kst 3.082000e-01   p_cons 4.225000e-02   p_joint 7.825000e-02

Joint ci ratio: 8.755303e-02	ci left: 5.988461e-02	ci right 6.540046e-02	k: 1878	n:30000
Cons ci ratio: 1.067247e-01	ci left: 4.073218e-02	ci right 4.535684e-02	k: 1290	n:30000
KS ci ratio: 3.420959e-02	ci left: 2.991955e-01	ci right 3.096424e-01	k: 9132	n:30000
TACC3   30000 perm   6 sec   (4923 perm/sec)   p_kst 3.044000e-01   p_cons 4.300000e-02   p_joint 6.260000e-02

Joint ci ratio: 7.111324e-02	ci left: 6.808387e-02	ci right 7.312868e-02	k: 2823	n:40000
Cons ci ratio: 9.226802e-02	ci left: 4.117946e-02	ci right 4.518720e-02	k: 1726	n:40000
KS ci ratio: 2.986299e-02	ci left: 2.965568e-01	ci right 3.055721e-01	k: 12042	n:40000
TACC3   40000 perm   8 sec   (4759 perm/sec)   p_kst 3.010500e-01   p_cons 4.315000e-02   p_joint 7.057500e-02

Outputting figure to mutsig2_images.part000000000170/TACC3.3_2577_40000_0.30105_0.04315_0.070575.png
                gene_name: TACC3
               theta_stop: 0.092 
                    nperm: 40000 
                     p_ks: 0.30 
        ci_ks_bounds_left: 0.30 
       ci_ks_bounds_right: 0.31 
                   p_cons: 0.043 
      ci_cons_bounds_left: 0.041 
     ci_cons_bounds_right: 0.045 
                  p_joint: 0.071 
     ci_joint_bounds_left: 0.068 
    ci_joint_bounds_right: 0.073 

Current progress: 33 percent done.
SYNJ1
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: 5.342080e-02	ci left: 3.405470e-01	ci right 3.593405e-01	k: 3499	n:10000
KS ci ratio: 3.399460e-02	ci left: 5.609292e-01	ci right 5.804296e-01	k: 5707	n:10000
SYNJ1   10000 perm   2 sec   (5192 perm/sec)   p_kst 5.707000e-01   p_cons 3.499000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000170/SYNJ1.2_5001_10000_0.5707_0.3499_1.png
                gene_name: SYNJ1
               theta_stop: 0.053 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   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: 44 percent done.
SYNPO
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.022342e-02	ci left: 7.816803e-01	ci right 7.977506e-01	k: 7898	n:10000
Cons ci ratio: 3.678368e-02	ci left: 5.218619e-01	ci right 5.415197e-01	k: 5317	n:10000
KS ci ratio: 4.362865e-02	ci left: 4.368230e-01	ci right 4.564081e-01	k: 4466	n:10000
SYNPO   10000 perm   2 sec   (5541 perm/sec)   p_kst 4.466000e-01   p_cons 5.317000e-01   p_joint 7.898000e-01

Outputting figure to mutsig2_images.part000000000170/SYNPO.2_3486_10000_0.4466_0.5317_0.7898.png
                gene_name: SYNPO
               theta_stop: 0.044 
                    nperm: 10000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.80 

Current progress: 56 percent done.
SYT10
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: 1.022202e-02	ci left: 9.314385e-01	ci right 9.411054e-01	k: 9364	n:10000
SYT10   10000 perm   2 sec   (6304 perm/sec)   p_kst 9.364000e-01   p_cons 5.485000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000170/SYT10.2_1600_10000_0.9364_0.5485_1.png
                gene_name: SYT10
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   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: 67 percent done.
SYT3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.185224e-02	ci left: 9.107001e-01	ci right 9.216561e-01	k: 9163	n:10000
Cons ci ratio: 3.111722e-02	ci left: 6.037736e-01	ci right 6.229603e-01	k: 6134	n:10000
KS ci ratio: 1.676522e-02	ci left: 8.381638e-01	ci right 8.524344e-01	k: 8454	n:10000
SYT3   10000 perm   2 sec   (6281 perm/sec)   p_kst 8.454000e-01   p_cons 6.134000e-01   p_joint 9.163000e-01

Outputting figure to mutsig2_images.part000000000170/SYT3.2_1805_10000_0.8454_0.6134_0.9163.png
                gene_name: SYT3
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.85 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.85 
                   p_cons: 0.61 
      ci_cons_bounds_left: 0.60 
     ci_cons_bounds_right: 0.62 
                  p_joint: 0.92 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 78 percent done.
SYTL2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.294682e-02	ci left: 4.446055e-01	ci right 4.642211e-01	k: 4544	n:10000
Cons ci ratio: 2.729154e-02	ci left: 6.642096e-01	ci right 6.826893e-01	k: 6735	n:10000
KS ci ratio: 8.440949e-02	ci left: 1.698592e-01	ci right 1.849292e-01	k: 1773	n:10000
SYTL2   10000 perm   2 sec   (5074 perm/sec)   p_kst 1.773000e-01   p_cons 6.735000e-01   p_joint 4.544000e-01

Outputting figure to mutsig2_images.part000000000170/SYTL2.2_5361_10000_0.1773_0.6735_0.4544.png
                gene_name: SYTL2
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.18 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.45 
     ci_joint_bounds_left: 0.44 
    ci_joint_bounds_right: 0.46 

Current progress: 89 percent done.
TAF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.695711e-02	ci left: 8.351090e-01	ci right 8.494910e-01	k: 8424	n:10000
Cons ci ratio: 7.333963e-02	ci left: 2.139851e-01	ci right 2.303771e-01	k: 2221	n:10000
KS ci ratio: 5.743326e-02	ci left: 3.085789e-01	ci right 3.269274e-01	k: 3177	n:10000
TAF1   10000 perm   2 sec   (4812 perm/sec)   p_kst 3.177000e-01   p_cons 2.221000e-01   p_joint 8.424000e-01

Outputting figure to mutsig2_images.part000000000170/TAF1.2_5834_10000_0.3177_0.2221_0.8424.png
                gene_name: TAF1
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.84 
     ci_joint_bounds_left: 0.84 
    ci_joint_bounds_right: 0.85 

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.165.3896/
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/181708/iteration1/scatter.0000000170
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 170 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120290: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000171> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:47:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000171.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000171.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 171  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     99.88 sec.
    Max Memory :       629 MB
    Max Swap   :      3422 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.165.3896/
-whichjob
171
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 171: processing genes 15381 - 15470
Calculating significance of each gene.
Using projection method.
15381	TAF6L	1
15382	TAF7	1
15383	TAF7L	2.620938e-02
15384	TAF8	1
15385	TAF9	1.725026e-01
15386	TAF9B	1
15387	TAGAP	1
15388	TAGLN	5.006900e-02
15389	TAGLN2	1
15390	TAGLN3	4.479424e-02
15391	TAL1	1
15392	TAL2	1
15393	TALDO1	1
15394	TANC1	2.576596e-01
15395	TANC2	1
15396	TANK	1
15397	TAOK1	1
15398	TAOK2	1.295615e-01
15399	TAOK3	1
15400	TAP1	1
15401	TAP2	7.172405e-02
15402	TAPBP	1
15403	TAPBPL	1
15404	TAPT1	1
15405	TARBP1	1
15406	TARBP2	1
15407	TARDBP	1
15408	TARP	5.013139e-02
15409	TARS	1
15410	TARS2	1
15411	TARSL2	1.755068e-01
15412	TAS1R1	2.826520e-01
15413	TAS1R2	1
15414	TAS1R3	3.148136e-01
15415	TAS2R1	1
15416	TAS2R10	1
15417	TAS2R13	1
15418	TAS2R14	1
15419	TAS2R16	1
15420	TAS2R19	1
15421	TAS2R20	1
15422	TAS2R3	1
15423	TAS2R30	1
15424	TAS2R31	1
15425	TAS2R38	1
15426	TAS2R39	3.373750e-02
15427	TAS2R4	1
15428	TAS2R40	1
15429	TAS2R41	1
15430	TAS2R42	1
15431	TAS2R43	1
15432	TAS2R46	1
15433	TAS2R5	1
15434	TAS2R50	3.519503e-02
15435	TAS2R60	1.285081e-01
15436	TAS2R7	1
15437	TAS2R8	1
15438	TAS2R9	1
15439	TASP1	7.850976e-03
15440	TAT	1
15441	TATDN1	1
15442	TATDN2	1
15443	TATDN3	1
15444	TAX1BP1	1
15445	TAX1BP3	1
15446	TAZ	1
15447	TBC1D1	3.128749e-01
15448	TBC1D10A	1.938354e-01
15449	TBC1D10B	1
15450	TBC1D10C	1
15451	TBC1D12	1
15452	TBC1D13	1
15453	TBC1D14	1
15454	TBC1D15	2.376367e-01
15455	TBC1D16	1
15456	TBC1D17	1
15457	TBC1D19	1
15458	TBC1D2	1
15459	TBC1D20	1
15460	TBC1D21	1.258403e-01
15461	TBC1D22A	1
15462	TBC1D22B	1
15463	TBC1D23	1
15464	TBC1D24	1
15465	TBC1D25	1.915119e-01
15466	TBC1D26	1
15467	TBC1D28	1
15468	TBC1D29	3.334571e-02
15469	TBC1D2B	1
15470	TBC1D3B	1
Done

Running MutSig 2:
Scatter job 171: processing genes 15381 - 15470
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TAF7L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.208946e-02	ci left: 2.199059e-01	ci right 2.364527e-01	k: 2281	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: 4.267076e-02	ci left: 4.477990e-01	ci right 4.674257e-01	k: 4576	n:10000
TAF7L   10000 perm   2 sec   (5477 perm/sec)   p_kst 4.576000e-01   p_cons 1.957000e-01   p_joint 2.281000e-01

Outputting figure to mutsig2_images.part000000000171/TAF7L.2_1441_10000_0.4576_0.1957_0.2281.png
                gene_name: TAF7L
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.46 
        ci_ks_bounds_left: 0.45 
       ci_ks_bounds_right: 0.47 
                   p_cons: 0.20 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.22 
    ci_joint_bounds_right: 0.24 

Current progress: 33 percent done.
TAOK2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.628446e-02	ci left: 5.286693e-01	ci right 5.483083e-01	k: 5385	n:10000
Cons ci ratio: 3.540304e-02	ci left: 5.408871e-01	ci right 5.604833e-01	k: 5507	n:10000
KS ci ratio: 4.488595e-02	ci left: 4.228604e-01	ci right 4.423788e-01	k: 4326	n:10000
TAOK2   10000 perm   2 sec   (5451 perm/sec)   p_kst 4.326000e-01   p_cons 5.507000e-01   p_joint 5.385000e-01

Outputting figure to mutsig2_images.part000000000171/TAOK2.2_4698_10000_0.4326_0.5507_0.5385.png
                gene_name: TAOK2
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.43 
        ci_ks_bounds_left: 0.42 
       ci_ks_bounds_right: 0.44 
                   p_cons: 0.55 
      ci_cons_bounds_left: 0.54 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.54 
     ci_joint_bounds_left: 0.53 
    ci_joint_bounds_right: 0.55 

Current progress: 67 percent done.
TASP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.918818e-03	ci left: 9.880698e-01	ci right 9.920369e-01	k: 9902	n:10000
Cons ci ratio: 2.859839e-02	ci left: 6.431744e-01	ci right 6.619367e-01	k: 6526	n:10000
KS ci ratio: 1.532928e-02	ci left: 8.605959e-01	ci right 8.739894e-01	k: 8674	n:10000
TASP1   10000 perm   2 sec   (5377 perm/sec)   p_kst 8.674000e-01   p_cons 6.526000e-01   p_joint 9.902000e-01

Outputting figure to mutsig2_images.part000000000171/TASP1.2_1315_10000_0.8674_0.6526_0.9902.png
                gene_name: TASP1
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.87 
                   p_cons: 0.65 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.66 
                  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.165.3896/
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/181708/iteration1/scatter.0000000171
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 171 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1542>
Subject: Job 1120293: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1542>, 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/181708/iteration1/scatter.0000000172> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:52:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000172.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000172.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 172  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    488.76 sec.
    Max Memory :      1283 MB
    Max Swap   :      3872 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.165.3896/
-whichjob
172
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 172: processing genes 15471 - 15561
Calculating significance of each gene.
Using projection method.
15471	TBC1D4	4.667755e-01
15472	TBC1D5	6.774830e-02
15473	TBC1D7	1
15474	TBC1D8	1
15475	TBC1D8B	1.183400e-01
15476	TBC1D9	1
15477	TBC1D9B	3.111696e-01
15478	TBCA	1
15479	TBCB	1
15480	TBCC	1.413031e-01
15481	TBCCD1	1
15482	TBCD	1
15483	TBCE	1
15484	TBCEL	1
15485	TBCK	1
15486	TBK1	1
15487	TBKBP1	1
15488	TBL1X	1
15489	TBL1XR1	3.882538e-02
15490	TBL1Y	1
15491	TBL2	1
15492	TBL3	1
15493	TBP	1
15494	TBPL1	1
15495	TBPL2	1
15496	TBR1	1
15497	TBRG1	1
15498	TBRG4	1
15499	TBX1	1
15500	TBX10	1
15501	TBX15	1
15502	TBX18	1
15503	TBX19	1
15504	TBX2	1
15505	TBX20	1
15506	TBX21	1
15507	TBX22	1
15508	TBX3	1.476086e-01
15509	TBX4	1.645254e-01
15510	TBX5	1.094192e-02
15511	TBX6	1
15512	TBXA2R	1
15513	TBXAS1	1.737883e-01
15514	TC2N	1
15515	TCAP	1
15516	TCEA1	1
15517	TCEA2	1
15518	TCEA3	1.666856e-01
15519	TCEAL1	1
15520	TCEAL2	1
15521	TCEAL3	1
15522	TCEAL4	1
15523	TCEAL5	1
15524	TCEAL6	1
15525	TCEAL7	1
15526	TCEAL8	1
15527	TCEANC	1
15528	TCEB1	1
15529	TCEB2	1
15530	TCEB3	1
15531	TCEB3B	1
15532	TCEB3C	1
15533	TCEB3CL	1
15534	TCERG1	1
15535	TCERG1L	1
15536	TCF12	2.496997e-01
15537	TCF19	1
15538	TCF20	1.157560e-01
15539	TCF21	1
15540	TCF23	1
15541	TCF25	2.019293e-01
15542	TCF3	1
15543	TCF4	7.136761e-02
15544	TCF7	1
15545	TCF7L1	1
15546	TCF7L2	1
15547	TCFL5	3.964486e-02
15548	TCHH	1
15549	TCHHL1	1
15550	TCHP	1
15551	TCIRG1	1
15552	TCL1A	1
15553	TCL1B	5.455845e-02
15554	TCN1	1
15555	TCN2	1
15556	TCOF1	1
15557	TCP1	1
15558	TCP10	9.065196e-03
15559	TCP10L	1
15560	TCP10L2	2.059423e-02
15561	TCP11	1
Done

Running MutSig 2:
Scatter job 172: processing genes 15471 - 15561
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TBCC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.134257e-01	ci left: 1.298624e-02	ci right 1.790194e-02	k: 153	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: 9.021878e-02	ci left: 1.515885e-01	ci right 1.660108e-01	k: 1587	n:10000
TBCC   10000 perm   2 sec   (6419 perm/sec)   p_kst 1.587000e-01   p_cons 2.500000e-03   p_joint 1.530000e-02

Joint ci ratio: 3.426791e-01	ci left: 5.387780e-03	ci right 7.659273e-03	k: 129	n:20000
Cons ci ratio: 5.481959e-01	ci left: 1.856100e-03	ci right 3.294626e-03	k: 50	n:20000
KS ci ratio: 6.290290e-02	ci left: 1.574610e-01	ci right 1.677373e-01	k: 3251	n:20000
TBCC   20000 perm   6 sec   (3143 perm/sec)   p_kst 1.625500e-01   p_cons 2.500000e-03   p_joint 6.450000e-03

Joint ci ratio: 2.580461e-01	ci left: 6.648515e-03	ci right 8.648608e-03	k: 228	n:30000
Cons ci ratio: 4.245739e-01	ci left: 2.233986e-03	ci right 3.465435e-03	k: 84	n:30000
KS ci ratio: 5.173435e-02	ci left: 1.564616e-01	ci right 1.648042e-01	k: 4818	n:30000
TBCC   30000 perm   8 sec   (3563 perm/sec)   p_kst 1.606000e-01   p_cons 2.800000e-03   p_joint 7.600000e-03

Joint ci ratio: 1.845774e-01	ci left: 1.012024e-02	ci right 1.220164e-02	k: 445	n:40000
Cons ci ratio: 3.588064e-01	ci left: 2.442383e-03	ci right 3.531758e-03	k: 118	n:40000
KS ci ratio: 4.480061e-02	ci left: 1.570389e-01	ci right 1.642605e-01	k: 6425	n:40000
TBCC   40000 perm   11 sec   (3805 perm/sec)   p_kst 1.606250e-01   p_cons 2.950000e-03   p_joint 1.112500e-02

Joint ci ratio: 2.109308e-01	ci left: 6.136311e-03	ci right 7.601822e-03	k: 342	n:50000
Cons ci ratio: 3.228373e-01	ci left: 2.466107e-03	ci right 3.433034e-03	k: 146	n:50000
KS ci ratio: 4.004570e-02	ci left: 1.575899e-01	ci right 1.640495e-01	k: 8040	n:50000
TBCC   50000 perm   13 sec   (3938 perm/sec)   p_kst 1.608000e-01   p_cons 2.920000e-03   p_joint 6.840000e-03

Joint ci ratio: 2.126167e-01	ci left: 5.034365e-03	ci right 6.247539e-03	k: 337	n:60000
Cons ci ratio: 2.893301e-01	ci left: 2.609169e-03	ci right 3.506634e-03	k: 182	n:60000
KS ci ratio: 3.665896e-02	ci left: 1.571244e-01	ci right 1.630085e-01	k: 9603	n:60000
TBCC   60000 perm   15 sec   (4014 perm/sec)   p_kst 1.600500e-01   p_cons 3.033333e-03   p_joint 5.616667e-03

Joint ci ratio: 1.225137e-01	ci left: 1.353050e-02	ci right 1.531009e-02	k: 1008	n:70000
Cons ci ratio: 2.713970e-01	ci left: 2.568479e-03	ci right 3.387867e-03	k: 207	n:70000
KS ci ratio: 3.391741e-02	ci left: 1.575182e-01	ci right 1.629672e-01	k: 11216	n:70000
TBCC   70000 perm   17 sec   (4050 perm/sec)   p_kst 1.602286e-01   p_cons 2.957143e-03   p_joint 1.440000e-02

Joint ci ratio: 1.070825e-01	ci left: 1.559207e-02	ci right 1.736825e-02	k: 1317	n:80000
Cons ci ratio: 2.526535e-01	ci left: 2.621186e-03	ci right 3.390558e-03	k: 239	n:80000
KS ci ratio: 3.172158e-02	ci left: 1.577389e-01	ci right 1.628357e-01	k: 12822	n:80000
TBCC   80000 perm   20 sec   (4062 perm/sec)   p_kst 1.602750e-01   p_cons 2.987500e-03   p_joint 1.646250e-02

Joint ci ratio: 1.011580e-01	ci left: 1.558029e-02	ci right 1.725109e-02	k: 1476	n:90000
Cons ci ratio: 2.386479e-01	ci left: 2.632345e-03	ci right 3.355833e-03	k: 268	n:90000
KS ci ratio: 2.990726e-02	ci left: 1.578864e-01	ci right 1.626911e-01	k: 14425	n:90000
TBCC   90000 perm   22 sec   (4056 perm/sec)   p_kst 1.602778e-01   p_cons 2.977778e-03   p_joint 1.640000e-02

Joint ci ratio: 1.070973e-01	ci left: 1.251151e-02	ci right 1.393693e-02	k: 1321	n:100000
Cons ci ratio: 2.302536e-01	ci left: 2.557354e-03	ci right 3.231992e-03	k: 288	n:100000
KS ci ratio: 2.837241e-02	ci left: 1.580111e-01	ci right 1.625687e-01	k: 16028	n:100000
TBCC   100000 perm   25 sec   (4024 perm/sec)   p_kst 1.602800e-01   p_cons 2.880000e-03   p_joint 1.321000e-02

Joint ci ratio: 1.047048e-01	ci left: 1.192261e-02	ci right 1.324873e-02	k: 1383	n:110000
Cons ci ratio: 2.216103e-01	ci left: 2.522123e-03	ci right 3.159084e-03	k: 311	n:110000
KS ci ratio: 2.708213e-02	ci left: 1.578199e-01	ci right 1.621617e-01	k: 17598	n:110000
TBCC   110000 perm   28 sec   (3976 perm/sec)   p_kst 1.599818e-01   p_cons 2.827273e-03   p_joint 1.257273e-02

Joint ci ratio: 1.014385e-01	ci left: 1.166777e-02	ci right 1.292263e-02	k: 1474	n:120000
Cons ci ratio: 2.101313e-01	ci left: 2.587862e-03	ci right 3.203218e-03	k: 346	n:120000
KS ci ratio: 2.587377e-02	ci left: 1.584852e-01	ci right 1.626479e-01	k: 19267	n:120000
TBCC   120000 perm   30 sec   (3946 perm/sec)   p_kst 1.605583e-01   p_cons 2.883333e-03   p_joint 1.228333e-02

Joint ci ratio: 1.042757e-01	ci left: 1.019277e-02	ci right 1.132152e-02	k: 1397	n:130000
Cons ci ratio: 2.040539e-01	ci left: 2.541952e-03	ci right 3.126729e-03	k: 367	n:130000
KS ci ratio: 2.486842e-02	ci left: 1.584624e-01	ci right 1.624604e-01	k: 20859	n:130000
TBCC   130000 perm   33 sec   (3911 perm/sec)   p_kst 1.604538e-01   p_cons 2.823077e-03   p_joint 1.074615e-02

Joint ci ratio: 1.009082e-01	ci left: 1.012585e-02	ci right 1.120884e-02	k: 1492	n:140000
Cons ci ratio: 1.964593e-01	ci left: 2.557144e-03	ci right 3.120902e-03	k: 396	n:140000
KS ci ratio: 2.400814e-02	ci left: 1.580405e-01	ci right 1.618879e-01	k: 22394	n:140000
TBCC   140000 perm   36 sec   (3870 perm/sec)   p_kst 1.599571e-01   p_cons 2.828571e-03   p_joint 1.065714e-02

Joint ci ratio: 9.132678e-02	ci left: 1.157889e-02	ci right 1.269342e-02	k: 1819	n:150000
Cons ci ratio: 1.885477e-01	ci left: 2.602420e-03	ci right 3.150410e-03	k: 430	n:150000
KS ci ratio: 2.319501e-02	ci left: 1.580949e-01	ci right 1.618116e-01	k: 23992	n:150000
TBCC   150000 perm   40 sec   (3779 perm/sec)   p_kst 1.599467e-01   p_cons 2.866667e-03   p_joint 1.212667e-02

Joint ci ratio: 9.313798e-02	ci left: 1.043972e-02	ci right 1.146561e-02	k: 1751	n:160000
Cons ci ratio: 1.821108e-01	ci left: 2.624534e-03	ci right 3.156233e-03	k: 461	n:160000
KS ci ratio: 2.243059e-02	ci left: 1.584867e-01	ci right 1.620881e-01	k: 25645	n:160000
TBCC   160000 perm   43 sec   (3706 perm/sec)   p_kst 1.602812e-01   p_cons 2.881250e-03   p_joint 1.094375e-02

Joint ci ratio: 9.940452e-02	ci left: 8.613885e-03	ci right 9.520623e-03	k: 1540	n:170000
Cons ci ratio: 1.762912e-01	ci left: 2.644327e-03	ci right 3.161092e-03	k: 492	n:170000
KS ci ratio: 2.175986e-02	ci left: 1.585530e-01	ci right 1.620468e-01	k: 27250	n:170000
TBCC   170000 perm   47 sec   (3652 perm/sec)   p_kst 1.602941e-01   p_cons 2.894118e-03   p_joint 9.058824e-03

Joint ci ratio: 9.762479e-02	ci left: 8.444164e-03	ci right 9.316208e-03	k: 1597	n:180000
Cons ci ratio: 1.709961e-01	ci left: 2.662160e-03	ci right 3.165172e-03	k: 523	n:180000
KS ci ratio: 2.115115e-02	ci left: 1.585470e-01	ci right 1.619418e-01	k: 28843	n:180000
TBCC   180000 perm   50 sec   (3576 perm/sec)   p_kst 1.602389e-01   p_cons 2.905556e-03   p_joint 8.872222e-03

Joint ci ratio: 8.472108e-02	ci left: 1.066981e-02	ci right 1.161888e-02	k: 2116	n:190000
Cons ci ratio: 1.651101e-01	ci left: 2.713642e-03	ci right 3.206979e-03	k: 561	n:190000
KS ci ratio: 2.059445e-02	ci left: 1.584956e-01	ci right 1.617989e-01	k: 30427	n:190000
TBCC   190000 perm   54 sec   (3522 perm/sec)   p_kst 1.601421e-01   p_cons 2.952632e-03   p_joint 1.113684e-02

Joint ci ratio: 7.918502e-02	ci left: 1.162542e-02	ci right 1.258880e-02	k: 2420	n:200000
Cons ci ratio: 1.612824e-01	ci left: 2.707446e-03	ci right 3.187140e-03	k: 588	n:200000
KS ci ratio: 2.004895e-02	ci left: 1.588588e-01	ci right 1.620810e-01	k: 32093	n:200000
TBCC   200000 perm   58 sec   (3452 perm/sec)   p_kst 1.604650e-01   p_cons 2.940000e-03   p_joint 1.210000e-02

Joint ci ratio: 7.746273e-02	ci left: 1.158070e-02	ci right 1.251856e-02	k: 2529	n:210000
Cons ci ratio: 1.568180e-01	ci left: 2.733985e-03	ci right 3.203711e-03	k: 622	n:210000
KS ci ratio: 1.958852e-02	ci left: 1.585861e-01	ci right 1.617280e-01	k: 33632	n:210000
TBCC   210000 perm   62 sec   (3389 perm/sec)   p_kst 1.601524e-01   p_cons 2.961905e-03   p_joint 1.204286e-02

Joint ci ratio: 7.275727e-02	ci left: 1.254867e-02	ci right 1.350058e-02	k: 2864	n:220000
Cons ci ratio: 1.532910e-01	ci left: 2.736417e-03	ci right 3.195016e-03	k: 651	n:220000
KS ci ratio: 1.914642e-02	ci left: 1.585065e-01	ci right 1.615752e-01	k: 35208	n:220000
TBCC   220000 perm   66 sec   (3355 perm/sec)   p_kst 1.600364e-01   p_cons 2.959091e-03   p_joint 1.301818e-02

Joint ci ratio: 6.406474e-02	ci left: 1.550398e-02	ci right 1.653436e-02	k: 3683	n:230000
Cons ci ratio: 1.502132e-01	ci left: 2.730375e-03	ci right 3.177949e-03	k: 678	n:230000
KS ci ratio: 1.873934e-02	ci left: 1.583436e-01	ci right 1.613432e-01	k: 36763	n:230000
TBCC   230000 perm   69 sec   (3321 perm/sec)   p_kst 1.598391e-01   p_cons 2.947826e-03   p_joint 1.601304e-02

Joint ci ratio: 6.267589e-02	ci left: 1.553459e-02	ci right 1.654381e-02	k: 3848	n:240000
Cons ci ratio: 1.461759e-01	ci left: 2.769077e-03	ci right 3.209729e-03	k: 716	n:240000
KS ci ratio: 1.833779e-02	ci left: 1.584772e-01	ci right 1.614143e-01	k: 38386	n:240000
TBCC   240000 perm   73 sec   (3287 perm/sec)   p_kst 1.599417e-01   p_cons 2.983333e-03   p_joint 1.603333e-02

Joint ci ratio: 6.853750e-02	ci left: 1.247311e-02	ci right 1.336223e-02	k: 3228	n:250000
Cons ci ratio: 1.429230e-01	ci left: 2.785541e-03	ci right 3.218108e-03	k: 749	n:250000
KS ci ratio: 1.796100e-02	ci left: 1.586007e-01	ci right 1.614791e-01	k: 40009	n:250000
TBCC   250000 perm   77 sec   (3252 perm/sec)   p_kst 1.600360e-01   p_cons 2.996000e-03   p_joint 1.291200e-02

Joint ci ratio: 5.112051e-02	ci left: 2.154973e-02	ci right 2.268404e-02	k: 5749	n:260000
Cons ci ratio: 1.398780e-01	ci left: 2.800840e-03	ci right 3.225743e-03	k: 782	n:260000
KS ci ratio: 1.761105e-02	ci left: 1.586464e-01	ci right 1.614689e-01	k: 41614	n:260000
TBCC   260000 perm   81 sec   (3217 perm/sec)   p_kst 1.600538e-01   p_cons 3.007692e-03   p_joint 2.211154e-02

Joint ci ratio: 5.068005e-02	ci left: 2.112810e-02	ci right 2.223035e-02	k: 5852	n:270000
Cons ci ratio: 1.369355e-01	ci left: 2.818672e-03	ci right 3.236553e-03	k: 816	n:270000
KS ci ratio: 1.728627e-02	ci left: 1.586042e-01	ci right 1.613735e-01	k: 43196	n:270000
TBCC   270000 perm   85 sec   (3183 perm/sec)   p_kst 1.599852e-01   p_cons 3.022222e-03   p_joint 2.167407e-02

Joint ci ratio: 4.968646e-02	ci left: 2.120583e-02	ci right 2.228982e-02	k: 6088	n:280000
Cons ci ratio: 1.348886e-01	ci left: 2.804254e-03	ci right 3.213283e-03	k: 841	n:280000
KS ci ratio: 1.697205e-02	ci left: 1.586723e-01	ci right 1.613919e-01	k: 44808	n:280000
TBCC   280000 perm   89 sec   (3147 perm/sec)   p_kst 1.600286e-01   p_cons 3.003571e-03   p_joint 2.174286e-02

Joint ci ratio: 4.885581e-02	ci left: 2.118640e-02	ci right 2.225078e-02	k: 6297	n:290000
Cons ci ratio: 1.322441e-01	ci left: 2.820881e-03	ci right 3.223635e-03	k: 875	n:290000
KS ci ratio: 1.668014e-02	ci left: 1.586433e-01	ci right 1.613152e-01	k: 46393	n:290000
TBCC   290000 perm   93 sec   (3112 perm/sec)   p_kst 1.599759e-01   p_cons 3.017241e-03   p_joint 2.171379e-02

Joint ci ratio: 4.963183e-02	ci left: 1.986419e-02	ci right 2.087844e-02	k: 6110	n:300000
Cons ci ratio: 1.303977e-01	ci left: 2.807446e-03	ci right 3.202252e-03	k: 900	n:300000
KS ci ratio: 1.639832e-02	ci left: 1.586898e-01	ci right 1.613168e-01	k: 48000	n:300000
TBCC   300000 perm   98 sec   (3076 perm/sec)   p_kst 1.600000e-01   p_cons 3.000000e-03   p_joint 2.036667e-02

Joint ci ratio: 5.484344e-02	ci left: 1.576806e-02	ci right 1.666038e-02	k: 5025	n:310000
Cons ci ratio: 1.288359e-01	ci left: 2.785548e-03	ci right 3.172224e-03	k: 922	n:310000
KS ci ratio: 1.612122e-02	ci left: 1.588847e-01	ci right 1.614701e-01	k: 49654	n:310000
TBCC   310000 perm   102 sec   (3040 perm/sec)   p_kst 1.601742e-01   p_cons 2.974194e-03   p_joint 1.620968e-02

Joint ci ratio: 6.015391e-02	ci left: 1.270274e-02	ci right 1.349361e-02	k: 4190	n:320000
Cons ci ratio: 1.266586e-01	ci left: 2.795304e-03	ci right 3.176285e-03	k: 954	n:320000
KS ci ratio: 1.587005e-02	ci left: 1.588590e-01	ci right 1.614034e-01	k: 51241	n:320000
TBCC   320000 perm   106 sec   (3006 perm/sec)   p_kst 1.601281e-01   p_cons 2.981250e-03   p_joint 1.309375e-02

Joint ci ratio: 5.299097e-02	ci left: 1.587968e-02	ci right 1.674703e-02	k: 5382	n:330000
Cons ci ratio: 1.237111e-01	ci left: 2.845632e-03	ci right 3.223785e-03	k: 1000	n:330000
KS ci ratio: 1.562006e-02	ci left: 1.590104e-01	ci right 1.615167e-01	k: 52886	n:330000
TBCC   330000 perm   111 sec   (2971 perm/sec)   p_kst 1.602606e-01   p_cons 3.030303e-03   p_joint 1.630909e-02

Joint ci ratio: 5.039403e-02	ci left: 1.704446e-02	ci right 1.792849e-02	k: 5944	n:340000
Cons ci ratio: 1.221956e-01	ci left: 2.833203e-03	ci right 3.204759e-03	k: 1025	n:340000
KS ci ratio: 1.539817e-02	ci left: 1.588630e-01	ci right 1.613311e-01	k: 54432	n:340000
TBCC   340000 perm   116 sec   (2938 perm/sec)   p_kst 1.600941e-01   p_cons 3.014706e-03   p_joint 1.748235e-02

Joint ci ratio: 4.961057e-02	ci left: 1.709074e-02	ci right 1.796299e-02	k: 6133	n:350000
Cons ci ratio: 1.202192e-01	ci left: 2.846454e-03	ci right 3.213280e-03	k: 1059	n:350000
KS ci ratio: 1.516725e-02	ci left: 1.590460e-01	ci right 1.614796e-01	k: 56091	n:350000
TBCC   350000 perm   120 sec   (2905 perm/sec)   p_kst 1.602600e-01   p_cons 3.025714e-03   p_joint 1.752286e-02

Joint ci ratio: 4.885861e-02	ci left: 1.713729e-02	ci right 1.799828e-02	k: 6323	n:360000
Cons ci ratio: 1.184988e-01	ci left: 2.850926e-03	ci right 3.212702e-03	k: 1090	n:360000
KS ci ratio: 1.495768e-02	ci left: 1.590170e-01	ci right 1.614162e-01	k: 57677	n:360000
TBCC   360000 perm   125 sec   (2872 perm/sec)   p_kst 1.602139e-01   p_cons 3.027778e-03   p_joint 1.756389e-02

Joint ci ratio: 4.821901e-02	ci left: 1.712533e-02	ci right 1.797415e-02	k: 6492	n:370000
Cons ci ratio: 1.166939e-01	ci left: 2.863064e-03	ci right 3.220465e-03	k: 1124	n:370000
KS ci ratio: 1.476101e-02	ci left: 1.589090e-01	ci right 1.612747e-01	k: 59233	n:370000
TBCC   370000 perm   130 sec   (2839 perm/sec)   p_kst 1.600892e-01   p_cons 3.037838e-03   p_joint 1.754595e-02

Joint ci ratio: 4.974450e-02	ci left: 1.567881e-02	ci right 1.648122e-02	k: 6109	n:380000
Cons ci ratio: 1.153188e-01	ci left: 2.856710e-03	ci right 3.208830e-03	k: 1151	n:380000
KS ci ratio: 1.456805e-02	ci left: 1.588776e-01	ci right 1.612118e-01	k: 60816	n:380000
TBCC   380000 perm   135 sec   (2808 perm/sec)   p_kst 1.600421e-01   p_cons 3.028947e-03   p_joint 1.607632e-02

Joint ci ratio: 4.881771e-02	ci left: 1.586690e-02	ci right 1.666338e-02	k: 6342	n:390000
Cons ci ratio: 1.134137e-01	ci left: 2.880603e-03	ci right 3.229410e-03	k: 1190	n:390000
KS ci ratio: 1.437396e-02	ci left: 1.590066e-01	ci right 1.613112e-01	k: 62461	n:390000
TBCC   390000 perm   140 sec   (2776 perm/sec)   p_kst 1.601564e-01   p_cons 3.051282e-03   p_joint 1.626154e-02

Joint ci ratio: 4.825886e-02	ci left: 1.583573e-02	ci right 1.662130e-02	k: 6490	n:400000
Cons ci ratio: 1.121039e-01	ci left: 2.876613e-03	ci right 3.220648e-03	k: 1218	n:400000
KS ci ratio: 1.419151e-02	ci left: 1.590521e-01	ci right 1.613279e-01	k: 64075	n:400000
TBCC   400000 perm   146 sec   (2734 perm/sec)   p_kst 1.601875e-01   p_cons 3.045000e-03   p_joint 1.622500e-02

Joint ci ratio: 4.764951e-02	ci left: 1.585193e-02	ci right 1.662810e-02	k: 6657	n:410000
Cons ci ratio: 1.108386e-01	ci left: 2.872840e-03	ci right 3.212292e-03	k: 1246	n:410000
KS ci ratio: 1.401495e-02	ci left: 1.591125e-01	ci right 1.613606e-01	k: 65696	n:410000
TBCC   410000 perm   152 sec   (2706 perm/sec)   p_kst 1.602341e-01   p_cons 3.039024e-03   p_joint 1.623659e-02

Joint ci ratio: 4.706969e-02	ci left: 1.586271e-02	ci right 1.662970e-02	k: 6822	n:420000
Cons ci ratio: 1.092717e-01	ci left: 2.887795e-03	ci right 3.223881e-03	k: 1282	n:420000
KS ci ratio: 1.384775e-02	ci left: 1.591132e-01	ci right 1.613343e-01	k: 67293	n:420000
TBCC   420000 perm   157 sec   (2676 perm/sec)   p_kst 1.602214e-01   p_cons 3.052381e-03   p_joint 1.624286e-02

Joint ci ratio: 4.655796e-02	ci left: 1.584086e-02	ci right 1.659824e-02	k: 6973	n:430000
Cons ci ratio: 1.082647e-01	ci left: 2.874931e-03	ci right 3.206240e-03	k: 1306	n:430000
KS ci ratio: 1.368984e-02	ci left: 1.590468e-01	ci right 1.612415e-01	k: 68861	n:430000
TBCC   430000 perm   163 sec   (2642 perm/sec)   p_kst 1.601419e-01   p_cons 3.037209e-03   p_joint 1.621628e-02

Joint ci ratio: 4.604286e-02	ci left: 1.583353e-02	ci right 1.658196e-02	k: 7130	n:440000
Cons ci ratio: 1.072042e-01	ci left: 2.867090e-03	ci right 3.194054e-03	k: 1332	n:440000
KS ci ratio: 1.353446e-02	ci left: 1.590380e-01	ci right 1.612074e-01	k: 70453	n:440000
TBCC   440000 perm   168 sec   (2612 perm/sec)   p_kst 1.601205e-01   p_cons 3.027273e-03   p_joint 1.620455e-02

Joint ci ratio: 4.556673e-02	ci left: 1.581118e-02	ci right 1.655062e-02	k: 7280	n:450000
Cons ci ratio: 1.061742e-01	ci left: 2.859612e-03	ci right 3.182395e-03	k: 1358	n:450000
KS ci ratio: 1.337983e-02	ci left: 1.591183e-01	ci right 1.612638e-01	k: 72085	n:450000
TBCC   450000 perm   174 sec   (2587 perm/sec)   p_kst 1.601889e-01   p_cons 3.017778e-03   p_joint 1.617778e-02

Joint ci ratio: 4.506195e-02	ci left: 1.581994e-02	ci right 1.655139e-02	k: 7444	n:460000
Cons ci ratio: 1.052497e-01	ci left: 2.848240e-03	ci right 3.166766e-03	k: 1382	n:460000
KS ci ratio: 1.323198e-02	ci left: 1.591628e-01	ci right 1.612850e-01	k: 73702	n:460000
TBCC   460000 perm   180 sec   (2561 perm/sec)   p_kst 1.602217e-01   p_cons 3.004348e-03   p_joint 1.618261e-02

Joint ci ratio: 4.462130e-02	ci left: 1.579471e-02	ci right 1.651766e-02	k: 7592	n:470000
Cons ci ratio: 1.044233e-01	ci left: 2.833220e-03	ci right 3.147425e-03	k: 1404	n:470000
KS ci ratio: 1.308614e-02	ci left: 1.592628e-01	ci right 1.613627e-01	k: 75346	n:470000
TBCC   470000 perm   185 sec   (2535 perm/sec)   p_kst 1.603106e-01   p_cons 2.987234e-03   p_joint 1.615319e-02

Joint ci ratio: 4.415565e-02	ci left: 1.579734e-02	ci right 1.651268e-02	k: 7753	n:480000
Cons ci ratio: 1.032178e-01	ci left: 2.841160e-03	ci right 3.152388e-03	k: 1437	n:480000
KS ci ratio: 1.296026e-02	ci left: 1.590429e-01	ci right 1.611196e-01	k: 76838	n:480000
TBCC   480000 perm   192 sec   (2497 perm/sec)   p_kst 1.600792e-01   p_cons 2.993750e-03   p_joint 1.615208e-02

Joint ci ratio: 4.372393e-02	ci left: 1.578578e-02	ci right 1.649343e-02	k: 7907	n:490000
Cons ci ratio: 1.025791e-01	ci left: 2.818964e-03	ci right 3.125735e-03	k: 1455	n:490000
KS ci ratio: 1.282585e-02	ci left: 1.590844e-01	ci right 1.611400e-01	k: 78454	n:490000
TBCC   490000 perm   200 sec   (2454 perm/sec)   p_kst 1.601102e-01   p_cons 2.969388e-03   p_joint 1.613673e-02

Joint ci ratio: 4.328827e-02	ci left: 1.578658e-02	ci right 1.648704e-02	k: 8067	n:500000
Cons ci ratio: 1.017101e-01	ci left: 2.811307e-03	ci right 3.114498e-03	k: 1480	n:500000
KS ci ratio: 1.269922e-02	ci left: 1.590467e-01	ci right 1.610813e-01	k: 80031	n:500000
TBCC   500000 perm   206 sec   (2429 perm/sec)   p_kst 1.600620e-01   p_cons 2.960000e-03   p_joint 1.613400e-02

Joint ci ratio: 4.287067e-02	ci left: 1.578351e-02	ci right 1.647691e-02	k: 8225	n:510000
Cons ci ratio: 1.006953e-01	ci left: 2.813518e-03	ci right 3.113741e-03	k: 1510	n:510000
KS ci ratio: 1.257783e-02	ci left: 1.589772e-01	ci right 1.609914e-01	k: 81591	n:510000
TBCC   510000 perm   212 sec   (2406 perm/sec)   p_kst 1.599824e-01   p_cons 2.960784e-03   p_joint 1.612745e-02

Joint ci ratio: 4.239048e-02	ci left: 1.583577e-02	ci right 1.652348e-02	k: 8412	n:520000
Cons ci ratio: 9.967783e-02	ci left: 2.817534e-03	ci right 3.114970e-03	k: 1541	n:520000
KS ci ratio: 1.245397e-02	ci left: 1.590371e-01	ci right 1.610321e-01	k: 83217	n:520000
TBCC   520000 perm   219 sec   (2380 perm/sec)   p_kst 1.600327e-01   p_cons 2.963462e-03   p_joint 1.617692e-02

Outputting figure to mutsig2_images.part000000000172/TBCC.3_1045_520000_0.16003_0.0029635_0.016177.png
                gene_name: TBCC
               theta_stop: 0.100 
                    nperm: 520000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.0030 
      ci_cons_bounds_left: 0.0028 
     ci_cons_bounds_right: 0.0031 
                  p_joint: 0.016 
     ci_joint_bounds_left: 0.016 
    ci_joint_bounds_right: 0.017 

Current progress: 17 percent done.
TCF20
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.602602e-01	ci left: 9.594514e-03	ci right 1.389697e-02	k: 116	n:10000
Cons ci ratio: 1.613966e-01	ci left: 5.118874e-02	ci right 6.027224e-02	k: 556	n:10000
KS ci ratio: 3.861344e-01	ci left: 8.233934e-03	ci right 1.225906e-02	k: 101	n:10000
TCF20   10000 perm   3 sec   (3389 perm/sec)   p_kst 1.010000e-02   p_cons 5.560000e-02   p_joint 1.160000e-02

Joint ci ratio: 2.265363e-01	ci left: 1.307791e-02	ci right 1.646531e-02	k: 294	n:20000
Cons ci ratio: 1.188317e-01	ci left: 4.852591e-02	ci right 5.470528e-02	k: 1031	n:20000
KS ci ratio: 2.509773e-01	ci left: 1.053722e-02	ci right 1.360709e-02	k: 240	n:20000
TCF20   20000 perm   6 sec   (3331 perm/sec)   p_kst 1.200000e-02   p_cons 5.155000e-02   p_joint 1.470000e-02

Joint ci ratio: 2.169337e-01	ci left: 9.598201e-03	ci right 1.196464e-02	k: 322	n:30000
Cons ci ratio: 9.769364e-02	ci left: 4.843977e-02	ci right 5.344765e-02	k: 1527	n:30000
KS ci ratio: 2.059352e-01	ci left: 1.070373e-02	ci right 1.319213e-02	k: 357	n:30000
TCF20   30000 perm   9 sec   (3214 perm/sec)   p_kst 1.190000e-02   p_cons 5.090000e-02   p_joint 1.073333e-02

Joint ci ratio: 1.669198e-01	ci left: 1.246390e-02	ci right 1.475752e-02	k: 543	n:40000
Cons ci ratio: 8.830621e-02	ci left: 4.487300e-02	ci right 4.904308e-02	k: 1877	n:40000
KS ci ratio: 1.780316e-01	ci left: 1.090819e-02	ci right 1.306353e-02	k: 478	n:40000
TCF20   40000 perm   14 sec   (2921 perm/sec)   p_kst 1.195000e-02   p_cons 4.692500e-02   p_joint 1.357500e-02

Joint ci ratio: 1.795772e-01	ci left: 8.591869e-03	ci right 1.030581e-02	k: 471	n:50000
Cons ci ratio: 7.532624e-02	ci left: 4.944133e-02	ci right 5.333096e-02	k: 2568	n:50000
KS ci ratio: 1.584020e-01	ci left: 1.114087e-02	ci right 1.307640e-02	k: 604	n:50000
TCF20   50000 perm   17 sec   (2927 perm/sec)   p_kst 1.208000e-02   p_cons 5.136000e-02   p_joint 9.420000e-03

Joint ci ratio: 1.723293e-01	ci left: 7.812861e-03	ci right 9.301928e-03	k: 512	n:60000
Cons ci ratio: 7.196806e-02	ci left: 4.541846e-02	ci right 4.882552e-02	k: 2826	n:60000
KS ci ratio: 1.432095e-01	ci left: 1.144946e-02	ci right 1.323151e-02	k: 739	n:60000
TCF20   60000 perm   20 sec   (2943 perm/sec)   p_kst 1.231667e-02   p_cons 4.710000e-02   p_joint 8.533333e-03

Joint ci ratio: 1.719300e-01	ci left: 6.737421e-03	ci right 8.018209e-03	k: 515	n:70000
Cons ci ratio: 6.639922e-02	ci left: 4.585156e-02	ci right 4.901466e-02	k: 3319	n:70000
KS ci ratio: 1.329246e-01	ci left: 1.145516e-02	ci right 1.309993e-02	k: 858	n:70000
TCF20   70000 perm   25 sec   (2857 perm/sec)   p_kst 1.225714e-02   p_cons 4.741429e-02   p_joint 7.357143e-03

Joint ci ratio: 1.637485e-01	ci left: 6.529866e-03	ci right 7.706304e-03	k: 568	n:80000
Cons ci ratio: 6.225121e-02	ci left: 4.575299e-02	ci right 4.870496e-02	k: 3777	n:80000
KS ci ratio: 1.225642e-01	ci left: 1.185066e-02	ci right 1.340998e-02	k: 1009	n:80000
TCF20   80000 perm   28 sec   (2851 perm/sec)   p_kst 1.261250e-02   p_cons 4.721250e-02   p_joint 7.100000e-03

Joint ci ratio: 1.684964e-01	ci left: 5.473942e-03	ci right 6.491628e-03	k: 537	n:90000
Cons ci ratio: 5.841926e-02	ci left: 4.625087e-02	ci right 4.904504e-02	k: 4287	n:90000
KS ci ratio: 1.151577e-01	ci left: 1.197862e-02	ci right 1.345304e-02	k: 1143	n:90000
TCF20   90000 perm   32 sec   (2840 perm/sec)   p_kst 1.270000e-02   p_cons 4.763333e-02   p_joint 5.966667e-03

Joint ci ratio: 1.761113e-01	ci left: 4.495741e-03	ci right 5.373352e-03	k: 492	n:100000
Cons ci ratio: 5.521149e-02	ci left: 4.666348e-02	ci right 4.932282e-02	k: 4798	n:100000
KS ci ratio: 1.083075e-01	ci left: 1.222922e-02	ci right 1.363924e-02	k: 1292	n:100000
TCF20   100000 perm   35 sec   (2824 perm/sec)   p_kst 1.292000e-02   p_cons 4.798000e-02   p_joint 4.920000e-03

Joint ci ratio: 1.347348e-01	ci left: 7.121611e-03	ci right 8.159147e-03	k: 839	n:110000
Cons ci ratio: 5.268879e-02	ci left: 4.664538e-02	ci right 4.917852e-02	k: 5269	n:110000
KS ci ratio: 1.030948e-01	ci left: 1.230349e-02	ci right 1.364965e-02	k: 1426	n:110000
TCF20   110000 perm   39 sec   (2798 perm/sec)   p_kst 1.296364e-02   p_cons 4.790000e-02   p_joint 7.627273e-03

Joint ci ratio: 1.371833e-01	ci left: 6.294510e-03	ci right 7.229566e-03	k: 810	n:120000
Cons ci ratio: 5.069201e-02	ci left: 4.626214e-02	ci right 4.867645e-02	k: 5695	n:120000
KS ci ratio: 9.809242e-02	ci left: 1.248869e-02	ci right 1.378500e-02	k: 1575	n:120000
TCF20   120000 perm   43 sec   (2780 perm/sec)   p_kst 1.312500e-02   p_cons 4.745833e-02   p_joint 6.750000e-03

Joint ci ratio: 1.434959e-01	ci left: 5.297976e-03	ci right 6.124307e-03	k: 741	n:130000
Cons ci ratio: 4.870609e-02	ci left: 4.630438e-02	ci right 4.862355e-02	k: 6169	n:130000
KS ci ratio: 9.411393e-02	ci left: 1.254905e-02	ci right 1.379588e-02	k: 1711	n:130000
TCF20   130000 perm   47 sec   (2760 perm/sec)   p_kst 1.316154e-02   p_cons 4.745385e-02   p_joint 5.700000e-03

Joint ci ratio: 1.455101e-01	ci left: 4.781764e-03	ci right 5.538954e-03	k: 721	n:140000
Cons ci ratio: 4.689221e-02	ci left: 4.642692e-02	ci right 4.866329e-02	k: 6655	n:140000
KS ci ratio: 9.033594e-02	ci left: 1.267154e-02	ci right 1.387732e-02	k: 1857	n:140000
TCF20   140000 perm   51 sec   (2737 perm/sec)   p_kst 1.326429e-02   p_cons 4.753571e-02   p_joint 5.150000e-03

Joint ci ratio: 1.420201e-01	ci left: 4.694331e-03	ci right 5.418337e-03	k: 757	n:150000
Cons ci ratio: 4.530362e-02	ci left: 4.646198e-02	ci right 4.862222e-02	k: 7130	n:150000
KS ci ratio: 8.682558e-02	ci left: 1.282422e-02	ci right 1.399470e-02	k: 2010	n:150000
TCF20   150000 perm   55 sec   (2713 perm/sec)   p_kst 1.340000e-02   p_cons 4.753333e-02   p_joint 5.046667e-03

Joint ci ratio: 1.452545e-01	ci left: 4.202019e-03	ci right 4.866131e-03	k: 724	n:160000
Cons ci ratio: 4.389960e-02	ci left: 4.642573e-02	ci right 4.851570e-02	k: 7594	n:160000
KS ci ratio: 8.401032e-02	ci left: 1.286067e-02	ci right 1.399456e-02	k: 2147	n:160000
TCF20   160000 perm   60 sec   (2689 perm/sec)   p_kst 1.341875e-02   p_cons 4.746250e-02   p_joint 4.525000e-03

Joint ci ratio: 1.469109e-01	ci left: 3.864114e-03	ci right 4.482395e-03	k: 708	n:170000
Cons ci ratio: 4.252995e-02	ci left: 4.658100e-02	ci right 4.861093e-02	k: 8090	n:170000
KS ci ratio: 8.165172e-02	ci left: 1.282998e-02	ci right 1.392789e-02	k: 2273	n:170000
TCF20   170000 perm   64 sec   (2665 perm/sec)   p_kst 1.337059e-02   p_cons 4.758824e-02   p_joint 4.164706e-03

Joint ci ratio: 1.643646e-01	ci left: 2.891055e-03	ci right 3.414039e-03	k: 566	n:180000
Cons ci ratio: 4.133660e-02	ci left: 4.659890e-02	ci right 4.857126e-02	k: 8564	n:180000
KS ci ratio: 7.976803e-02	ci left: 1.271050e-02	ci right 1.377193e-02	k: 2382	n:180000
TCF20   180000 perm   68 sec   (2641 perm/sec)   p_kst 1.323333e-02   p_cons 4.757778e-02   p_joint 3.144444e-03

Joint ci ratio: 1.770398e-01	ci left: 2.345823e-03	ci right 2.806405e-03	k: 488	n:190000
Cons ci ratio: 4.031571e-02	ci left: 4.644360e-02	ci right 4.835971e-02	k: 9005	n:190000
KS ci ratio: 7.752174e-02	ci left: 1.276389e-02	ci right 1.379840e-02	k: 2522	n:190000
TCF20   190000 perm   73 sec   (2616 perm/sec)   p_kst 1.327368e-02   p_cons 4.739474e-02   p_joint 2.568421e-03

Joint ci ratio: 1.488656e-01	ci left: 3.197744e-03	ci right 3.716812e-03	k: 690	n:200000
Cons ci ratio: 3.755370e-02	ci left: 5.069396e-02	ci right 5.263906e-02	k: 10332	n:200000
KS ci ratio: 7.541208e-02	ci left: 1.282704e-02	ci right 1.383714e-02	k: 2665	n:200000
TCF20   200000 perm   77 sec   (2592 perm/sec)   p_kst 1.332500e-02   p_cons 5.166000e-02   p_joint 3.450000e-03

Joint ci ratio: 1.410994e-01	ci left: 3.403459e-03	ci right 3.924675e-03	k: 768	n:210000
Cons ci ratio: 3.664092e-02	ci left: 5.073791e-02	ci right 5.263639e-02	k: 10853	n:210000
KS ci ratio: 7.357202e-02	ci left: 1.284712e-02	ci right 1.383305e-02	k: 2800	n:210000
TCF20   210000 perm   82 sec   (2566 perm/sec)   p_kst 1.333333e-02   p_cons 5.168095e-02   p_joint 3.657143e-03

Joint ci ratio: 1.382537e-01	ci left: 3.389126e-03	ci right 3.896817e-03	k: 800	n:220000
Cons ci ratio: 3.579991e-02	ci left: 5.075586e-02	ci right 5.261052e-02	k: 11369	n:220000
KS ci ratio: 7.186040e-02	ci left: 1.286564e-02	ci right 1.382906e-02	k: 2935	n:220000
TCF20   220000 perm   87 sec   (2542 perm/sec)   p_kst 1.334091e-02   p_cons 5.167727e-02   p_joint 3.636364e-03

Joint ci ratio: 1.398504e-01	ci left: 3.166209e-03	ci right 3.646440e-03	k: 782	n:230000
Cons ci ratio: 3.499411e-02	ci left: 5.082876e-02	ci right 5.264343e-02	k: 11898	n:230000
KS ci ratio: 7.017036e-02	ci left: 1.291697e-02	ci right 1.386057e-02	k: 3078	n:230000
TCF20   230000 perm   91 sec   (2517 perm/sec)   p_kst 1.338261e-02   p_cons 5.173043e-02   p_joint 3.400000e-03

Joint ci ratio: 9.931036e-02	ci left: 6.129554e-03	ci right 6.774119e-03	k: 1547	n:240000
Cons ci ratio: 3.421570e-02	ci left: 5.096627e-02	ci right 5.274457e-02	k: 12444	n:240000
KS ci ratio: 6.939543e-02	ci left: 1.266529e-02	ci right 1.357986e-02	k: 3148	n:240000
TCF20   240000 perm   96 sec   (2493 perm/sec)   p_kst 1.311667e-02   p_cons 5.185000e-02   p_joint 6.445833e-03

Outputting figure to mutsig2_images.part000000000172/TCF20.3_5921_240000_0.013117_0.05185_0.0064458.png
                gene_name: TCF20
               theta_stop: 0.099 
                    nperm: 240000 
                     p_ks: 0.013 
        ci_ks_bounds_left: 0.013 
       ci_ks_bounds_right: 0.014 
                   p_cons: 0.052 
      ci_cons_bounds_left: 0.051 
     ci_cons_bounds_right: 0.053 
                  p_joint: 0.0064 
     ci_joint_bounds_left: 0.0061 
    ci_joint_bounds_right: 0.0068 

Current progress: 33 percent done.
TBC1D5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.413521e-02	ci left: 4.311373e-01	ci right 4.506972e-01	k: 4409	n:10000
Cons ci ratio: 8.964901e-02	ci left: 1.532571e-01	ci right 1.677413e-01	k: 1604	n:10000
KS ci ratio: 7.995015e-02	ci left: 1.859943e-01	ci right 2.015845e-01	k: 1937	n:10000
TBC1D5   10000 perm   2 sec   (5910 perm/sec)   p_kst 1.937000e-01   p_cons 1.604000e-01   p_joint 4.409000e-01

Outputting figure to mutsig2_images.part000000000172/TBC1D5.2_2538_10000_0.1937_0.1604_0.4409.png
                gene_name: TBC1D5
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.16 
      ci_cons_bounds_left: 0.15 
     ci_cons_bounds_right: 0.17 
                  p_joint: 0.44 
     ci_joint_bounds_left: 0.43 
    ci_joint_bounds_right: 0.45 

Current progress: 50 percent done.
TBC1D8B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.256589e-03	ci left: 9.534652e-01	ci right 9.614655e-01	k: 9576	n:10000
Cons ci ratio: 4.018442e-02	ci left: 4.777063e-01	ci right 4.973985e-01	k: 4875	n:9999
KS ci ratio: 7.501285e-02	ci left: 2.063903e-01	ci right 2.225764e-01	k: 2144	n:10000
TBC1D8B   10000 perm   2 sec   (5282 perm/sec)   p_kst 2.144000e-01   p_cons 4.875488e-01   p_joint 9.576000e-01

Outputting figure to mutsig2_images.part000000000172/TBC1D8B.2_3513_10000_0.2144_0.48755_0.9576.png
                gene_name: TBC1D8B
               theta_stop: 0.075 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.49 
      ci_cons_bounds_left: 0.48 
     ci_cons_bounds_right: 0.50 
                  p_joint: 0.96 
     ci_joint_bounds_left: 0.95 
    ci_joint_bounds_right: 0.96 

Current progress: 67 percent done.
TBX5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.440813e-02	ci left: 7.116922e-01	ci right 7.293792e-01	k: 7206	n:10000
Cons ci ratio: 1.371419e-02	ci left: 8.847277e-01	ci right 8.970435e-01	k: 8910	n:10000
KS ci ratio: 7.494614e-02	ci left: 2.066861e-01	ci right 2.228804e-01	k: 2147	n:10000
TBX5   10000 perm   2 sec   (5642 perm/sec)   p_kst 2.147000e-01   p_cons 8.910000e-01   p_joint 7.206000e-01

Outputting figure to mutsig2_images.part000000000172/TBX5.2_1656_10000_0.2147_0.891_0.7206.png
                gene_name: TBX5
               theta_stop: 0.075 
                    nperm: 10000 
                     p_ks: 0.21 
        ci_ks_bounds_left: 0.21 
       ci_ks_bounds_right: 0.22 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.90 
                  p_joint: 0.72 
     ci_joint_bounds_left: 0.71 
    ci_joint_bounds_right: 0.73 

Current progress: 83 percent done.
TCHH
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.778928e-02	ci left: 6.561554e-01	ci right 6.747481e-01	k: 6655	n:10000
Cons ci ratio: 6.202778e-02	ci left: 2.764632e-01	ci right 2.942620e-01	k: 2853	n:10000
KS ci ratio: 1.407139e-02	ci left: 8.795059e-01	ci right 8.920683e-01	k: 8859	n:10000
TCHH   10000 perm   2 sec   (4273 perm/sec)   p_kst 8.859000e-01   p_cons 2.853000e-01   p_joint 6.655000e-01

Outputting figure to mutsig2_images.part000000000172/TCHH.2_5840_10000_0.8859_0.2853_0.6655.png
                gene_name: TCHH
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.28 
     ci_cons_bounds_right: 0.29 
                  p_joint: 0.67 
     ci_joint_bounds_left: 0.66 
    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.165.3896/
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/181708/iteration1/scatter.0000000172
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 172 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120296: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000173> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:47:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000173.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000173.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 173  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    118.32 sec.
    Max Memory :      1281 MB
    Max Swap   :      3911 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.165.3896/
-whichjob
173
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 173: processing genes 15562 - 15651
Calculating significance of each gene.
Using projection method.
15562	TCP11L1	1
15563	TCP11L2	1.936036e-02
15564	TCTA	1
15565	TCTE1	1
15566	TCTE3	1
15567	TCTEX1D1	1
15568	TCTEX1D2	1
15569	TCTEX1D4	1
15570	TCTN1	1.912210e-01
15571	TCTN2	1
15572	TCTN3	1.646489e-01
15573	TDG	1
15574	TDGF1	1
15575	TDO2	9.112593e-02
15576	TDP1	2.706900e-01
15577	TDP2	1
15578	TDRD1	4.597417e-01
15579	TDRD10	1
15580	TDRD3	1.559650e-01
15581	TDRD5	1
15582	TDRD6	4.742328e-01
15583	TDRD7	1
15584	TDRD9	1
15585	TDRKH	1
15586	TEAD1	1
15587	TEAD2	1
15588	TEAD3	1.316803e-01
15589	TEAD4	1
15590	TEC	1
15591	TECPR1	1.632651e-01
15592	TECPR2	1
15593	TECR	1
15594	TECRL	1
15595	TECTA	1
15596	TECTB	1
15597	TEDDM1	1
15598	TEF	1
15599	TEK	1
15600	TEKT1	1
15601	TEKT2	1
15602	TEKT3	1
15603	TEKT4	1
15604	TEKT5	1
15605	TELO2	1
15606	TENC1	1
15607	TEP1	1
15608	TEPP	1.250255e-02
15609	TERF1	1
15610	TERF2	1
15611	TERF2IP	1
15612	TERT	1
15613	TES	1
15614	TESC	1
15615	TESK1	1
15616	TESK2	1
15617	TET1	1
15618	TET2	1.925011e-01
15619	TET3	3.980000e-01
15620	TEX10	1
15621	TEX101	1
15622	TEX11	1
15623	TEX12	1
15624	TEX13A	1
15625	TEX13B	1
15626	TEX14	3.081592e-01
15627	TEX15	5.704752e-01
15628	TEX19	1
15629	TEX2	2.942473e-01
15630	TEX261	1
15631	TEX264	1
15632	TEX9	1
15633	TF	1
15634	TFAM	1
15635	TFAP2A	1
15636	TFAP2B	1
15637	TFAP2C	9.686340e-02
15638	TFAP2D	1
15639	TFAP2E	1
15640	TFAP4	1
15641	TFB1M	3.618640e-02
15642	TFB2M	1
15643	TFCP2	1
15644	TFCP2L1	1
15645	TFDP1	1
15646	TFDP2	1
15647	TFDP3	1
15648	TFE3	5.495053e-02
15649	TFEB	1
15650	TFEC	8.997013e-03
15651	TFF1	1
Done

Running MutSig 2:
Scatter job 173: processing genes 15562 - 15651
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TCP11L2
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: 3.633558e-02	ci left: 5.279684e-01	ci right 5.476096e-01	k: 5378	n:10000
KS ci ratio: 1.497436e-02	ci left: 8.660086e-01	ci right 8.791735e-01	k: 8727	n:10000
TCP11L2   10000 perm   2 sec   (6243 perm/sec)   p_kst 8.727000e-01   p_cons 5.378000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000173/TCP11L2.2_1596_10000_0.8727_0.5378_1.png
                gene_name: TCP11L2
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.87 
        ci_ks_bounds_left: 0.87 
       ci_ks_bounds_right: 0.88 
                   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: 33 percent done.
TET2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.111979e-01	ci left: 2.977507e-02	ci right 3.690017e-02	k: 332	n:10000
Cons ci ratio: 4.502334e-02	ci left: 4.213649e-01	ci right 4.408752e-01	k: 4311	n:10000
KS ci ratio: 1.809983e-01	ci left: 4.073298e-02	ci right 4.893483e-02	k: 447	n:10000
TET2   10000 perm   2 sec   (4610 perm/sec)   p_kst 4.470000e-02   p_cons 4.311000e-01   p_joint 3.320000e-02

Joint ci ratio: 1.126358e-01	ci left: 5.387513e-02	ci right 6.035438e-02	k: 1141	n:20000
Cons ci ratio: 3.350697e-02	ci left: 3.994324e-01	ci right 4.130948e-01	k: 8125	n:20000
KS ci ratio: 1.301312e-01	ci left: 4.056926e-02	ci right 4.626445e-02	k: 867	n:20000
TET2   20000 perm   5 sec   (4253 perm/sec)   p_kst 4.335000e-02   p_cons 4.062500e-01   p_joint 5.705000e-02

Joint ci ratio: 5.222582e-02	ci left: 1.539552e-01	ci right 1.622445e-01	k: 4742	n:30000
Cons ci ratio: 2.717012e-02	ci left: 4.040276e-01	ci right 4.151899e-01	k: 12288	n:30000
KS ci ratio: 1.081327e-01	ci left: 3.969301e-02	ci right 4.426290e-02	k: 1258	n:30000
TET2   30000 perm   7 sec   (4114 perm/sec)   p_kst 4.193333e-02   p_cons 4.096000e-01   p_joint 1.580667e-01

Joint ci ratio: 1.939843e-02	ci left: 5.002376e-01	ci right 5.100616e-01	k: 20206	n:40000
Cons ci ratio: 2.358764e-02	ci left: 4.036023e-01	ci right 4.132610e-01	k: 16337	n:40000
KS ci ratio: 9.392864e-02	ci left: 3.976182e-02	ci right 4.370506e-02	k: 1668	n:40000
TET2   40000 perm   10 sec   (4030 perm/sec)   p_kst 4.170000e-02   p_cons 4.084250e-01   p_joint 5.051500e-01

Outputting figure to mutsig2_images.part000000000173/TET2.2_6134_40000_0.0417_0.40842_0.50515.png
                gene_name: TET2
               theta_stop: 0.094 
                    nperm: 40000 
                     p_ks: 0.042 
        ci_ks_bounds_left: 0.040 
       ci_ks_bounds_right: 0.044 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.41 
                  p_joint: 0.51 
     ci_joint_bounds_left: 0.50 
    ci_joint_bounds_right: 0.51 

Current progress: 67 percent done.
TFEC
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: 1.019010e-01	ci left: 1.222933e-01	ci right 1.355237e-01	k: 1288	n:10000
KS ci ratio: 1.942301e-02	ci left: 7.949654e-01	ci right 8.106578e-01	k: 8029	n:10000
TFEC   10000 perm   1 sec   (6896 perm/sec)   p_kst 8.029000e-01   p_cons 1.288000e-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: 7.002759e-02	ci left: 1.306864e-01	ci right 1.402199e-01	k: 2708	n:20000
KS ci ratio: 1.374904e-02	ci left: 7.969643e-01	ci right 8.080477e-01	k: 16051	n:20000
TFEC   20000 perm   3 sec   (6091 perm/sec)   p_kst 8.025500e-01   p_cons 1.354000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000173/TFEC.2_1072_20000_0.80255_0.1354_1.png
                gene_name: TFEC
               theta_stop: 0.070 
                    nperm: 20000 
                     p_ks: 0.80 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.81 
                   p_cons: 0.14 
      ci_cons_bounds_left: 0.13 
     ci_cons_bounds_right: 0.14 
                  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.165.3896/
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/181708/iteration1/scatter.0000000173
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 173 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1702>
Subject: Job 1120300: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1702>, 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/181708/iteration1/scatter.0000000174> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:47:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000174.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000174.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 174  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    137.61 sec.
    Max Memory :      1091 MB
    Max Swap   :      3816 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.165.3896/
-whichjob
174
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 174: processing genes 15652 - 15742
Calculating significance of each gene.
Using projection method.
15652	TFF2	1
15653	TFF3	1
15654	TFG	1
15655	TFIP11	1.638451e-01
15656	TFPI	1
15657	TFPI2	9.352692e-02
15658	TFPT	1
15659	TFR2	1
15660	TFRC	1.659414e-01
15661	TG	1
15662	TGDS	1
15663	TGFA	1
15664	TGFB1	1
15665	TGFB1I1	1
15666	TGFB2	1
15667	TGFB3	1
15668	TGFBI	1
15669	TGFBR1	1
15670	TGFBR2	1
15671	TGFBR3	1.096262e-02
15672	TGFBRAP1	2.412338e-01
15673	TGIF1	1
15674	TGIF2	1
15675	TGIF2LX	6.319328e-02
15676	TGIF2LY	1
15677	TGM1	1
15678	TGM2	1
15679	TGM3	1.804643e-01
15680	TGM4	1
15681	TGM5	2.639676e-01
15682	TGM6	1
15683	TGM7	1
15684	TGOLN2	1
15685	TGS1	2.196390e-01
15686	TH	1
15687	TH1L	1
15688	THADA	1.554644e-02
15689	THAP1	1
15690	THAP10	1.159740e-01
15691	THAP11	1
15692	THAP2	1
15693	THAP3	1
15694	THAP4	1
15695	THAP5	1
15696	THAP6	1
15697	THAP7	1
15698	THAP8	1
15699	THAP9	1.585996e-01
15700	THBD	1
15701	THBS1	1
15702	THBS2	4.379898e-01
15703	THBS3	1
15704	THBS4	1
15705	THEG	1
15706	THEM4	1
15707	THEM5	1
15708	THEMIS	2.003310e-03
15709	THG1L	1
15710	THNSL1	1
15711	THNSL2	1
15712	THOC1	1.033837e-01
15713	THOC2	1
15714	THOC3	1
15715	THOC4	1
15716	THOC5	1
15717	THOC6	1
15718	THOC7	1
15719	THOP1	1
15720	THPO	1
15721	THRA	1
15722	THRAP3	1
15723	THRB	1
15724	THRSP	1
15725	THSD1	1
15726	THSD4	9.509814e-02
15727	THSD7A	1
15728	THSD7B	4.274274e-01
15729	THTPA	1
15730	THUMPD1	8.653767e-02
15731	THUMPD2	1
15732	THUMPD3	1
15733	THY1	1
15734	THYN1	1
15735	TIA1	1
15736	TIAF1	5.918348e-02
15737	TIAL1	1
15738	TIAM1	3.209653e-01
15739	TIAM2	1
15740	TICAM1	6.262465e-02
15741	TIE1	3.459342e-01
15742	TIFA	1
Done

Running MutSig 2:
Scatter job 174: processing genes 15652 - 15742
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TGFBR3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.661620e-02	ci left: 2.485560e-01	ci right 2.657857e-01	k: 2571	n:10000
Cons ci ratio: 1.539580e-02	ci left: 8.595750e-01	ci right 8.730108e-01	k: 8664	n:10000
KS ci ratio: 1.342088e-01	ci left: 7.330186e-02	ci right 8.394515e-02	k: 785	n:10000
TGFBR3   10000 perm   2 sec   (5383 perm/sec)   p_kst 7.850000e-02   p_cons 8.664000e-01   p_joint 2.571000e-01

Joint ci ratio: 5.561903e-02	ci left: 1.933869e-01	ci right 2.045007e-01	k: 3978	n:20000
Cons ci ratio: 1.089732e-02	ci left: 8.613529e-01	ci right 8.708404e-01	k: 17323	n:20000
KS ci ratio: 9.671650e-02	ci left: 7.221756e-02	ci right 7.960630e-02	k: 1517	n:20000
TGFBR3   20000 perm   6 sec   (3127 perm/sec)   p_kst 7.585000e-02   p_cons 8.661500e-01   p_joint 1.989000e-01

Outputting figure to mutsig2_images.part000000000174/TGFBR3.3_2620_20000_0.07585_0.86615_0.1989.png
                gene_name: TGFBR3
               theta_stop: 0.097 
                    nperm: 20000 
                     p_ks: 0.076 
        ci_ks_bounds_left: 0.072 
       ci_ks_bounds_right: 0.080 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.87 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.20 

Current progress: 20 percent done.
THADA
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.985136e-02	ci left: 2.310633e-01	ci right 2.478887e-01	k: 2394	n:10000
Cons ci ratio: 9.408979e-03	ci left: 9.409733e-01	ci right 9.499650e-01	k: 9456	n:10000
KS ci ratio: 1.692637e-01	ci left: 4.657748e-02	ci right 5.528648e-02	k: 508	n:10000
THADA   10000 perm   2 sec   (4622 perm/sec)   p_kst 5.080000e-02   p_cons 9.456000e-01   p_joint 2.394000e-01

Joint ci ratio: 7.725382e-02	ci left: 1.096268e-01	ci right 1.184858e-01	k: 2280	n:20000
Cons ci ratio: 6.618419e-03	ci left: 9.428799e-01	ci right 9.491896e-01	k: 18922	n:20000
KS ci ratio: 1.231716e-01	ci left: 4.522388e-02	ci right 5.120834e-02	k: 963	n:20000
THADA   20000 perm   5 sec   (4191 perm/sec)   p_kst 4.815000e-02   p_cons 9.461000e-01   p_joint 1.140000e-01

Joint ci ratio: 7.285774e-02	ci left: 8.478483e-02	ci right 9.122855e-02	k: 2639	n:30000
Cons ci ratio: 5.371422e-03	ci left: 9.440979e-01	ci right 9.492152e-01	k: 28401	n:30000
KS ci ratio: 1.002064e-01	ci left: 4.609628e-02	ci right 5.099163e-02	k: 1455	n:30000
THADA   30000 perm   7 sec   (4033 perm/sec)   p_kst 4.850000e-02   p_cons 9.467000e-01   p_joint 8.796667e-02

Joint ci ratio: 5.641564e-02	ci left: 1.046534e-01	ci right 1.107537e-01	k: 4307	n:40000
Cons ci ratio: 4.672199e-03	ci left: 9.439948e-01	ci right 9.484401e-01	k: 37850	n:40000
KS ci ratio: 8.641580e-02	ci left: 4.680689e-02	ci right 5.105890e-02	k: 1956	n:40000
THADA   40000 perm   10 sec   (3922 perm/sec)   p_kst 4.890000e-02   p_cons 9.462500e-01   p_joint 1.076750e-01

Outputting figure to mutsig2_images.part000000000174/THADA.3_6010_40000_0.0489_0.94625_0.10768.png
                gene_name: THADA
               theta_stop: 0.086 
                    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: 0.11 
     ci_joint_bounds_left: 0.10 
    ci_joint_bounds_right: 0.11 

Current progress: 40 percent done.
THEMIS
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: 1.496089e-02	ci left: 8.662129e-01	ci right 8.793691e-01	k: 8729	n:10000
KS ci ratio: 1.978425e-02	ci left: 7.889804e-01	ci right 8.048463e-01	k: 7970	n:10000
THEMIS   10000 perm   2 sec   (5526 perm/sec)   p_kst 7.970000e-01   p_cons 8.729000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000174/THEMIS.3_2071_10000_0.797_0.8729_1.png
                gene_name: THEMIS
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.80 
        ci_ks_bounds_left: 0.79 
       ci_ks_bounds_right: 0.80 
                   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: 60 percent done.
TGS1
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: 1.176235e-03	ci left: 9.984243e-01	ci right 9.996546e-01	k: 9992	n:10000
KS ci ratio: 1.429301e-02	ci left: 8.762316e-01	ci right 8.889446e-01	k: 8827	n:10000
TGS1   10000 perm   2 sec   (5939 perm/sec)   p_kst 8.827000e-01   p_cons 9.992000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000174/TGS1.2_2614_10000_0.8827_0.9992_1.png
                gene_name: TGS1
               theta_stop: 0.014 
                    nperm: 10000 
                     p_ks: 0.88 
        ci_ks_bounds_left: 0.88 
       ci_ks_bounds_right: 0.89 
                   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: 80 percent done.
TICAM1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.185486e-02	ci left: 4.573820e-01	ci right 4.770371e-01	k: 4672	n:10000
Cons ci ratio: 3.220355e-02	ci left: 5.873093e-01	ci right 6.066342e-01	k: 5970	n:10000
KS ci ratio: 6.673845e-02	ci left: 2.478638e-01	ci right 2.650783e-01	k: 2564	n:10000
TICAM1   10000 perm   2 sec   (5836 perm/sec)   p_kst 2.564000e-01   p_cons 5.970000e-01   p_joint 4.672000e-01

Outputting figure to mutsig2_images.part000000000174/TICAM1.2_2143_10000_0.2564_0.597_0.4672.png
                gene_name: TICAM1
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.60 
      ci_cons_bounds_left: 0.59 
     ci_cons_bounds_right: 0.61 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    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.165.3896/
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/181708/iteration1/scatter.0000000174
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 174 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120303: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000175> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:47:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000175.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000175.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 175  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    133.46 sec.
    Max Memory :      1090 MB
    Max Swap   :      3818 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.165.3896/
-whichjob
175
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 175: processing genes 15743 - 15832
Calculating significance of each gene.
Using projection method.
15743	TIFAB	1
15744	TIGD2	1.149269e-01
15745	TIGD3	7.136235e-02
15746	TIGD4	1
15747	TIGD5	1.020085e-01
15748	TIGD6	1
15749	TIGD7	1
15750	TIGIT	1
15751	TIMD4	1
15752	TIMELESS	2.876540e-01
15753	TIMM10	1
15754	TIMM13	1
15755	TIMM16	1
15756	TIMM17A	1
15757	TIMM17B	1
15758	TIMM22	1
15759	TIMM23	1
15760	TIMM44	2.330735e-01
15761	TIMM50	1
15762	TIMM8A	1
15763	TIMM8B	1
15764	TIMM9	1
15765	TIMP1	1
15766	TIMP2	1
15767	TIMP3	1
15768	TIMP4	1
15769	TINAG	1
15770	TINAGL1	1
15771	TINF2	1
15772	TIPARP	1
15773	TIPIN	1
15774	TIPRL	1
15775	TIRAP	1
15776	TJAP1	1.515597e-01
15777	TJP1	1
15778	TJP2	1
15779	TJP3	1
15780	TK1	1.016049e-01
15781	TK2	1
15782	TKT	1
15783	TKTL1	3.008800e-02
15784	TKTL2	1
15785	TLCD1	1
15786	TLE1	1
15787	TLE2	1
15788	TLE3	2.056660e-01
15789	TLE4	1
15790	TLE6	1
15791	TLK1	1
15792	TLK2	8.014919e-02
15793	TLL1	1
15794	TLL2	1
15795	TLN1	1
15796	TLN2	1
15797	TLR1	1
15798	TLR10	4.049154e-02
15799	TLR2	1
15800	TLR3	1
15801	TLR4	1
15802	TLR5	7.429094e-02
15803	TLR6	2.812280e-01
15804	TLR7	1
15805	TLR8	1
15806	TLR9	1
15807	TLX1	1
15808	TLX1NB	1
15809	TLX2	1
15810	TLX3	1
15811	TM2D1	1
15812	TM2D2	1
15813	TM2D3	1
15814	TM4SF1	1
15815	TM4SF18	1
15816	TM4SF19	1
15817	TM4SF20	1
15818	TM4SF4	1
15819	TM4SF5	1
15820	TM6SF1	1.786952e-01
15821	TM6SF2	1
15822	TM7SF2	8.596414e-02
15823	TM7SF3	1
15824	TM7SF4	1.297359e-01
15825	TM9SF1	1
15826	TM9SF2	1
15827	TM9SF3	1
15828	TM9SF4	2.084709e-01
15829	TMBIM1	1
15830	TMBIM4	1
15831	TMBIM6	6.558914e-02
15832	TMC1	1
Done

Running MutSig 2:
Scatter job 175: processing genes 15743 - 15832
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TKTL1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.151716e-02	ci left: 9.151276e-01	ci right 9.258259e-01	k: 9206	n:10000
Cons ci ratio: 2.607094e-02	ci left: 6.841568e-01	ci right 7.023305e-01	k: 6933	n:10000
KS ci ratio: 2.793293e-02	ci left: 6.538404e-01	ci right 6.724645e-01	k: 6632	n:10000
TKTL1   10000 perm   2 sec   (5651 perm/sec)   p_kst 6.632000e-01   p_cons 6.933000e-01   p_joint 9.206000e-01

Outputting figure to mutsig2_images.part000000000175/TKTL1.2_1843_10000_0.6632_0.6933_0.9206.png
                gene_name: TKTL1
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.66 
        ci_ks_bounds_left: 0.65 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.69 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.70 
                  p_joint: 0.92 
     ci_joint_bounds_left: 0.92 
    ci_joint_bounds_right: 0.93 

Current progress: 33 percent done.
TLR10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.402266e-02	ci left: 8.802224e-01	ci right 8.927514e-01	k: 8866	n:10000
Cons ci ratio: 1.004954e-02	ci left: 9.335086e-01	ci right 9.430341e-01	k: 9384	n:10000
KS ci ratio: 4.661919e-02	ci left: 4.044221e-01	ci right 4.238280e-01	k: 4141	n:10000
TLR10   10000 perm   2 sec   (5473 perm/sec)   p_kst 4.141000e-01   p_cons 9.384000e-01   p_joint 8.866000e-01

Outputting figure to mutsig2_images.part000000000175/TLR10.2_2440_10000_0.4141_0.9384_0.8866.png
                gene_name: TLR10
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.94 
      ci_cons_bounds_left: 0.93 
     ci_cons_bounds_right: 0.94 
                  p_joint: 0.89 
     ci_joint_bounds_left: 0.88 
    ci_joint_bounds_right: 0.89 

Current progress: 67 percent done.
TLR5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.115002e-02	ci left: 6.032715e-01	ci right 6.224627e-01	k: 6129	n:10000
Cons ci ratio: 3.434269e-02	ci left: 5.559172e-01	ci right 5.754445e-01	k: 5657	n:10000
KS ci ratio: 6.533341e-02	ci left: 2.559738e-01	ci right 2.733635e-01	k: 2646	n:10000
TLR5   10000 perm   2 sec   (5575 perm/sec)   p_kst 2.646000e-01   p_cons 5.657000e-01   p_joint 6.129000e-01

Outputting figure to mutsig2_images.part000000000175/TLR5.2_2581_10000_0.2646_0.5657_0.6129.png
                gene_name: TLR5
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.26 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.57 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.58 
                  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.165.3896/
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/181708/iteration1/scatter.0000000175
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 175 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1701>
Subject: Job 1120306: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1701>, 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/181708/iteration1/scatter.0000000176> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:54:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000176.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000176.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 176  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    560.19 sec.
    Max Memory :      1292 MB
    Max Swap   :      3894 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.165.3896/
-whichjob
176
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 176: processing genes 15833 - 15923
Calculating significance of each gene.
Using projection method.
15833	TMC2	1
15834	TMC3	7.964958e-02
15835	TMC4	1
15836	TMC5	1
15837	TMC6	1
15838	TMC7	1
15839	TMC8	1.360028e-01
15840	TMCC1	1
15841	TMCC2	1
15842	TMCC3	1
15843	TMCO1	1
15844	TMCO2	1.909129e-03
15845	TMCO3	1
15846	TMCO4	1
15847	TMCO5A	1
15848	TMCO6	5.651618e-02
15849	TMCO7	1
15850	TMED1	1
15851	TMED10	1
15852	TMED2	1
15853	TMED3	1
15854	TMED4	1
15855	TMED5	1
15856	TMED6	1
15857	TMED7	4.869557e-02
15858	TMED7-TICAM2	1
15859	TMED8	1
15860	TMED9	1
15861	TMEFF1	1
15862	TMEFF2	1
15863	TMEM100	1
15864	TMEM101	1
15865	TMEM102	1
15866	TMEM104	1
15867	TMEM105	1
15868	TMEM106A	1
15869	TMEM106B	1
15870	TMEM106C	1
15871	TMEM107	1
15872	TMEM108	1
15873	TMEM109	1
15874	TMEM11	1
15875	TMEM110	1
15876	TMEM111	7.513896e-02
15877	TMEM115	1
15878	TMEM116	1
15879	TMEM117	7.238411e-02
15880	TMEM119	1
15881	TMEM120A	1
15882	TMEM120B	1
15883	TMEM123	2.501696e-02
15884	TMEM125	1
15885	TMEM126A	1
15886	TMEM126B	1
15887	TMEM127	1
15888	TMEM128	1
15889	TMEM130	1.474941e-01
15890	TMEM131	2.966551e-01
15891	TMEM132A	1
15892	TMEM132B	1
15893	TMEM132D	5.964592e-02
15894	TMEM132E	1
15895	TMEM133	1
15896	TMEM134	1
15897	TMEM135	1
15898	TMEM136	1
15899	TMEM138	1
15900	TMEM139	1
15901	TMEM140	1
15902	TMEM141	1
15903	TMEM143	1
15904	TMEM144	1
15905	TMEM145	2.041753e-01
15906	TMEM146	2.091766e-01
15907	TMEM147	1
15908	TMEM149	1
15909	TMEM14A	1
15910	TMEM14B	1
15911	TMEM14C	1
15912	TMEM14E	1
15913	TMEM150A	1
15914	TMEM150B	1
15915	TMEM150C	1
15916	TMEM151A	1
15917	TMEM154	1
15918	TMEM155	1
15919	TMEM156	1
15920	TMEM159	1
15921	TMEM161A	1
15922	TMEM161B	1
15923	TMEM163	1
Done

Running MutSig 2:
Scatter job 176: processing genes 15833 - 15923
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TMC3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.118942e-02	ci left: 6.026690e-01	ci right 6.218656e-01	k: 6123	n:10000
Cons ci ratio: 3.437065e-02	ci left: 5.555163e-01	ci right 5.750457e-01	k: 5653	n:10000
KS ci ratio: 7.881696e-02	ci left: 1.904255e-01	ci right 2.061507e-01	k: 1982	n:10000
TMC3   10000 perm   2 sec   (4446 perm/sec)   p_kst 1.982000e-01   p_cons 5.653000e-01   p_joint 6.123000e-01

Outputting figure to mutsig2_images.part000000000176/TMC3.2_3391_10000_0.1982_0.5653_0.6123.png
                gene_name: TMC3
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.57 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.58 
                  p_joint: 0.61 
     ci_joint_bounds_left: 0.60 
    ci_joint_bounds_right: 0.62 

Current progress: 33 percent done.
TMCO2
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: 1.423778e-02	ci left: 8.770500e-01	ci right 8.897257e-01	k: 8835	n:10000
KS ci ratio: 9.791669e-01	ci left: 8.397740e-04	ci right 2.472817e-03	k: 15	n:10000
TMCO2   10000 perm   1 sec   (7097 perm/sec)   p_kst 1.500000e-03   p_cons 8.835000e-01   p_joint 1.060000e-02

Joint ci ratio: 1.445823e-01	ci left: 3.288174e-02	ci right 3.805446e-02	k: 708	n:20000
Cons ci ratio: 9.874887e-03	ci left: 8.829377e-01	ci right 8.917493e-01	k: 17748	n:20000
KS ci ratio: 6.438316e-01	ci left: 1.261006e-03	ci right 2.491096e-03	k: 36	n:20000
TMCO2   20000 perm   3 sec   (6160 perm/sec)   p_kst 1.800000e-03   p_cons 8.874000e-01   p_joint 3.540000e-02

Joint ci ratio: 1.838116e-01	ci left: 1.355952e-02	ci right 1.633558e-02	k: 447	n:30000
Cons ci ratio: 8.654752e-03	ci left: 8.686055e-01	ci right 8.761889e-01	k: 26173	n:30000
KS ci ratio: 5.595332e-01	ci left: 1.179942e-03	ci right 2.120815e-03	k: 48	n:30000
TMCO2   30000 perm   5 sec   (5844 perm/sec)   p_kst 1.600000e-03   p_cons 8.724333e-01   p_joint 1.490000e-02

Joint ci ratio: 1.627253e-01	ci left: 1.313539e-02	ci right 1.548590e-02	k: 571	n:40000
Cons ci ratio: 7.499608e-03	ci left: 8.689897e-01	ci right 8.755561e-01	k: 34892	n:40000
KS ci ratio: 4.615547e-01	ci left: 1.386542e-03	ci right 2.238401e-03	k: 71	n:40000
TMCO2   40000 perm   7 sec   (5640 perm/sec)   p_kst 1.775000e-03   p_cons 8.723000e-01   p_joint 1.427500e-02

Joint ci ratio: 1.927977e-01	ci left: 7.409151e-03	ci right 9.008737e-03	k: 409	n:50000
Cons ci ratio: 6.680671e-03	ci left: 8.702517e-01	ci right 8.761049e-01	k: 43660	n:50000
KS ci ratio: 4.273434e-01	ci left: 1.322391e-03	ci right 2.057410e-03	k: 83	n:50000
TMCO2   50000 perm   9 sec   (5490 perm/sec)   p_kst 1.660000e-03   p_cons 8.732000e-01   p_joint 8.180000e-03

Joint ci ratio: 1.761803e-01	ci left: 7.462067e-03	ci right 8.919440e-03	k: 490	n:60000
Cons ci ratio: 6.089829e-03	ci left: 8.708306e-01	ci right 8.761665e-01	k: 52411	n:60000
KS ci ratio: 4.039969e-01	ci left: 1.251227e-03	ci right 1.898523e-03	k: 93	n:60000
TMCO2   60000 perm   11 sec   (5262 perm/sec)   p_kst 1.550000e-03   p_cons 8.735167e-01   p_joint 8.166667e-03

Joint ci ratio: 1.601546e-01	ci left: 7.805784e-03	ci right 9.178283e-03	k: 593	n:70000
Cons ci ratio: 5.631195e-03	ci left: 8.713030e-01	ci right 8.762374e-01	k: 61165	n:70000
KS ci ratio: 3.751728e-01	ci left: 1.265802e-03	ci right 1.862455e-03	k: 108	n:70000
TMCO2   70000 perm   14 sec   (5154 perm/sec)   p_kst 1.542857e-03   p_cons 8.737857e-01   p_joint 8.471429e-03

Joint ci ratio: 1.636037e-01	ci left: 6.541857e-03	ci right 7.719311e-03	k: 569	n:80000
Cons ci ratio: 5.285335e-03	ci left: 8.707107e-01	ci right 8.753372e-01	k: 69843	n:80000
KS ci ratio: 3.546272e-01	ci left: 1.255186e-03	ci right 1.806978e-03	k: 121	n:80000
TMCO2   80000 perm   16 sec   (5053 perm/sec)   p_kst 1.512500e-03   p_cons 8.730375e-01   p_joint 7.112500e-03

Joint ci ratio: 1.434100e-01	ci left: 7.642592e-03	ci right 8.833875e-03	k: 740	n:90000
Cons ci ratio: 4.968647e-03	ci left: 8.714898e-01	ci right 8.758417e-01	k: 78631	n:90000
KS ci ratio: 3.241565e-01	ci left: 1.359717e-03	ci right 1.895450e-03	k: 145	n:90000
TMCO2   90000 perm   18 sec   (4923 perm/sec)   p_kst 1.611111e-03   p_cons 8.736778e-01   p_joint 8.222222e-03

Joint ci ratio: 1.369197e-01	ci left: 7.573072e-03	ci right 8.695738e-03	k: 812	n:100000
Cons ci ratio: 4.709343e-03	ci left: 8.718065e-01	ci right 8.759318e-01	k: 87388	n:100000
KS ci ratio: 3.126028e-01	ci left: 1.324954e-03	ci right 1.824671e-03	k: 156	n:100000
TMCO2   100000 perm   21 sec   (4775 perm/sec)   p_kst 1.560000e-03   p_cons 8.738800e-01   p_joint 8.120000e-03

Joint ci ratio: 1.300576e-01	ci left: 7.657927e-03	ci right 8.731882e-03	k: 900	n:110000
Cons ci ratio: 4.172050e-03	ci left: 8.873394e-01	ci right 8.910582e-01	k: 97813	n:110000
KS ci ratio: 2.960870e-01	ci left: 1.355657e-03	ci right 1.834874e-03	k: 174	n:110000
TMCO2   110000 perm   23 sec   (4693 perm/sec)   p_kst 1.581818e-03   p_cons 8.892091e-01   p_joint 8.181818e-03

Joint ci ratio: 1.243874e-01	ci left: 7.697504e-03	ci right 8.726475e-03	k: 984	n:120000
Cons ci ratio: 3.993935e-03	ci left: 8.874441e-01	ci right 8.910038e-01	k: 106708	n:120000
KS ci ratio: 2.797701e-01	ci left: 1.405063e-03	ci right 1.869555e-03	k: 195	n:120000
TMCO2   120000 perm   26 sec   (4616 perm/sec)   p_kst 1.625000e-03   p_cons 8.892333e-01   p_joint 8.200000e-03

Joint ci ratio: 1.302131e-01	ci left: 6.472083e-03	ci right 7.380890e-03	k: 899	n:130000
Cons ci ratio: 3.836394e-03	ci left: 8.875586e-01	ci right 8.909778e-01	k: 115606	n:130000
KS ci ratio: 2.683728e-01	ci left: 1.418769e-03	ci right 1.865472e-03	k: 212	n:130000
TMCO2   130000 perm   29 sec   (4522 perm/sec)   p_kst 1.630769e-03   p_cons 8.892769e-01   p_joint 6.915385e-03

Joint ci ratio: 1.257532e-01	ci left: 6.459211e-03	ci right 7.332828e-03	k: 964	n:140000
Cons ci ratio: 3.698146e-03	ci left: 8.875514e-01	ci right 8.908468e-01	k: 124489	n:140000
KS ci ratio: 2.588280e-01	ci left: 1.424165e-03	ci right 1.854042e-03	k: 228	n:140000
TMCO2   140000 perm   31 sec   (4453 perm/sec)   p_kst 1.628571e-03   p_cons 8.892071e-01   p_joint 6.885714e-03

Joint ci ratio: 1.207812e-01	ci left: 6.551968e-03	ci right 7.400591e-03	k: 1045	n:150000
Cons ci ratio: 3.569730e-03	ci left: 8.877751e-01	ci right 8.909565e-01	k: 133406	n:150000
KS ci ratio: 2.477151e-01	ci left: 1.460341e-03	ci right 1.879299e-03	k: 249	n:150000
TMCO2   150000 perm   34 sec   (4388 perm/sec)   p_kst 1.660000e-03   p_cons 8.893733e-01   p_joint 6.966667e-03

Joint ci ratio: 1.039329e-01	ci left: 8.354256e-03	ci right 9.276175e-03	k: 1409	n:160000
Cons ci ratio: 3.454587e-03	ci left: 8.879285e-01	ci right 8.910074e-01	k: 142316	n:160000
KS ci ratio: 2.370460e-01	ci left: 1.504098e-03	ci right 1.914297e-03	k: 272	n:160000
TMCO2   160000 perm   37 sec   (4325 perm/sec)   p_kst 1.700000e-03   p_cons 8.894750e-01   p_joint 8.806250e-03

Joint ci ratio: 1.021140e-01	ci left: 8.155056e-03	ci right 9.038296e-03	k: 1460	n:170000
Cons ci ratio: 3.350812e-03	ci left: 8.880119e-01	ci right 8.909983e-01	k: 151217	n:170000
KS ci ratio: 2.315987e-01	ci left: 1.487602e-03	ci right 1.882645e-03	k: 285	n:170000
TMCO2   170000 perm   40 sec   (4260 perm/sec)   p_kst 1.676471e-03   p_cons 8.895118e-01   p_joint 8.588235e-03

Joint ci ratio: 1.017880e-01	ci left: 7.756055e-03	ci right 8.593235e-03	k: 1470	n:180000
Cons ci ratio: 3.258897e-03	ci left: 8.879029e-01	ci right 8.908067e-01	k: 160085	n:180000
KS ci ratio: 2.261320e-01	ci left: 1.478275e-03	ci right 1.860284e-03	k: 299	n:180000
TMCO2   180000 perm   43 sec   (4186 perm/sec)   p_kst 1.661111e-03   p_cons 8.893611e-01   p_joint 8.166667e-03

Joint ci ratio: 7.386838e-02	ci left: 1.406545e-02	ci right 1.514943e-02	k: 2774	n:190000
Cons ci ratio: 3.172111e-03	ci left: 8.879335e-01	ci right 8.907598e-01	k: 168977	n:190000
KS ci ratio: 2.192930e-01	ci left: 1.494895e-03	ci right 1.867941e-03	k: 318	n:190000
TMCO2   190000 perm   46 sec   (4098 perm/sec)   p_kst 1.673684e-03   p_cons 8.893526e-01   p_joint 1.460000e-02

Joint ci ratio: 9.249830e-02	ci left: 8.488134e-03	ci right 9.316194e-03	k: 1779	n:200000
Cons ci ratio: 3.087981e-03	ci left: 8.882134e-01	ci right 8.909653e-01	k: 177919	n:200000
KS ci ratio: 2.117875e-01	ci left: 1.528947e-03	ci right 1.895738e-03	k: 341	n:200000
TMCO2   200000 perm   50 sec   (4003 perm/sec)   p_kst 1.705000e-03   p_cons 8.895950e-01   p_joint 8.895000e-03

Joint ci ratio: 6.930713e-02	ci left: 1.448444e-02	ci right 1.552901e-02	k: 3150	n:210000
Cons ci ratio: 3.015528e-03	ci left: 8.881178e-01	ci right 8.908047e-01	k: 186788	n:210000
KS ci ratio: 2.061379e-01	ci left: 1.541883e-03	ci right 1.900667e-03	k: 360	n:210000
TMCO2   210000 perm   53 sec   (3944 perm/sec)   p_kst 1.714286e-03   p_cons 8.894667e-01   p_joint 1.500000e-02

Joint ci ratio: 6.757918e-02	ci left: 1.455430e-02	ci right 1.557671e-02	k: 3313	n:220000
Cons ci ratio: 2.948895e-03	ci left: 8.879678e-01	ci right 8.905947e-01	k: 195643	n:220000
KS ci ratio: 2.006533e-01	ci left: 1.558079e-03	ci right 1.909803e-03	k: 380	n:220000
TMCO2   220000 perm   57 sec   (3888 perm/sec)   p_kst 1.727273e-03   p_cons 8.892864e-01   p_joint 1.505909e-02

Joint ci ratio: 6.613870e-02	ci left: 1.454568e-02	ci right 1.554486e-02	k: 3459	n:230000
Cons ci ratio: 2.883175e-03	ci left: 8.880587e-01	ci right 8.906271e-01	k: 204550	n:230000
KS ci ratio: 1.960747e-01	ci left: 1.564711e-03	ci right 1.908910e-03	k: 398	n:230000
TMCO2   230000 perm   60 sec   (3834 perm/sec)   p_kst 1.730435e-03   p_cons 8.893478e-01   p_joint 1.503913e-02

Joint ci ratio: 6.489628e-02	ci left: 1.448878e-02	ci right 1.546465e-02	k: 3593	n:240000
Cons ci ratio: 2.822975e-03	ci left: 8.880505e-01	ci right 8.905651e-01	k: 213435	n:240000
KS ci ratio: 1.906544e-01	ci left: 1.590711e-03	ci right 1.929836e-03	k: 421	n:240000
TMCO2   240000 perm   64 sec   (3779 perm/sec)   p_kst 1.754167e-03   p_cons 8.893125e-01   p_joint 1.497083e-02

Joint ci ratio: 6.198059e-02	ci left: 1.525965e-02	ci right 1.623962e-02	k: 3936	n:250000
Cons ci ratio: 2.769821e-03	ci left: 8.877983e-01	ci right 8.902647e-01	k: 222259	n:250000
KS ci ratio: 1.865016e-01	ci left: 1.599496e-03	ci right 1.932226e-03	k: 440	n:250000
TMCO2   250000 perm   67 sec   (3724 perm/sec)   p_kst 1.760000e-03   p_cons 8.890360e-01   p_joint 1.574400e-02

Joint ci ratio: 6.020055e-02	ci left: 1.556286e-02	ci right 1.653259e-02	k: 4171	n:260000
Cons ci ratio: 2.714886e-03	ci left: 8.879061e-01	ci right 8.903237e-01	k: 231171	n:260000
KS ci ratio: 1.840168e-01	ci left: 1.581989e-03	ci right 1.906203e-03	k: 452	n:260000
TMCO2   260000 perm   71 sec   (3671 perm/sec)   p_kst 1.738462e-03   p_cons 8.891192e-01   p_joint 1.604231e-02

Joint ci ratio: 5.922447e-02	ci left: 1.549357e-02	ci right 1.644279e-02	k: 4310	n:270000
Cons ci ratio: 2.666996e-03	ci left: 8.877161e-01	ci right 8.900904e-01	k: 240005	n:270000
KS ci ratio: 1.806583e-01	ci left: 1.583486e-03	ci right 1.901436e-03	k: 469	n:270000
TMCO2   270000 perm   75 sec   (3623 perm/sec)   p_kst 1.737037e-03   p_cons 8.889074e-01   p_joint 1.596296e-02

Joint ci ratio: 5.643505e-02	ci left: 1.646101e-02	ci right 1.742046e-02	k: 4742	n:280000
Cons ci ratio: 2.617331e-03	ci left: 8.878593e-01	ci right 8.901897e-01	k: 248928	n:280000
KS ci ratio: 1.762132e-01	ci left: 1.608821e-03	ci right 1.923064e-03	k: 493	n:280000
TMCO2   280000 perm   78 sec   (3572 perm/sec)   p_kst 1.760714e-03   p_cons 8.890286e-01   p_joint 1.693571e-02

Joint ci ratio: 5.855832e-02	ci left: 1.477143e-02	ci right 1.566589e-02	k: 4412	n:290000
Cons ci ratio: 2.570831e-03	ci left: 8.879550e-01	ci right 8.902441e-01	k: 257840	n:290000
KS ci ratio: 1.724145e-01	ci left: 1.625898e-03	ci right 1.935918e-03	k: 515	n:290000
TMCO2   290000 perm   82 sec   (3526 perm/sec)   p_kst 1.775862e-03   p_cons 8.891034e-01   p_joint 1.521379e-02

Joint ci ratio: 5.754319e-02	ci left: 1.479479e-02	ci right 1.567461e-02	k: 4569	n:300000
Cons ci ratio: 2.525656e-03	ci left: 8.881283e-01	ci right 8.903775e-01	k: 266777	n:300000
KS ci ratio: 1.696429e-01	ci left: 1.625943e-03	ci right 1.930478e-03	k: 532	n:300000
TMCO2   300000 perm   86 sec   (3481 perm/sec)   p_kst 1.773333e-03   p_cons 8.892567e-01   p_joint 1.523000e-02

Joint ci ratio: 5.660950e-02	ci left: 1.480086e-02	ci right 1.566630e-02	k: 4721	n:310000
Cons ci ratio: 2.484690e-03	ci left: 8.881384e-01	ci right 8.903511e-01	k: 275667	n:310000
KS ci ratio: 1.666974e-01	ci left: 1.632204e-03	ci right 1.932071e-03	k: 551	n:310000
TMCO2   310000 perm   90 sec   (3436 perm/sec)   p_kst 1.777419e-03   p_cons 8.892484e-01   p_joint 1.522903e-02

Joint ci ratio: 5.348478e-02	ci left: 1.606762e-02	ci right 1.695367e-02	k: 5282	n:320000
Cons ci ratio: 2.446934e-03	ci left: 8.880446e-01	ci right 8.902233e-01	k: 284524	n:320000
KS ci ratio: 1.627619e-01	ci left: 1.662097e-03	ci right 1.959541e-03	k: 578	n:320000
TMCO2   320000 perm   94 sec   (3394 perm/sec)   p_kst 1.806250e-03   p_cons 8.891375e-01   p_joint 1.650625e-02

Joint ci ratio: 5.481548e-02	ci left: 1.484211e-02	ci right 1.568158e-02	k: 5035	n:330000
Cons ci ratio: 2.409699e-03	ci left: 8.880511e-01	ci right 8.901966e-01	k: 293412	n:330000
KS ci ratio: 1.602895e-01	ci left: 1.664071e-03	ci right 1.956910e-03	k: 596	n:330000
TMCO2   330000 perm   98 sec   (3353 perm/sec)   p_kst 1.806061e-03   p_cons 8.891273e-01   p_joint 1.525758e-02

Joint ci ratio: 5.413385e-02	ci left: 1.477691e-02	ci right 1.560197e-02	k: 5163	n:340000
Cons ci ratio: 2.373156e-03	ci left: 8.881372e-01	ci right 8.902503e-01	k: 302327	n:340000
KS ci ratio: 1.575419e-01	ci left: 1.674437e-03	ci right 1.963571e-03	k: 617	n:340000
TMCO2   340000 perm   103 sec   (3309 perm/sec)   p_kst 1.814706e-03   p_cons 8.891971e-01   p_joint 1.518529e-02

Joint ci ratio: 5.336960e-02	ci left: 1.477470e-02	ci right 1.558764e-02	k: 5312	n:350000
Cons ci ratio: 2.336802e-03	ci left: 8.883391e-01	ci right 8.904202e-01	k: 311284	n:350000
KS ci ratio: 1.555418e-01	ci left: 1.670519e-03	ci right 1.954973e-03	k: 633	n:350000
TMCO2   350000 perm   107 sec   (3265 perm/sec)   p_kst 1.808571e-03   p_cons 8.893829e-01   p_joint 1.517714e-02

Joint ci ratio: 5.267602e-02	ci left: 1.475076e-02	ci right 1.555152e-02	k: 5453	n:360000
Cons ci ratio: 2.301899e-03	ci left: 8.885439e-01	ci right 8.905943e-01	k: 320246	n:360000
KS ci ratio: 1.530275e-01	ci left: 1.680198e-03	ci right 1.961251e-03	k: 654	n:360000
TMCO2   360000 perm   112 sec   (3223 perm/sec)   p_kst 1.816667e-03   p_cons 8.895722e-01   p_joint 1.514722e-02

Joint ci ratio: 5.029726e-02	ci left: 1.574495e-02	ci right 1.655995e-02	k: 5975	n:370000
Cons ci ratio: 2.269946e-03	ci left: 8.886129e-01	ci right 8.906350e-01	k: 329162	n:370000
KS ci ratio: 1.507430e-01	ci left: 1.686787e-03	ci right 1.964351e-03	k: 674	n:370000
TMCO2   370000 perm   116 sec   (3183 perm/sec)   p_kst 1.821622e-03   p_cons 8.896270e-01   p_joint 1.614865e-02

Joint ci ratio: 4.961672e-02	ci left: 1.575939e-02	ci right 1.656380e-02	k: 6140	n:380000
Cons ci ratio: 2.240607e-03	ci left: 8.885623e-01	ci right 8.905581e-01	k: 338034	n:380000
KS ci ratio: 1.492045e-01	ci left: 1.677857e-03	ci right 1.950882e-03	k: 688	n:380000
TMCO2   380000 perm   121 sec   (3146 perm/sec)   p_kst 1.810526e-03   p_cons 8.895632e-01   p_joint 1.615789e-02

Joint ci ratio: 4.723391e-02	ci left: 1.694378e-02	ci right 1.776598e-02	k: 6767	n:390000
Cons ci ratio: 2.212347e-03	ci left: 8.885170e-01	ci right 8.904874e-01	k: 346907	n:390000
KS ci ratio: 1.467739e-01	ci left: 1.691627e-03	ci right 1.962015e-03	k: 711	n:390000
TMCO2   390000 perm   125 sec   (3110 perm/sec)   p_kst 1.823077e-03   p_cons 8.895051e-01   p_joint 1.735128e-02

Joint ci ratio: 4.835740e-02	ci left: 1.577151e-02	ci right 1.655553e-02	k: 6464	n:400000
Cons ci ratio: 2.182963e-03	ci left: 8.886699e-01	ci right 8.906144e-01	k: 355858	n:400000
KS ci ratio: 1.451524e-01	ci left: 1.687875e-03	ci right 1.954425e-03	k: 727	n:400000
TMCO2   400000 perm   130 sec   (3074 perm/sec)   p_kst 1.817500e-03   p_cons 8.896450e-01   p_joint 1.616000e-02

Joint ci ratio: 4.779566e-02	ci left: 1.575552e-02	ci right 1.652939e-02	k: 6617	n:410000
Cons ci ratio: 2.155332e-03	ci left: 8.887592e-01	ci right 8.906792e-01	k: 364786	n:410000
KS ci ratio: 1.433906e-01	ci left: 1.689025e-03	ci right 1.952242e-03	k: 745	n:410000
TMCO2   410000 perm   135 sec   (3039 perm/sec)   p_kst 1.817073e-03   p_cons 8.897220e-01   p_joint 1.613902e-02

Joint ci ratio: 4.439638e-02	ci left: 1.781906e-02	ci right 1.863046e-02	k: 7653	n:420000
Cons ci ratio: 2.128464e-03	ci left: 8.888682e-01	ci right 8.907645e-01	k: 373724	n:420000
KS ci ratio: 1.408626e-01	ci left: 1.710811e-03	ci right 1.972328e-03	k: 772	n:420000
TMCO2   420000 perm   140 sec   (3005 perm/sec)   p_kst 1.838095e-03   p_cons 8.898190e-01   p_joint 1.822143e-02

Joint ci ratio: 4.664301e-02	ci left: 1.578339e-02	ci right 1.653943e-02	k: 6948	n:430000
Cons ci ratio: 2.104547e-03	ci left: 8.887879e-01	ci right 8.906627e-01	k: 382583	n:430000
KS ci ratio: 1.393390e-01	ci left: 1.709174e-03	ci right 1.967380e-03	k: 789	n:430000
TMCO2   430000 perm   145 sec   (2972 perm/sec)   p_kst 1.834884e-03   p_cons 8.897279e-01   p_joint 1.615814e-02

Joint ci ratio: 4.611522e-02	ci left: 1.578409e-02	ci right 1.653139e-02	k: 7108	n:440000
Cons ci ratio: 2.079850e-03	ci left: 8.888596e-01	ci right 8.907125e-01	k: 391507	n:440000
KS ci ratio: 1.382074e-01	ci left: 1.698848e-03	ci right 1.953238e-03	k: 802	n:440000
TMCO2   440000 perm   150 sec   (2939 perm/sec)   p_kst 1.822727e-03   p_cons 8.897886e-01   p_joint 1.615455e-02

Joint ci ratio: 4.294359e-02	ci left: 1.778944e-02	ci right 1.857233e-02	k: 8180	n:450000
Cons ci ratio: 2.057516e-03	ci left: 8.887833e-01	ci right 8.906161e-01	k: 400366	n:450000
KS ci ratio: 1.372715e-01	ci left: 1.684697e-03	ci right 1.935120e-03	k: 813	n:450000
TMCO2   450000 perm   155 sec   (2907 perm/sec)   p_kst 1.806667e-03   p_cons 8.897022e-01   p_joint 1.817778e-02

Joint ci ratio: 4.107740e-02	ci left: 1.901412e-02	ci right 1.981369e-02	k: 8929	n:460000
Cons ci ratio: 2.034173e-03	ci left: 8.888763e-01	ci right 8.906884e-01	k: 409301	n:460000
KS ci ratio: 1.356968e-01	ci left: 1.687968e-03	ci right 1.935766e-03	k: 832	n:460000
TMCO2   460000 perm   160 sec   (2877 perm/sec)   p_kst 1.808696e-03   p_cons 8.897848e-01   p_joint 1.941087e-02

Joint ci ratio: 4.301405e-02	ci left: 1.699020e-02	ci right 1.773917e-02	k: 8160	n:470000
Cons ci ratio: 2.011779e-03	ci left: 8.889483e-01	ci right 8.907405e-01	k: 418228	n:470000
KS ci ratio: 1.345712e-01	ci left: 1.680833e-03	ci right 1.925374e-03	k: 846	n:470000
TMCO2   470000 perm   165 sec   (2849 perm/sec)   p_kst 1.800000e-03   p_cons 8.898468e-01   p_joint 1.736170e-02

Joint ci ratio: 4.413251e-02	ci left: 1.581383e-02	ci right 1.652953e-02	k: 7761	n:480000
Cons ci ratio: 1.991082e-03	ci left: 8.889212e-01	ci right 8.906949e-01	k: 427109	n:480000
KS ci ratio: 1.333182e-01	ci left: 1.678032e-03	ci right 1.919712e-03	k: 862	n:480000
TMCO2   480000 perm   170 sec   (2819 perm/sec)   p_kst 1.795833e-03   p_cons 8.898104e-01   p_joint 1.616875e-02

Joint ci ratio: 4.369586e-02	ci left: 1.580597e-02	ci right 1.651405e-02	k: 7917	n:490000
Cons ci ratio: 1.972036e-03	ci left: 8.887929e-01	ci right 8.905494e-01	k: 435940	n:490000
KS ci ratio: 1.322504e-01	ci left: 1.671408e-03	ci right 1.910054e-03	k: 876	n:490000
TMCO2   490000 perm   176 sec   (2790 perm/sec)   p_kst 1.787755e-03   p_cons 8.896735e-01   p_joint 1.615714e-02

Joint ci ratio: 4.324471e-02	ci left: 1.581824e-02	ci right 1.651938e-02	k: 8083	n:500000
Cons ci ratio: 2.106987e-03	ci left: 8.728583e-01	ci right 8.747013e-01	k: 436891	n:500000
KS ci ratio: 1.313555e-01	ci left: 1.661188e-03	ci right 1.896645e-03	k: 888	n:500000
TMCO2   500000 perm   181 sec   (2761 perm/sec)   p_kst 1.776000e-03   p_cons 8.737820e-01   p_joint 1.616600e-02

Joint ci ratio: 4.276511e-02	ci left: 1.586111e-02	ci right 1.655616e-02	k: 8265	n:510000
Cons ci ratio: 2.087263e-03	ci left: 8.727577e-01	ci right 8.745832e-01	k: 445573	n:510000
KS ci ratio: 1.301894e-01	ci left: 1.658962e-03	ci right 1.891854e-03	k: 904	n:510000
TMCO2   510000 perm   187 sec   (2732 perm/sec)   p_kst 1.772549e-03   p_cons 8.736725e-01   p_joint 1.620588e-02

Joint ci ratio: 4.230367e-02	ci left: 1.590047e-02	ci right 1.658955e-02	k: 8446	n:520000
Cons ci ratio: 2.066946e-03	ci left: 8.727825e-01	ci right 8.745903e-01	k: 454318	n:520000
KS ci ratio: 1.289837e-01	ci left: 1.658691e-03	ci right 1.889224e-03	k: 921	n:520000
TMCO2   520000 perm   192 sec   (2703 perm/sec)   p_kst 1.771154e-03   p_cons 8.736885e-01   p_joint 1.624231e-02

Joint ci ratio: 4.187412e-02	ci left: 1.592532e-02	ci right 1.660829e-02	k: 8620	n:530000
Cons ci ratio: 2.047142e-03	ci left: 8.728140e-01	ci right 8.746045e-01	k: 463067	n:530000
KS ci ratio: 1.276068e-01	ci left: 1.663920e-03	ci right 1.892524e-03	k: 941	n:530000
TMCO2   530000 perm   198 sec   (2675 perm/sec)   p_kst 1.775472e-03   p_cons 8.737113e-01   p_joint 1.626415e-02

Joint ci ratio: 4.140717e-02	ci left: 1.598776e-02	ci right 1.666559e-02	k: 8815	n:540000
Cons ci ratio: 2.028610e-03	ci left: 8.727665e-01	ci right 8.745406e-01	k: 471774	n:540000
KS ci ratio: 1.265369e-01	ci left: 1.661795e-03	ci right 1.888049e-03	k: 957	n:540000
TMCO2   540000 perm   204 sec   (2647 perm/sec)   p_kst 1.772222e-03   p_cons 8.736556e-01   p_joint 1.632407e-02

Joint ci ratio: 4.102265e-02	ci left: 1.599579e-02	ci right 1.666750e-02	k: 8981	n:550000
Cons ci ratio: 2.010308e-03	ci left: 8.727499e-01	ci right 8.745080e-01	k: 480497	n:550000
KS ci ratio: 1.255581e-01	ci left: 1.657993e-03	ci right 1.881853e-03	k: 972	n:550000
TMCO2   550000 perm   210 sec   (2621 perm/sec)   p_kst 1.767273e-03   p_cons 8.736309e-01   p_joint 1.632909e-02

Joint ci ratio: 4.066673e-02	ci left: 1.598941e-02	ci right 1.665490e-02	k: 9139	n:560000
Cons ci ratio: 1.992090e-03	ci left: 8.727788e-01	ci right 8.745209e-01	k: 489245	n:560000
KS ci ratio: 1.247282e-01	ci left: 1.650873e-03	ci right 1.872190e-03	k: 985	n:560000
TMCO2   560000 perm   216 sec   (2594 perm/sec)   p_kst 1.758929e-03   p_cons 8.736518e-01   p_joint 1.631964e-02

Joint ci ratio: 4.028469e-02	ci left: 1.601107e-02	ci right 1.667105e-02	k: 9313	n:570000
Cons ci ratio: 1.973793e-03	ci left: 8.728700e-01	ci right 8.745963e-01	k: 498029	n:570000
KS ci ratio: 1.232978e-01	ci left: 1.661010e-03	ci right 1.880946e-03	k: 1008	n:570000
TMCO2   570000 perm   222 sec   (2569 perm/sec)   p_kst 1.768421e-03   p_cons 8.737351e-01   p_joint 1.633860e-02

Joint ci ratio: 3.995176e-02	ci left: 1.600128e-02	ci right 1.665529e-02	k: 9469	n:580000
Cons ci ratio: 1.955516e-03	ci left: 8.730118e-01	ci right 8.747224e-01	k: 506844	n:580000
KS ci ratio: 1.228735e-01	ci left: 1.644068e-03	ci right 1.860957e-03	k: 1015	n:580000
TMCO2   580000 perm   228 sec   (2543 perm/sec)   p_kst 1.750000e-03   p_cons 8.738690e-01   p_joint 1.632586e-02

Joint ci ratio: 3.962278e-02	ci left: 1.599521e-02	ci right 1.664345e-02	k: 9627	n:590000
Cons ci ratio: 1.939420e-03	ci left: 8.729568e-01	ci right 8.746531e-01	k: 515546	n:590000
KS ci ratio: 1.215639e-01	ci left: 1.652351e-03	ci right 1.867842e-03	k: 1037	n:590000
TMCO2   590000 perm   234 sec   (2518 perm/sec)   p_kst 1.757627e-03   p_cons 8.738068e-01   p_joint 1.631695e-02

Joint ci ratio: 3.932426e-02	ci left: 1.597120e-02	ci right 1.661349e-02	k: 9774	n:600000
Cons ci ratio: 1.923220e-03	ci left: 8.729605e-01	ci right 8.746426e-01	k: 524282	n:600000
KS ci ratio: 1.205806e-01	ci left: 1.652287e-03	ci right 1.865903e-03	k: 1054	n:600000
TMCO2   600000 perm   241 sec   (2493 perm/sec)   p_kst 1.756667e-03   p_cons 8.738033e-01   p_joint 1.629000e-02

Joint ci ratio: 3.901041e-02	ci left: 1.596585e-02	ci right 1.660269e-02	k: 9932	n:610000
Cons ci ratio: 1.907759e-03	ci left: 8.729246e-01	ci right 8.745931e-01	k: 532994	n:610000
KS ci ratio: 1.196766e-01	ci left: 1.650642e-03	ci right 1.862332e-03	k: 1070	n:610000
TMCO2   610000 perm   247 sec   (2470 perm/sec)   p_kst 1.754098e-03   p_cons 8.737607e-01   p_joint 1.628197e-02

Joint ci ratio: 3.867669e-02	ci left: 1.598307e-02	ci right 1.661501e-02	k: 10104	n:620000
Cons ci ratio: 1.891711e-03	ci left: 8.730016e-01	ci right 8.746562e-01	k: 541775	n:620000
KS ci ratio: 1.189024e-01	ci left: 1.645925e-03	ci right 1.855548e-03	k: 1084	n:620000
TMCO2   620000 perm   253 sec   (2446 perm/sec)   p_kst 1.748387e-03   p_cons 8.738306e-01   p_joint 1.629677e-02

Joint ci ratio: 3.834949e-02	ci left: 1.600133e-02	ci right 1.662853e-02	k: 10277	n:630000
Cons ci ratio: 1.876993e-03	ci left: 8.729663e-01	ci right 8.746080e-01	k: 550487	n:630000
KS ci ratio: 1.180891e-01	ci left: 1.642903e-03	ci right 1.850610e-03	k: 1099	n:630000
TMCO2   630000 perm   260 sec   (2424 perm/sec)   p_kst 1.744444e-03   p_cons 8.737889e-01   p_joint 1.631270e-02

Joint ci ratio: 3.806565e-02	ci left: 1.598963e-02	ci right 1.661163e-02	k: 10431	n:640000
Cons ci ratio: 1.861808e-03	ci left: 8.730278e-01	ci right 8.746563e-01	k: 559260	n:640000
KS ci ratio: 1.171346e-01	ci left: 1.644530e-03	ci right 1.850647e-03	k: 1117	n:640000
TMCO2   640000 perm   266 sec   (2402 perm/sec)   p_kst 1.745312e-03   p_cons 8.738438e-01   p_joint 1.629844e-02

Joint ci ratio: 3.775360e-02	ci left: 1.600727e-02	ci right 1.662474e-02	k: 10604	n:650000
Cons ci ratio: 1.846237e-03	ci left: 8.731769e-01	ci right 8.747920e-01	k: 568091	n:650000
KS ci ratio: 1.159475e-01	ci left: 1.653584e-03	ci right 1.858590e-03	k: 1140	n:650000
TMCO2   650000 perm   273 sec   (2380 perm/sec)   p_kst 1.753846e-03   p_cons 8.739862e-01   p_joint 1.631385e-02

Joint ci ratio: 3.746323e-02	ci left: 1.601239e-02	ci right 1.662520e-02	k: 10769	n:660000
Cons ci ratio: 1.832447e-03	ci left: 8.731529e-01	ci right 8.747559e-01	k: 576811	n:660000
KS ci ratio: 1.152930e-01	ci left: 1.647656e-03	ci right 1.850697e-03	k: 1153	n:660000
TMCO2   660000 perm   280 sec   (2358 perm/sec)   p_kst 1.746970e-03   p_cons 8.739561e-01   p_joint 1.631667e-02

Joint ci ratio: 3.719849e-02	ci left: 1.600110e-02	ci right 1.660906e-02	k: 10923	n:670000
Cons ci ratio: 1.819972e-03	ci left: 8.730070e-01	ci right 8.745987e-01	k: 585449	n:670000
KS ci ratio: 1.144531e-01	ci left: 1.647708e-03	ci right 1.849176e-03	k: 1170	n:670000
TMCO2   670000 perm   287 sec   (2336 perm/sec)   p_kst 1.746269e-03   p_cons 8.738045e-01   p_joint 1.630299e-02

Joint ci ratio: 3.692064e-02	ci left: 1.600619e-02	ci right 1.660971e-02	k: 11088	n:680000
Cons ci ratio: 1.806794e-03	ci left: 8.729819e-01	ci right 8.745620e-01	k: 594166	n:680000
KS ci ratio: 1.134878e-01	ci left: 1.652051e-03	ci right 1.852232e-03	k: 1190	n:680000
TMCO2   680000 perm   294 sec   (2313 perm/sec)   p_kst 1.750000e-03   p_cons 8.737735e-01   p_joint 1.630588e-02

Joint ci ratio: 3.665391e-02	ci left: 1.600684e-02	ci right 1.660593e-02	k: 11250	n:690000
Cons ci ratio: 1.793132e-03	ci left: 8.730520e-01	ci right 8.746203e-01	k: 602948	n:690000
KS ci ratio: 1.125466e-01	ci left: 1.656275e-03	ci right 1.855192e-03	k: 1210	n:690000
TMCO2   690000 perm   301 sec   (2292 perm/sec)   p_kst 1.753623e-03   p_cons 8.738377e-01   p_joint 1.630435e-02

Joint ci ratio: 3.643670e-02	ci left: 1.596926e-02	ci right 1.656333e-02	k: 11385	n:700000
Cons ci ratio: 1.780051e-03	ci left: 8.730857e-01	ci right 8.746426e-01	k: 611706	n:700000
KS ci ratio: 1.119477e-01	ci left: 1.650663e-03	ci right 1.847782e-03	k: 1223	n:700000
TMCO2   700000 perm   308 sec   (2272 perm/sec)   p_kst 1.747143e-03   p_cons 8.738657e-01   p_joint 1.626429e-02

Joint ci ratio: 3.618980e-02	ci left: 1.596206e-02	ci right 1.655175e-02	k: 11541	n:710000
Cons ci ratio: 1.768009e-03	ci left: 8.730239e-01	ci right 8.745702e-01	k: 620397	n:710000
KS ci ratio: 1.112681e-01	ci left: 1.647951e-03	ci right 1.843474e-03	k: 1238	n:710000
TMCO2   710000 perm   315 sec   (2253 perm/sec)   p_kst 1.743662e-03   p_cons 8.737986e-01   p_joint 1.625493e-02

Joint ci ratio: 3.593536e-02	ci left: 1.596609e-02	ci right 1.655170e-02	k: 11705	n:720000
Cons ci ratio: 1.755533e-03	ci left: 8.730489e-01	ci right 8.745842e-01	k: 629149	n:720000
KS ci ratio: 1.105126e-01	ci left: 1.648019e-03	ci right 1.842136e-03	k: 1255	n:720000
TMCO2   720000 perm   322 sec   (2234 perm/sec)   p_kst 1.743056e-03   p_cons 8.738181e-01   p_joint 1.625694e-02

Joint ci ratio: 3.567247e-02	ci left: 1.598224e-02	ci right 1.656407e-02	k: 11878	n:730000
Cons ci ratio: 1.743004e-03	ci left: 8.731130e-01	ci right 8.746375e-01	k: 637930	n:730000
KS ci ratio: 1.098155e-01	ci left: 1.646758e-03	ci right 1.839423e-03	k: 1271	n:730000
TMCO2   730000 perm   329 sec   (2216 perm/sec)   p_kst 1.741096e-03   p_cons 8.738767e-01   p_joint 1.627123e-02

Joint ci ratio: 3.542274e-02	ci left: 1.599128e-02	ci right 1.656927e-02	k: 12046	n:740000
Cons ci ratio: 1.731831e-03	ci left: 8.730358e-01	ci right 8.745504e-01	k: 646608	n:740000
KS ci ratio: 1.087094e-01	ci left: 1.658680e-03	ci right 1.850660e-03	k: 1297	n:740000
TMCO2   740000 perm   337 sec   (2196 perm/sec)   p_kst 1.752703e-03   p_cons 8.737946e-01   p_joint 1.627838e-02

Joint ci ratio: 3.519429e-02	ci left: 1.598555e-02	ci right 1.655953e-02	k: 12203	n:750000
Cons ci ratio: 1.720330e-03	ci left: 8.730303e-01	ci right 8.745348e-01	k: 655338	n:750000
KS ci ratio: 1.078813e-01	ci left: 1.662508e-03	ci right 1.853373e-03	k: 1317	n:750000
TMCO2   750000 perm   344 sec   (2179 perm/sec)   p_kst 1.756000e-03   p_cons 8.737840e-01   p_joint 1.627067e-02

Joint ci ratio: 3.495727e-02	ci left: 1.599172e-02	ci right 1.656198e-02	k: 12369	n:760000
Cons ci ratio: 1.709217e-03	ci left: 8.730038e-01	ci right 8.744986e-01	k: 664052	n:760000
KS ci ratio: 1.071521e-01	ci left: 1.663681e-03	ci right 1.853307e-03	k: 1335	n:760000
TMCO2   760000 perm   352 sec   (2161 perm/sec)   p_kst 1.756579e-03   p_cons 8.737526e-01   p_joint 1.627500e-02

Joint ci ratio: 3.473765e-02	ci left: 1.598615e-02	ci right 1.655256e-02	k: 12526	n:770000
Cons ci ratio: 1.698127e-03	ci left: 8.730028e-01	ci right 8.744878e-01	k: 672785	n:770000
KS ci ratio: 1.065162e-01	ci left: 1.662298e-03	ci right 1.850573e-03	k: 1351	n:770000
TMCO2   770000 perm   359 sec   (2143 perm/sec)   p_kst 1.754545e-03   p_cons 8.737468e-01   p_joint 1.626753e-02

Joint ci ratio: 3.450830e-02	ci left: 1.599345e-02	ci right 1.655631e-02	k: 12693	n:780000
Cons ci ratio: 1.687466e-03	ci left: 8.729736e-01	ci right 8.744492e-01	k: 681496	n:780000
KS ci ratio: 1.056213e-01	ci left: 1.669692e-03	ci right 1.857116e-03	k: 1374	n:780000
TMCO2   780000 perm   367 sec   (2126 perm/sec)   p_kst 1.761538e-03   p_cons 8.737128e-01   p_joint 1.627308e-02

Joint ci ratio: 3.429292e-02	ci left: 1.599179e-02	ci right 1.655101e-02	k: 12853	n:790000
Cons ci ratio: 1.676186e-03	ci left: 8.730530e-01	ci right 8.745189e-01	k: 690292	n:790000
KS ci ratio: 1.047109e-01	ci left: 1.678138e-03	ci right 1.864786e-03	k: 1398	n:790000
TMCO2   790000 perm   375 sec   (2109 perm/sec)   p_kst 1.769620e-03   p_cons 8.737873e-01   p_joint 1.626962e-02

Joint ci ratio: 3.407353e-02	ci left: 1.599762e-02	ci right 1.655339e-02	k: 13019	n:800000
Cons ci ratio: 1.665751e-03	ci left: 8.730478e-01	ci right 8.745045e-01	k: 699022	n:800000
KS ci ratio: 1.042281e-01	ci left: 1.672986e-03	ci right 1.858151e-03	k: 1411	n:800000
TMCO2   800000 perm   382 sec   (2092 perm/sec)   p_kst 1.763750e-03   p_cons 8.737775e-01   p_joint 1.627375e-02

Joint ci ratio: 3.383354e-02	ci left: 1.602658e-02	ci right 1.657936e-02	k: 13204	n:810000
Cons ci ratio: 1.654971e-03	ci left: 8.731145e-01	ci right 8.745619e-01	k: 707810	n:810000
KS ci ratio: 1.034975e-01	ci left: 1.676382e-03	ci right 1.860544e-03	k: 1431	n:810000
TMCO2   810000 perm   390 sec   (2075 perm/sec)   p_kst 1.766667e-03   p_cons 8.738395e-01   p_joint 1.630123e-02

Joint ci ratio: 3.364455e-02	ci left: 1.601130e-02	ci right 1.656041e-02	k: 13353	n:820000
Cons ci ratio: 1.645071e-03	ci left: 8.730891e-01	ci right 8.745278e-01	k: 716524	n:820000
KS ci ratio: 1.029955e-01	ci left: 1.672571e-03	ci right 1.855368e-03	k: 1445	n:820000
TMCO2   820000 perm   398 sec   (2059 perm/sec)   p_kst 1.762195e-03   p_cons 8.738098e-01   p_joint 1.628415e-02

Joint ci ratio: 3.344484e-02	ci left: 1.600955e-02	ci right 1.655528e-02	k: 13513	n:830000
Cons ci ratio: 1.635265e-03	ci left: 8.730752e-01	ci right 8.745053e-01	k: 725247	n:830000
KS ci ratio: 1.021857e-01	ci left: 1.679419e-03	ci right 1.861435e-03	k: 1468	n:830000
TMCO2   830000 perm   406 sec   (2042 perm/sec)   p_kst 1.768675e-03   p_cons 8.737916e-01   p_joint 1.628072e-02

Joint ci ratio: 3.322767e-02	ci left: 1.602792e-02	ci right 1.657066e-02	k: 13690	n:840000
Cons ci ratio: 1.625212e-03	ci left: 8.731190e-01	ci right 8.745403e-01	k: 734018	n:840000
KS ci ratio: 1.013607e-01	ci left: 1.687271e-03	ci right 1.868574e-03	k: 1492	n:840000
TMCO2   840000 perm   415 sec   (2024 perm/sec)   p_kst 1.776190e-03   p_cons 8.738310e-01   p_joint 1.629762e-02

Joint ci ratio: 3.303404e-02	ci left: 1.602720e-02	ci right 1.656669e-02	k: 13851	n:850000
Cons ci ratio: 1.615290e-03	ci left: 8.731688e-01	ci right 8.745816e-01	k: 742795	n:850000
KS ci ratio: 1.008555e-01	ci left: 1.684621e-03	ci right 1.864684e-03	k: 1507	n:850000
TMCO2   850000 perm   423 sec   (2008 perm/sec)   p_kst 1.772941e-03   p_cons 8.738765e-01   p_joint 1.629529e-02

Joint ci ratio: 3.283066e-02	ci left: 1.603919e-02	ci right 1.657570e-02	k: 14023	n:860000
Cons ci ratio: 1.605666e-03	ci left: 8.732012e-01	ci right 8.746056e-01	k: 751558	n:860000
KS ci ratio: 1.001603e-01	ci left: 1.688838e-03	ci right 1.868033e-03	k: 1528	n:860000
TMCO2   860000 perm   432 sec   (1992 perm/sec)   p_kst 1.776744e-03   p_cons 8.739047e-01   p_joint 1.630581e-02

Joint ci ratio: 3.264386e-02	ci left: 1.603838e-02	ci right 1.657175e-02	k: 14184	n:870000
Cons ci ratio: 1.596146e-03	ci left: 8.732421e-01	ci right 8.746382e-01	k: 760329	n:870000
KS ci ratio: 9.947931e-02	ci left: 1.692961e-03	ci right 1.871302e-03	k: 1549	n:870000
TMCO2   870000 perm   440 sec   (1977 perm/sec)   p_kst 1.780460e-03   p_cons 8.739414e-01   p_joint 1.630345e-02

Outputting figure to mutsig2_images.part000000000176/TMCO2.2_557_870000_0.0017805_0.87394_0.016303.png
                gene_name: TMCO2
               theta_stop: 0.099 
                    nperm: 870000 
                     p_ks: 0.0018 
        ci_ks_bounds_left: 0.0017 
       ci_ks_bounds_right: 0.0019 
                   p_cons: 0.87 
      ci_cons_bounds_left: 0.87 
     ci_cons_bounds_right: 0.87 
                  p_joint: 0.016 
     ci_joint_bounds_left: 0.016 
    ci_joint_bounds_right: 0.017 

Current progress: 67 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: 2.827121e-02	ci left: 6.484061e-01	ci right 6.671019e-01	k: 6578	n:10000
KS ci ratio: 3.129460e-02	ci left: 6.010623e-01	ci right 6.202732e-01	k: 6107	n:10000
TMEM132D   10000 perm   2 sec   (5088 perm/sec)   p_kst 6.107000e-01   p_cons 6.578000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000176/TMEM132D.2_3336_10000_0.6107_0.6578_1.png
                gene_name: TMEM132D
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.62 
                   p_cons: 0.66 
      ci_cons_bounds_left: 0.65 
     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.165.3896/
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/181708/iteration1/scatter.0000000176
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 176 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120309: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000177> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:47:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000177.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000177.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 177  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    108.46 sec.
    Max Memory :       612 MB
    Max Swap   :      3510 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.165.3896/
-whichjob
177
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 177: processing genes 15924 - 16013
Calculating significance of each gene.
Using projection method.
15924	TMEM164	1
15925	TMEM165	1
15926	TMEM167A	1
15927	TMEM167B	1
15928	TMEM168	1
15929	TMEM169	1
15930	TMEM17	1
15931	TMEM170A	1
15932	TMEM170B	1
15933	TMEM171	1
15934	TMEM173	1
15935	TMEM174	1
15936	TMEM175	1
15937	TMEM176A	1
15938	TMEM176B	1
15939	TMEM177	1
15940	TMEM178	1
15941	TMEM179	1
15942	TMEM179B	1
15943	TMEM18	1
15944	TMEM180	1
15945	TMEM181	1
15946	TMEM182	1
15947	TMEM183A	1
15948	TMEM183B	1
15949	TMEM184A	4.060474e-02
15950	TMEM184B	2.616427e-02
15951	TMEM184C	1
15952	TMEM185A	1
15953	TMEM186	1
15954	TMEM187	1
15955	TMEM188	1
15956	TMEM189	1
15957	TMEM189-UBE2V1	1
15958	TMEM19	3.453446e-02
15959	TMEM190	1
15960	TMEM192	1
15961	TMEM194A	1
15962	TMEM195	1
15963	TMEM196	1
15964	TMEM198	1
15965	TMEM199	1
15966	TMEM2	3.558274e-01
15967	TMEM20	1
15968	TMEM200A	1
15969	TMEM200B	1
15970	TMEM200C	1
15971	TMEM201	1
15972	TMEM202	1
15973	TMEM203	1
15974	TMEM204	1
15975	TMEM205	1
15976	TMEM206	1
15977	TMEM207	1
15978	TMEM208	1
15979	TMEM209	1
15980	TMEM211	1
15981	TMEM213	1
15982	TMEM214	1
15983	TMEM215	1
15984	TMEM216	1
15985	TMEM217	1
15986	TMEM218	1
15987	TMEM219	1
15988	TMEM22	1
15989	TMEM220	1
15990	TMEM222	1
15991	TMEM223	1
15992	TMEM225	1
15993	TMEM229B	1
15994	TMEM231	1
15995	TMEM25	1
15996	TMEM26	1
15997	TMEM27	1
15998	TMEM30A	1
15999	TMEM30B	1
16000/18094 16000	TMEM31	1
16001	TMEM33	1
16002	TMEM35	1
16003	TMEM37	1
16004	TMEM38A	1
16005	TMEM38B	1
16006	TMEM39A	1
16007	TMEM39B	1
16008	TMEM40	1.229691e-01
16009	TMEM41A	1
16010	TMEM41B	1.077368e-01
16011	TMEM42	1
16012	TMEM43	1
16013	TMEM44	1
Done

Running MutSig 2:
Scatter job 177: processing genes 15924 - 16013
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TMEM41B
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: 3.303319e-02	ci left: 5.749683e-01	ci right 5.943823e-01	k: 5847	n:10000
KS ci ratio: 3.625527e-02	ci left: 5.290697e-01	ci right 5.487076e-01	k: 5389	n:10000
TMEM41B   10000 perm   2 sec   (6360 perm/sec)   p_kst 5.389000e-01   p_cons 5.847000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000177/TMEM41B.2_920_10000_0.5389_0.5847_1.png
                gene_name: TMEM41B
               theta_stop: 0.036 
                    nperm: 10000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.55 
                   p_cons: 0.58 
      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.165.3896/
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/181708/iteration1/scatter.0000000177
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 177 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1714>
Subject: Job 1120310: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1714>, 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/181708/iteration1/scatter.0000000178> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:47:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000178.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000178.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 178  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    107.23 sec.
    Max Memory :      1156 MB
    Max Swap   :      3839 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.165.3896/
-whichjob
178
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 178: processing genes 16014 - 16104
Calculating significance of each gene.
Using projection method.
16014	TMEM45A	1
16015	TMEM45B	1
16016	TMEM47	1
16017	TMEM48	1
16018	TMEM49	1
16019	TMEM5	1
16020	TMEM50A	1
16021	TMEM50B	1
16022	TMEM51	1
16023	TMEM52	1
16024	TMEM53	1.175348e-01
16025	TMEM54	1
16026	TMEM55A	1
16027	TMEM55B	1
16028	TMEM56	1
16029	TMEM57	1
16030	TMEM59	1
16031	TMEM59L	1
16032	TMEM60	1
16033	TMEM61	1
16034	TMEM62	1.176954e-02
16035	TMEM63A	1
16036	TMEM63B	1
16037	TMEM63C	1
16038	TMEM64	1
16039	TMEM65	1
16040	TMEM66	1
16041	TMEM67	1
16042	TMEM68	1
16043	TMEM69	1
16044	TMEM70	1
16045	TMEM71	1
16046	TMEM72	1
16047	TMEM74	1
16048	TMEM79	7.591483e-02
16049	TMEM80	1
16050	TMEM81	1
16051	TMEM82	1
16052	TMEM85	1
16053	TMEM86A	1
16054	TMEM86B	1
16055	TMEM87A	1
16056	TMEM87B	1
16057	TMEM88	1
16058	TMEM89	1
16059	TMEM8A	1
16060	TMEM8B	1
16061	TMEM8C	1
16062	TMEM9	1
16063	TMEM90A	1
16064	TMEM90B	1
16065	TMEM91	1
16066	TMEM92	1
16067	TMEM93	1
16068	TMEM95	1
16069	TMEM97	1
16070	TMEM98	1
16071	TMEM99	1
16072	TMEM9B	1
16073	TMF1	1
16074	TMIE	1
16075	TMIGD1	1
16076	TMIGD2	1
16077	TMLHE	1
16078	TMOD1	1.147750e-01
16079	TMOD2	1.807374e-01
16080	TMOD3	1
16081	TMOD4	1
16082	TMPO	2.004209e-01
16083	TMPPE	1
16084	TMPRSS11A	1
16085	TMPRSS11B	1
16086	TMPRSS11D	1
16087	TMPRSS11E	1
16088	TMPRSS11F	1
16089	TMPRSS12	1.059335e-01
16090	TMPRSS13	1
16091	TMPRSS15	1
16092	TMPRSS2	1
16093	TMPRSS3	1
16094	TMPRSS4	1
16095	TMPRSS5	1
16096	TMPRSS6	1
16097	TMPRSS7	2.481447e-01
16098	TMPRSS9	2.678650e-01
16099	TMSB10	1
16100	TMSB15A	1
16101	TMSB15B	1
16102	TMSB4X	1
16103	TMSB4Y	1
16104	TMSL3	1
Done

Running MutSig 2:
Scatter job 178: processing genes 16014 - 16104
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TMEM62
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.844806e-02	ci left: 8.110065e-01	ci right 8.262075e-01	k: 8187	n:10000
Cons ci ratio: 6.748140e-02	ci left: 2.437115e-01	ci right 2.608330e-01	k: 2522	n:10000
KS ci ratio: 2.656849e-02	ci left: 6.759943e-01	ci right 6.942978e-01	k: 6852	n:10000
TMEM62   10000 perm   2 sec   (5769 perm/sec)   p_kst 6.852000e-01   p_cons 2.522000e-01   p_joint 8.187000e-01

Outputting figure to mutsig2_images.part000000000178/TMEM62.2_1988_10000_0.6852_0.2522_0.8187.png
                gene_name: TMEM62
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.69 
        ci_ks_bounds_left: 0.68 
       ci_ks_bounds_right: 0.69 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.83 

Current progress: 50 percent done.
TMPRSS11F
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.362151e-02	ci left: 5.663433e-01	ci right 5.858123e-01	k: 5761	n:10000
Cons ci ratio: 1.423087e-02	ci left: 8.771523e-01	ci right 8.898233e-01	k: 8836	n:10000
KS ci ratio: 5.688161e-02	ci left: 3.127459e-01	ci right 3.311579e-01	k: 3219	n:10000
TMPRSS11F   10000 perm   1 sec   (6740 perm/sec)   p_kst 3.219000e-01   p_cons 8.836000e-01   p_joint 5.761000e-01

Outputting figure to mutsig2_images.part000000000178/TMPRSS11F.2_1357_10000_0.3219_0.8836_0.5761.png
                gene_name: TMPRSS11F
               theta_stop: 0.057 
                    nperm: 10000 
                     p_ks: 0.32 
        ci_ks_bounds_left: 0.31 
       ci_ks_bounds_right: 0.33 
                   p_cons: 0.88 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  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.165.3896/
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/181708/iteration1/scatter.0000000178
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 178 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1653>
Subject: Job 1120313: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1653>, 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/181708/iteration1/scatter.0000000179> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:47:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000179.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000179.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 179  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    103.87 sec.
    Max Memory :       616 MB
    Max Swap   :      3411 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.165.3896/
-whichjob
179
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 179: processing genes 16105 - 16194
Calculating significance of each gene.
Using projection method.
16105	TMTC1	1
16106	TMTC2	1.501628e-01
16107	TMTC3	1
16108	TMTC4	3.134801e-01
16109	TMUB1	1
16110	TMUB2	1
16111	TMX1	8.658296e-02
16112	TMX2	1.392697e-01
16113	TMX3	7.926176e-02
16114	TMX4	1
16115	TNC	1.229219e-01
16116	TNF	1
16117	TNFAIP1	1
16118	TNFAIP2	1
16119	TNFAIP3	1
16120	TNFAIP6	1
16121	TNFAIP8	1
16122	TNFAIP8L1	1
16123	TNFAIP8L2	1
16124	TNFAIP8L3	1
16125	TNFRSF10A	1
16126	TNFRSF10B	1
16127	TNFRSF10C	1
16128	TNFRSF10D	1
16129	TNFRSF11A	1
16130	TNFRSF11B	1
16131	TNFRSF12A	1
16132	TNFRSF13B	1
16133	TNFRSF13C	4.240523e-02
16134	TNFRSF14	1
16135	TNFRSF17	1
16136	TNFRSF18	1
16137	TNFRSF19	1
16138	TNFRSF1A	1
16139	TNFRSF1B	1.281175e-01
16140	TNFRSF21	1
16141	TNFRSF25	9.910482e-02
16142	TNFRSF4	1
16143	TNFRSF6B	1
16144	TNFRSF8	1.179211e-01
16145	TNFRSF9	2.971673e-02
16146	TNFSF10	1
16147	TNFSF11	1.442367e-01
16148	TNFSF12	1
16149	TNFSF12-TNFSF13	1
16150	TNFSF13	1
16151	TNFSF13B	1
16152	TNFSF14	1
16153	TNFSF15	1
16154	TNFSF18	1
16155	TNFSF4	2.554289e-02
16156	TNFSF8	6.842838e-02
16157	TNFSF9	1
16158	TNIK	1
16159	TNIP1	1
16160	TNIP2	1
16161	TNIP3	1
16162	TNK1	1
16163	TNK2	1
16164	TNKS	1
16165	TNKS1BP1	1
16166	TNKS2	4.381592e-01
16167	TNMD	1
16168	TNN	1
16169	TNNC1	1
16170	TNNC2	1
16171	TNNI1	1
16172	TNNI2	6.256067e-02
16173	TNNI3	6.618015e-02
16174	TNNI3K	1
16175	TNNT1	1
16176	TNNT2	1
16177	TNNT3	1
16178	TNP1	1
16179	TNP2	3.270721e-02
16180	TNPO1	2.683089e-01
16181	TNPO2	1
16182	TNPO3	1
16183	TNR	1.866938e-01
16184	TNRC18	4.015220e-01
16185	TNRC6A	3.160928e-01
16186	TNRC6B	1
16187	TNRC6C	3.858148e-01
16188	TNS1	6.158827e-01
16189	TNS3	5.281468e-01
16190	TNS4	1
16191	TNXB	6.173816e-01
16192	TOB1	1
16193	TOB2	1
16194	TOE1	1
Done

Running MutSig 2:
Scatter job 179: processing genes 16105 - 16194
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TNC
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.827391e-02	ci left: 8.138514e-01	ci right 8.289609e-01	k: 8215	n:10000
Cons ci ratio: 3.688720e-02	ci left: 5.204606e-01	ci right 5.401218e-01	k: 5303	n:10000
KS ci ratio: 1.866511e-02	ci left: 8.074513e-01	ci right 8.227647e-01	k: 8152	n:10000
TNC   10000 perm   2 sec   (4407 perm/sec)   p_kst 8.152000e-01   p_cons 5.303000e-01   p_joint 8.215000e-01

Outputting figure to mutsig2_images.part000000000179/TNC.2_6714_10000_0.8152_0.5303_0.8215.png
                gene_name: TNC
               theta_stop: 0.037 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.53 
      ci_cons_bounds_left: 0.52 
     ci_cons_bounds_right: 0.54 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.83 

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.165.3896/
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/181708/iteration1/scatter.0000000179
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 179 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1550>
Subject: Job 1120316: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1550>, 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/181708/iteration1/scatter.0000000180> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 14:09:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000180.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000180.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 180  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :  12977.53 sec.
    Max Memory :      1275 MB
    Max Swap   :      3885 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.165.3896/
-whichjob
180
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 180: processing genes 16195 - 16285
Calculating significance of each gene.
Using projection method.
16195	TOLLIP	1
16196	TOM1	1
16197	TOM1L1	1
16198	TOM1L2	1
16199	TOMM20	1
16200	TOMM20L	1
16201	TOMM22	1
16202	TOMM34	1
16203	TOMM40	1
16204	TOMM40L	1
16205	TOMM5	1
16206	TOMM7	1
16207	TOMM70A	1
16208	TOP1	9.325265e-02
16209	TOP1MT	1
16210	TOP2A	1
16211	TOP2B	1
16212	TOP3A	1.612689e-01
16213	TOP3B	1
16214	TOPBP1	3.007799e-01
16215	TOPORS	8.258319e-02
16216	TOR1A	1
16217	TOR1AIP1	2.816393e-01
16218	TOR1AIP2	1
16219	TOR1B	1
16220	TOR2A	1
16221	TOR3A	1.155634e-01
16222	TOX	1
16223	TOX2	1
16224	TOX3	1
16225	TOX4	1
16226	TP53	1.110223e-16
16227	TP53AIP1	1
16228	TP53BP1	1.168172e-01
16229	TP53BP2	1
16230	TP53I11	1
16231	TP53I13	1.522026e-02
16232	TP53I3	1.345625e-02
16233	TP53INP1	1
16234	TP53INP2	6.720182e-02
16235	TP53RK	1
16236	TP53TG5	1
16237	TP63	7.567918e-02
16238	TP73	1
16239	TPBG	1
16240	TPCN1	1
16241	TPCN2	2.376979e-01
16242	TPD52	1
16243	TPD52L1	1
16244	TPD52L2	1
16245	TPD52L3	1
16246	TPH1	1
16247	TPH2	1
16248	TPI1	1
16249	TPK1	3.871947e-03
16250	TPM1	1
16251	TPM2	1.826087e-01
16252	TPM3	1
16253	TPM4	1
16254	TPMT	1
16255	TPO	3.999739e-02
16256	TPP1	1
16257	TPP2	1
16258	TPPP	1
16259	TPPP2	1
16260	TPPP3	1
16261	TPR	2.370214e-02
16262	TPRA1	1
16263	TPRG1	1.542275e-01
16264	TPRG1L	1
16265	TPRKB	1
16266	TPRN	1
16267	TPRX1	1
16268	TPSAB1	1
16269	TPSB2	1
16270	TPSD1	1
16271	TPSG1	1
16272	TPST1	1
16273	TPST2	1
16274	TPT1	1
16275	TPTE	1.364547e-01
16276	TPTE2	2.035165e-01
16277	TPX2	2.332366e-01
16278	TRA2A	1
16279	TRA2B	1.306378e-01
16280	TRABD	1
16281	TRADD	1
16282	TRAF1	1
16283	TRAF2	2.493132e-01
16284	TRAF3	1
16285	TRAF3IP1	1
Done

Running MutSig 2:
Scatter job 180: processing genes 16195 - 16285
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TP53
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: 1.011330e+00	ci left: 7.655977e-04	ci right 2.347848e-03	k: 14	n:10000
KS ci ratio: 2.771443e+00	ci left: 2.531778e-06	ci right 5.570370e-04	k: 1	n:10000
TP53   10000 perm   3 sec   (3798 perm/sec)   p_kst 1.000000e-04   p_cons 1.400000e-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: 6.438316e-01	ci left: 1.261006e-03	ci right 2.491096e-03	k: 36	n:20000
KS ci ratio: 2.771651e+00	ci left: 1.265890e-06	ci right 2.785503e-04	k: 1	n:20000
TP53   20000 perm   8 sec   (2385 perm/sec)   p_kst 5.000000e-05   p_cons 1.800000e-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: 5.379686e-01	ci left: 1.294799e-03	ci right 2.272423e-03	k: 52	n:30000
KS ci ratio: 2.771720e+00	ci left: 8.439266e-07	ci right 1.857073e-04	k: 1	n:30000
TP53   30000 perm   11 sec   (2655 perm/sec)   p_kst 3.333333e-05   p_cons 1.733333e-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: 4.714995e-01	ci left: 1.320351e-03	ci right 2.154664e-03	k: 68	n:40000
KS ci ratio: 2.263100e+00	ci left: 6.055289e-06	ci right 1.806054e-04	k: 2	n:40000
TP53   40000 perm   14 sec   (2828 perm/sec)   p_kst 5.000000e-05   p_cons 1.700000e-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: 3.976255e-01	ci left: 1.555474e-03	ci right 2.344151e-03	k: 96	n:50000
KS ci ratio: 2.263123e+00	ci left: 4.844222e-06	ci right 1.444862e-04	k: 2	n:50000
TP53   50000 perm   17 sec   (2924 perm/sec)   p_kst 4.000000e-05   p_cons 1.920000e-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: 3.620476e-01	ci left: 1.597806e-03	ci right 2.318402e-03	k: 116	n:60000
KS ci ratio: 2.263138e+00	ci left: 4.036847e-06	ci right 1.204062e-04	k: 2	n:60000
TP53   60000 perm   20 sec   (2980 perm/sec)   p_kst 3.333333e-05   p_cons 1.933333e-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: 3.370520e-01	ci left: 1.604141e-03	ci right 2.266808e-03	k: 134	n:70000
KS ci ratio: 1.959930e+00	ci left: 8.838260e-06	ci right 1.252416e-04	k: 3	n:70000
TP53   70000 perm   23 sec   (2996 perm/sec)   p_kst 4.285714e-05   p_cons 1.914286e-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: 3.275117e-01	ci left: 1.495268e-03	ci right 2.091794e-03	k: 142	n:80000
KS ci ratio: 1.959939e+00	ci left: 7.733468e-06	ci right 1.095870e-04	k: 3	n:80000
TP53   80000 perm   27 sec   (2999 perm/sec)   p_kst 3.750000e-05   p_cons 1.775000e-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: 3.039686e-01	ci left: 1.564468e-03	ci right 2.135075e-03	k: 165	n:90000
KS ci ratio: 1.959946e+00	ci left: 6.874187e-06	ci right 9.741102e-05	k: 3	n:90000
TP53   90000 perm   30 sec   (2997 perm/sec)   p_kst 3.333333e-05   p_cons 1.833333e-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: 2.887188e-01	ci left: 1.574649e-03	ci right 2.114902e-03	k: 183	n:100000
KS ci ratio: 1.753025e+00	ci left: 1.089876e-05	ci right 1.024127e-04	k: 4	n:100000
TP53   100000 perm   34 sec   (2967 perm/sec)   p_kst 4.000000e-05   p_cons 1.830000e-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: 2.819189e-01	ci left: 1.507456e-03	ci right 2.010307e-03	k: 192	n:110000
KS ci ratio: 1.753029e+00	ci left: 9.907953e-06	ci right 9.310271e-05	k: 4	n:110000
TP53   110000 perm   37 sec   (2946 perm/sec)   p_kst 3.636364e-05   p_cons 1.745455e-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: 2.689877e-01	ci left: 1.529240e-03	ci right 2.012016e-03	k: 211	n:120000
KS ci ratio: 1.753033e+00	ci left: 9.082284e-06	ci right 8.534435e-05	k: 4	n:120000
TP53   120000 perm   41 sec   (2910 perm/sec)   p_kst 3.333333e-05   p_cons 1.758333e-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: 2.593796e-01	ci left: 1.526534e-03	ci right 1.988453e-03	k: 227	n:130000
KS ci ratio: 1.753037e+00	ci left: 8.383641e-06	ci right 7.877956e-05	k: 4	n:130000
TP53   130000 perm   45 sec   (2901 perm/sec)   p_kst 3.076923e-05   p_cons 1.746154e-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: 2.472054e-01	ci left: 1.571363e-03	ci right 2.021103e-03	k: 250	n:140000
KS ci ratio: 1.600293e+00	ci left: 1.159643e-05	ci right 8.334324e-05	k: 5	n:140000
TP53   140000 perm   49 sec   (2884 perm/sec)   p_kst 3.571429e-05   p_cons 1.785714e-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: 2.383480e-01	ci left: 1.585570e-03	ci right 2.020716e-03	k: 269	n:150000
KS ci ratio: 1.600296e+00	ci left: 1.082333e-05	ci right 7.778715e-05	k: 5	n:150000
TP53   150000 perm   52 sec   (2860 perm/sec)   p_kst 3.333333e-05   p_cons 1.793333e-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: 2.235108e-01	ci left: 1.704368e-03	ci right 2.138998e-03	k: 306	n:160000
KS ci ratio: 1.600298e+00	ci left: 1.014687e-05	ci right 7.292556e-05	k: 5	n:160000
TP53   160000 perm   56 sec   (2837 perm/sec)   p_kst 3.125000e-05   p_cons 1.912500e-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: 2.172339e-01	ci left: 1.704150e-03	ci right 2.124891e-03	k: 324	n:170000
KS ci ratio: 1.600300e+00	ci left: 9.549987e-06	ci right 6.863590e-05	k: 5	n:170000
TP53   170000 perm   61 sec   (2801 perm/sec)   p_kst 2.941176e-05   p_cons 1.905882e-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: 2.108428e-01	ci left: 1.714632e-03	ci right 2.123898e-03	k: 344	n:180000
KS ci ratio: 1.481588e+00	ci left: 1.223284e-05	ci right 7.255121e-05	k: 6	n:180000
TP53   180000 perm   65 sec   (2755 perm/sec)   p_kst 3.333333e-05   p_cons 1.911111e-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: 2.058337e-01	ci left: 1.709194e-03	ci right 2.106250e-03	k: 361	n:190000
KS ci ratio: 1.481590e+00	ci left: 1.158900e-05	ci right 6.873280e-05	k: 6	n:190000
TP53   190000 perm   70 sec   (2715 perm/sec)   p_kst 3.157895e-05   p_cons 1.900000e-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: 2.003725e-01	ci left: 1.718650e-03	ci right 2.106015e-03	k: 381	n:200000
KS ci ratio: 1.481591e+00	ci left: 1.100955e-05	ci right 6.529622e-05	k: 6	n:200000
TP53   200000 perm   74 sec   (2697 perm/sec)   p_kst 3.000000e-05   p_cons 1.905000e-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: 1.950812e-01	ci left: 1.731861e-03	ci right 2.110671e-03	k: 402	n:210000
KS ci ratio: 1.481593e+00	ci left: 1.048528e-05	ci right 6.218693e-05	k: 6	n:210000
TP53   210000 perm   78 sec   (2679 perm/sec)   p_kst 2.857143e-05   p_cons 1.914286e-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: 1.886343e-01	ci left: 1.774304e-03	ci right 2.148104e-03	k: 430	n:220000
KS ci ratio: 1.481594e+00	ci left: 1.000867e-05	ci right 5.936029e-05	k: 6	n:220000
TP53   220000 perm   83 sec   (2658 perm/sec)   p_kst 2.727273e-05   p_cons 1.954545e-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: 1.852290e-01	ci left: 1.763470e-03	ci right 2.127526e-03	k: 446	n:230000
KS ci ratio: 1.481595e+00	ci left: 9.573512e-06	ci right 5.677945e-05	k: 6	n:230000
TP53   230000 perm   87 sec   (2636 perm/sec)   p_kst 2.608696e-05   p_cons 1.939130e-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: 1.818051e-01	ci left: 1.757571e-03	ci right 2.112964e-03	k: 463	n:240000
KS ci ratio: 1.481596e+00	ci left: 9.174613e-06	ci right 5.441367e-05	k: 6	n:240000
TP53   240000 perm   92 sec   (2614 perm/sec)   p_kst 2.500000e-05   p_cons 1.929167e-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: 1.789373e-01	ci left: 1.744558e-03	ci right 2.091153e-03	k: 478	n:250000
KS ci ratio: 1.481597e+00	ci left: 8.807626e-06	ci right 5.223716e-05	k: 6	n:250000
TP53   250000 perm   96 sec   (2593 perm/sec)   p_kst 2.400000e-05   p_cons 1.912000e-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: 1.753145e-01	ci left: 1.750973e-03	ci right 2.091053e-03	k: 498	n:260000
KS ci ratio: 1.481598e+00	ci left: 8.468870e-06	ci right 5.022806e-05	k: 6	n:260000
TP53   260000 perm   101 sec   (2570 perm/sec)   p_kst 2.307692e-05   p_cons 1.915385e-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: 1.822185e-01	ci left: 1.555200e-03	ci right 1.870465e-03	k: 461	n:270000
KS ci ratio: 1.481599e+00	ci left: 8.155206e-06	ci right 4.836779e-05	k: 6	n:270000
TP53   270000 perm   106 sec   (2548 perm/sec)   p_kst 2.222222e-05   p_cons 1.707407e-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: 1.782120e-01	ci left: 1.571275e-03	ci right 1.882041e-03	k: 482	n:280000
KS ci ratio: 1.481600e+00	ci left: 7.863947e-06	ci right 4.664039e-05	k: 6	n:280000
TP53   280000 perm   111 sec   (2526 perm/sec)   p_kst 2.142857e-05   p_cons 1.721429e-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: 1.756850e-01	ci left: 1.563231e-03	ci right 1.867556e-03	k: 496	n:290000
KS ci ratio: 1.481600e+00	ci left: 7.592775e-06	ci right 4.503212e-05	k: 6	n:290000
TP53   290000 perm   116 sec   (2504 perm/sec)   p_kst 2.068966e-05   p_cons 1.710345e-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: 1.724196e-01	ci left: 1.571698e-03	ci right 1.871393e-03	k: 515	n:300000
KS ci ratio: 1.385909e+00	ci left: 9.381260e-06	ci right 4.807499e-05	k: 7	n:300000
TP53   300000 perm   121 sec   (2483 perm/sec)   p_kst 2.333333e-05   p_cons 1.716667e-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: 1.702890e-01	ci left: 1.561134e-03	ci right 1.854758e-03	k: 528	n:310000
KS ci ratio: 1.385909e+00	ci left: 9.078637e-06	ci right 4.652420e-05	k: 7	n:310000
TP53   310000 perm   126 sec   (2460 perm/sec)   p_kst 2.258065e-05   p_cons 1.703226e-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: 1.646239e-01	ci left: 1.623133e-03	ci right 1.917257e-03	k: 565	n:320000
KS ci ratio: 1.385910e+00	ci left: 8.794928e-06	ci right 4.507034e-05	k: 7	n:320000
TP53   320000 perm   131 sec   (2438 perm/sec)   p_kst 2.187500e-05   p_cons 1.765625e-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: 1.634750e-01	ci left: 1.597193e-03	ci right 1.884397e-03	k: 573	n:330000
KS ci ratio: 1.385910e+00	ci left: 8.528414e-06	ci right 4.370459e-05	k: 7	n:330000
TP53   330000 perm   137 sec   (2416 perm/sec)   p_kst 2.121212e-05   p_cons 1.736364e-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: 1.619323e-01	ci left: 1.581251e-03	ci right 1.862645e-03	k: 584	n:340000
KS ci ratio: 1.385911e+00	ci left: 8.277577e-06	ci right 4.241917e-05	k: 7	n:340000
TP53   340000 perm   142 sec   (2394 perm/sec)   p_kst 2.058824e-05   p_cons 1.717647e-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: 1.612475e-01	ci left: 1.549779e-03	ci right 1.824292e-03	k: 589	n:350000
KS ci ratio: 1.385911e+00	ci left: 8.041074e-06	ci right 4.120721e-05	k: 7	n:350000
TP53   350000 perm   148 sec   (2373 perm/sec)   p_kst 2.000000e-05   p_cons 1.682857e-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: 1.593685e-01	ci left: 1.544058e-03	ci right 1.814065e-03	k: 603	n:360000
KS ci ratio: 1.385912e+00	ci left: 7.817710e-06	ci right 4.006257e-05	k: 7	n:360000
TP53   360000 perm   153 sec   (2351 perm/sec)   p_kst 1.944444e-05   p_cons 1.675000e-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: 1.574260e-01	ci left: 1.541260e-03	ci right 1.807183e-03	k: 618	n:370000
KS ci ratio: 1.385912e+00	ci left: 7.606419e-06	ci right 3.897981e-05	k: 7	n:370000
TP53   370000 perm   159 sec   (2330 perm/sec)   p_kst 1.891892e-05   p_cons 1.670270e-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: 1.554302e-01	ci left: 1.541157e-03	ci right 1.803378e-03	k: 634	n:380000
KS ci ratio: 1.385913e+00	ci left: 7.406250e-06	ci right 3.795404e-05	k: 7	n:380000
TP53   380000 perm   165 sec   (2308 perm/sec)   p_kst 1.842105e-05   p_cons 1.668421e-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: 1.537452e-01	ci left: 1.536149e-03	ci right 1.794422e-03	k: 648	n:390000
KS ci ratio: 1.385913e+00	ci left: 7.216345e-06	ci right 3.698087e-05	k: 7	n:390000
TP53   390000 perm   171 sec   (2284 perm/sec)   p_kst 1.794872e-05   p_cons 1.661538e-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: 1.512028e-01	ci left: 1.550648e-03	ci right 1.806658e-03	k: 670	n:400000
KS ci ratio: 1.385914e+00	ci left: 7.035936e-06	ci right 3.605635e-05	k: 7	n:400000
TP53   400000 perm   177 sec   (2264 perm/sec)   p_kst 1.750000e-05   p_cons 1.675000e-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: 1.485678e-01	ci left: 1.569170e-03	ci right 1.823322e-03	k: 694	n:410000
KS ci ratio: 1.385914e+00	ci left: 6.864327e-06	ci right 3.517694e-05	k: 7	n:410000
TP53   410000 perm   183 sec   (2238 perm/sec)   p_kst 1.707317e-05   p_cons 1.692683e-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: 1.465774e-01	ci left: 1.575376e-03	ci right 1.826816e-03	k: 713	n:420000
KS ci ratio: 1.385914e+00	ci left: 6.700890e-06	ci right 3.433940e-05	k: 7	n:420000
TP53   420000 perm   190 sec   (2209 perm/sec)   p_kst 1.666667e-05   p_cons 1.697619e-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: 1.452616e-01	ci left: 1.567868e-03	ci right 1.815668e-03	k: 726	n:430000
KS ci ratio: 1.306651e+00	ci left: 8.032201e-06	ci right 3.665825e-05	k: 8	n:430000
TP53   430000 perm   197 sec   (2185 perm/sec)   p_kst 1.860465e-05   p_cons 1.688372e-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: 1.433033e-01	ci left: 1.576049e-03	ci right 1.821497e-03	k: 746	n:440000
KS ci ratio: 1.306652e+00	ci left: 7.849650e-06	ci right 3.582511e-05	k: 8	n:440000
TP53   440000 perm   204 sec   (2161 perm/sec)   p_kst 1.818182e-05   p_cons 1.695455e-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: 1.415146e-01	ci left: 1.581744e-03	ci right 1.824744e-03	k: 765	n:450000
KS ci ratio: 1.306652e+00	ci left: 7.675213e-06	ci right 3.502901e-05	k: 8	n:450000
TP53   450000 perm   211 sec   (2134 perm/sec)   p_kst 1.777778e-05   p_cons 1.700000e-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: 1.400596e-01	ci left: 1.580915e-03	ci right 1.821083e-03	k: 781	n:460000
KS ci ratio: 1.306652e+00	ci left: 7.508360e-06	ci right 3.426751e-05	k: 8	n:460000
TP53   460000 perm   218 sec   (2112 perm/sec)   p_kst 1.739130e-05   p_cons 1.697826e-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: 1.386485e-01	ci left: 1.580135e-03	ci right 1.817565e-03	k: 797	n:470000
KS ci ratio: 1.306653e+00	ci left: 7.348607e-06	ci right 3.353842e-05	k: 8	n:470000
TP53   470000 perm   224 sec   (2094 perm/sec)   p_kst 1.702128e-05   p_cons 1.695745e-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: 1.369426e-01	ci left: 1.587446e-03	ci right 1.822801e-03	k: 817	n:480000
KS ci ratio: 1.306653e+00	ci left: 7.195510e-06	ci right 3.283971e-05	k: 8	n:480000
TP53   480000 perm   232 sec   (2068 perm/sec)   p_kst 1.666667e-05   p_cons 1.702083e-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: 1.352174e-01	ci left: 1.596447e-03	ci right 1.829916e-03	k: 838	n:490000
KS ci ratio: 1.306653e+00	ci left: 7.048663e-06	ci right 3.216952e-05	k: 8	n:490000
TP53   490000 perm   240 sec   (2044 perm/sec)   p_kst 1.632653e-05   p_cons 1.710204e-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: 1.334780e-01	ci left: 1.607040e-03	ci right 1.838795e-03	k: 860	n:500000
KS ci ratio: 1.306654e+00	ci left: 6.907689e-06	ci right 3.152613e-05	k: 8	n:500000
TP53   500000 perm   247 sec   (2026 perm/sec)   p_kst 1.600000e-05   p_cons 1.720000e-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: 1.318790e-01	ci left: 1.615340e-03	ci right 1.845282e-03	k: 881	n:510000
KS ci ratio: 1.306654e+00	ci left: 6.772244e-06	ci right 3.090798e-05	k: 8	n:510000
TP53   510000 perm   254 sec   (2010 perm/sec)   p_kst 1.568627e-05   p_cons 1.727451e-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: 1.310650e-01	ci left: 1.604733e-03	ci right 1.831646e-03	k: 892	n:520000
KS ci ratio: 1.306654e+00	ci left: 6.642008e-06	ci right 3.031360e-05	k: 8	n:520000
TP53   520000 perm   261 sec   (1995 perm/sec)   p_kst 1.538462e-05   p_cons 1.715385e-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: 1.296212e-01	ci left: 1.610961e-03	ci right 1.836051e-03	k: 912	n:530000
KS ci ratio: 1.306654e+00	ci left: 6.516686e-06	ci right 2.974165e-05	k: 8	n:530000
TP53   530000 perm   268 sec   (1980 perm/sec)   p_kst 1.509434e-05   p_cons 1.720755e-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: 1.282929e-01	ci left: 1.615179e-03	ci right 1.838370e-03	k: 931	n:540000
KS ci ratio: 1.306655e+00	ci left: 6.396007e-06	ci right 2.919088e-05	k: 8	n:540000
TP53   540000 perm   275 sec   (1965 perm/sec)   p_kst 1.481481e-05   p_cons 1.724074e-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: 1.274755e-01	ci left: 1.606931e-03	ci right 1.827461e-03	k: 943	n:550000
KS ci ratio: 1.306655e+00	ci left: 6.279715e-06	ci right 2.866014e-05	k: 8	n:550000
TP53   550000 perm   282 sec   (1950 perm/sec)   p_kst 1.454545e-05   p_cons 1.714545e-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: 1.153751e-01	ci left: 1.938429e-03	ci right 2.177484e-03	k: 1151	n:560000
KS ci ratio: 1.239601e+00	ci left: 7.348906e-06	ci right 3.050836e-05	k: 9	n:560000
TP53   560000 perm   289 sec   (1935 perm/sec)   p_kst 1.607143e-05   p_cons 2.055357e-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: 1.145335e-01	ci left: 1.933388e-03	ci right 2.169964e-03	k: 1168	n:570000
KS ci ratio: 1.239601e+00	ci left: 7.219977e-06	ci right 2.997313e-05	k: 9	n:570000
TP53   570000 perm   297 sec   (1921 perm/sec)   p_kst 1.578947e-05   p_cons 2.049123e-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: 1.134706e-01	ci left: 1.936904e-03	ci right 2.171563e-03	k: 1190	n:580000
KS ci ratio: 1.239601e+00	ci left: 7.095495e-06	ci right 2.945635e-05	k: 9	n:580000
TP53   580000 perm   304 sec   (1906 perm/sec)   p_kst 1.551724e-05   p_cons 2.051724e-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: 1.124833e-01	ci left: 1.938662e-03	ci right 2.171355e-03	k: 1211	n:590000
KS ci ratio: 1.239601e+00	ci left: 6.975232e-06	ci right 2.895710e-05	k: 9	n:590000
TP53   590000 perm   312 sec   (1891 perm/sec)   p_kst 1.525424e-05   p_cons 2.052542e-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: 1.119313e-01	ci left: 1.925789e-03	ci right 2.155728e-03	k: 1223	n:600000
KS ci ratio: 1.239601e+00	ci left: 6.858977e-06	ci right 2.847448e-05	k: 9	n:600000
TP53   600000 perm   320 sec   (1875 perm/sec)   p_kst 1.500000e-05   p_cons 2.038333e-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: 1.108940e-01	ci left: 1.930873e-03	ci right 2.159143e-03	k: 1246	n:610000
KS ci ratio: 1.239602e+00	ci left: 6.746535e-06	ci right 2.800769e-05	k: 9	n:610000
TP53   610000 perm   329 sec   (1857 perm/sec)   p_kst 1.475410e-05   p_cons 2.042623e-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: 1.097121e-01	ci left: 1.942078e-03	ci right 2.169067e-03	k: 1273	n:620000
KS ci ratio: 1.181913e+00	ci left: 7.734524e-06	ci right 2.966166e-05	k: 10	n:620000
TP53   620000 perm   337 sec   (1838 perm/sec)   p_kst 1.612903e-05   p_cons 2.053226e-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: 1.089031e-01	ci left: 1.940585e-03	ci right 2.165620e-03	k: 1292	n:630000
KS ci ratio: 1.181913e+00	ci left: 7.611753e-06	ci right 2.919085e-05	k: 10	n:630000
TP53   630000 perm   345 sec   (1825 perm/sec)   p_kst 1.587302e-05   p_cons 2.050794e-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: 1.077830e-01	ci left: 1.951308e-03	ci right 2.175112e-03	k: 1319	n:640000
KS ci ratio: 1.181913e+00	ci left: 7.492819e-06	ci right 2.873474e-05	k: 10	n:640000
TP53   640000 perm   353 sec   (1812 perm/sec)   p_kst 1.562500e-05   p_cons 2.060937e-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: 1.070157e-01	ci left: 1.949734e-03	ci right 2.171665e-03	k: 1338	n:650000
KS ci ratio: 1.181914e+00	ci left: 7.377545e-06	ci right 2.829267e-05	k: 10	n:650000
TP53   650000 perm   361 sec   (1799 perm/sec)   p_kst 1.538462e-05   p_cons 2.058462e-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: 1.063038e-01	ci left: 1.946737e-03	ci right 2.166761e-03	k: 1356	n:660000
KS ci ratio: 1.181914e+00	ci left: 7.265764e-06	ci right 2.786400e-05	k: 10	n:660000
TP53   660000 perm   370 sec   (1785 perm/sec)   p_kst 1.515152e-05   p_cons 2.054545e-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: 1.055675e-01	ci left: 1.945288e-03	ci right 2.163531e-03	k: 1375	n:670000
KS ci ratio: 1.131596e+00	ci left: 8.195789e-06	ci right 2.937599e-05	k: 11	n:670000
TP53   670000 perm   378 sec   (1771 perm/sec)   p_kst 1.641791e-05   p_cons 2.052239e-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: 1.050350e-01	ci left: 1.936727e-03	ci right 2.152845e-03	k: 1389	n:680000
KS ci ratio: 1.131596e+00	ci left: 8.075263e-06	ci right 2.894399e-05	k: 11	n:680000
TP53   680000 perm   387 sec   (1758 perm/sec)   p_kst 1.617647e-05   p_cons 2.042647e-03   p_joint 0

Joint ci ratio: 4.587767e-01	ci left: 8.164662e-05	ci right 1.314070e-04	k: 72	n:690000
Cons ci ratio: 1.042874e-01	ci left: 1.936885e-03	ci right 2.151388e-03	k: 1409	n:690000
KS ci ratio: 1.087201e+00	ci left: 8.986372e-06	ci right 3.037891e-05	k: 12	n:690000
TP53   690000 perm   395 sec   (1746 perm/sec)   p_kst 1.739130e-05   p_cons 2.042029e-03   p_joint 1.043478e-04

Joint ci ratio: 4.587770e-01	ci left: 8.048022e-05	ci right 1.295298e-04	k: 72	n:700000
Cons ci ratio: 1.034469e-01	ci left: 1.941219e-03	ci right 2.154364e-03	k: 1432	n:700000
KS ci ratio: 1.087202e+00	ci left: 8.857995e-06	ci right 2.994493e-05	k: 12	n:700000
TP53   700000 perm   405 sec   (1730 perm/sec)   p_kst 1.714286e-05   p_cons 2.045714e-03   p_joint 1.028571e-04

Joint ci ratio: 4.861936e-01	ci left: 6.942010e-05	ci right 1.151064e-04	k: 64	n:710000
Cons ci ratio: 1.027326e-01	ci left: 1.941321e-03	ci right 2.152916e-03	k: 1452	n:710000
KS ci ratio: 1.087202e+00	ci left: 8.733234e-06	ci right 2.952317e-05	k: 12	n:710000
TP53   710000 perm   413 sec   (1719 perm/sec)   p_kst 1.690141e-05   p_cons 2.045070e-03   p_joint 9.014085e-05

Joint ci ratio: 4.824962e-01	ci left: 6.967515e-05	ci right 1.150650e-04	k: 65	n:720000
Cons ci ratio: 1.018252e-01	ci left: 1.949546e-03	ci right 2.160049e-03	k: 1478	n:720000
KS ci ratio: 1.087202e+00	ci left: 8.611939e-06	ci right 2.911313e-05	k: 12	n:720000
TP53   720000 perm   422 sec   (1707 perm/sec)   p_kst 1.666667e-05   p_cons 2.052778e-03   p_joint 9.027778e-05

Joint ci ratio: 4.788819e-01	ci left: 6.992450e-05	ci right 1.150235e-04	k: 66	n:730000
Cons ci ratio: 1.010761e-01	ci left: 1.952212e-03	ci right 2.161360e-03	k: 1500	n:730000
KS ci ratio: 1.087202e+00	ci left: 8.493966e-06	ci right 2.871432e-05	k: 12	n:730000
TP53   730000 perm   431 sec   (1695 perm/sec)   p_kst 1.643836e-05   p_cons 2.054795e-03   p_joint 9.041096e-05

Joint ci ratio: 4.753477e-01	ci left: 7.016834e-05	ci right 1.149819e-04	k: 67	n:740000
Cons ci ratio: 1.003433e-01	ci left: 1.954812e-03	ci right 2.162631e-03	k: 1522	n:740000
KS ci ratio: 1.087202e+00	ci left: 8.379183e-06	ci right 2.832629e-05	k: 12	n:740000
TP53   740000 perm   440 sec   (1682 perm/sec)   p_kst 1.621622e-05   p_cons 2.056757e-03   p_joint 9.054054e-05

Joint ci ratio: 4.753480e-01	ci left: 6.923276e-05	ci right 1.134488e-04	k: 67	n:750000
Cons ci ratio: 9.972331e-02	ci left: 1.953447e-03	ci right 2.159763e-03	k: 1541	n:750000
KS ci ratio: 1.087202e+00	ci left: 8.267460e-06	ci right 2.794861e-05	k: 12	n:750000
TP53   750000 perm   449 sec   (1670 perm/sec)   p_kst 1.600000e-05   p_cons 2.054667e-03   p_joint 8.933333e-05

Joint ci ratio: 4.685077e-01	ci left: 7.064029e-05	ci right 1.148985e-04	k: 69	n:760000
Cons ci ratio: 9.927410e-02	ci left: 1.945706e-03	ci right 2.150224e-03	k: 1555	n:760000
KS ci ratio: 1.047654e+00	ci left: 9.107863e-06	ci right 2.925034e-05	k: 13	n:760000
TP53   760000 perm   459 sec   (1655 perm/sec)   p_kst 1.710526e-05   p_cons 2.046053e-03   p_joint 9.078947e-05

Joint ci ratio: 4.685080e-01	ci left: 6.972288e-05	ci right 1.134063e-04	k: 69	n:770000
Cons ci ratio: 9.857955e-02	ci left: 1.948302e-03	ci right 2.151577e-03	k: 1577	n:770000
KS ci ratio: 1.047654e+00	ci left: 8.989578e-06	ci right 2.887047e-05	k: 13	n:770000
TP53   770000 perm   469 sec   (1641 perm/sec)   p_kst 1.688312e-05   p_cons 2.048052e-03   p_joint 8.961039e-05

Joint ci ratio: 4.651969e-01	ci left: 6.996018e-05	ci right 1.133843e-04	k: 70	n:780000
Cons ci ratio: 9.771595e-02	ci left: 1.958340e-03	ci right 2.160771e-03	k: 1605	n:780000
KS ci ratio: 1.047654e+00	ci left: 8.874327e-06	ci right 2.850034e-05	k: 13	n:780000
TP53   780000 perm   479 sec   (1630 perm/sec)   p_kst 1.666667e-05   p_cons 2.057692e-03   p_joint 8.974359e-05

Joint ci ratio: 4.651972e-01	ci left: 6.907460e-05	ci right 1.119491e-04	k: 70	n:790000
Cons ci ratio: 9.687465e-02	ci left: 1.968132e-03	ci right 2.169724e-03	k: 1633	n:790000
KS ci ratio: 1.047654e+00	ci left: 8.761993e-06	ci right 2.813958e-05	k: 13	n:790000
TP53   790000 perm   488 sec   (1619 perm/sec)   p_kst 1.645570e-05   p_cons 2.067089e-03   p_joint 8.860759e-05

Joint ci ratio: 4.587801e-01	ci left: 7.042010e-05	ci right 1.133388e-04	k: 72	n:800000
Cons ci ratio: 9.622893e-02	ci left: 1.970367e-03	ci right 2.170766e-03	k: 1655	n:800000
KS ci ratio: 1.047654e+00	ci left: 8.652468e-06	ci right 2.778783e-05	k: 13	n:800000
TP53   800000 perm   497 sec   (1609 perm/sec)   p_kst 1.625000e-05   p_cons 2.068750e-03   p_joint 9.000000e-05

Joint ci ratio: 4.556696e-01	ci left: 7.064305e-05	ci right 1.133154e-04	k: 73	n:810000
Cons ci ratio: 9.551044e-02	ci left: 1.976166e-03	ci right 2.175570e-03	k: 1680	n:810000
KS ci ratio: 1.047654e+00	ci left: 8.545647e-06	ci right 2.744478e-05	k: 13	n:810000
TP53   810000 perm   508 sec   (1595 perm/sec)   p_kst 1.604938e-05   p_cons 2.074074e-03   p_joint 9.012346e-05

Joint ci ratio: 4.496337e-01	ci left: 7.194244e-05	ci right 1.146489e-04	k: 75	n:820000
Cons ci ratio: 9.491937e-02	ci left: 1.977066e-03	ci right 2.175258e-03	k: 1701	n:820000
KS ci ratio: 1.047654e+00	ci left: 8.441432e-06	ci right 2.711009e-05	k: 13	n:820000
TP53   820000 perm   519 sec   (1580 perm/sec)   p_kst 1.585366e-05   p_cons 2.074390e-03   p_joint 9.146341e-05

Joint ci ratio: 4.467045e-01	ci left: 7.214446e-05	ci right 1.146075e-04	k: 76	n:830000
Cons ci ratio: 9.420227e-02	ci left: 1.983831e-03	ci right 2.181116e-03	k: 1727	n:830000
KS ci ratio: 1.047655e+00	ci left: 8.339727e-06	ci right 2.678346e-05	k: 13	n:830000
TP53   830000 perm   529 sec   (1569 perm/sec)   p_kst 1.566265e-05   p_cons 2.080723e-03   p_joint 9.156627e-05

Joint ci ratio: 4.718929e-01	ci left: 6.286322e-05	ci right 1.026253e-04	k: 68	n:840000
Cons ci ratio: 9.374250e-02	ci left: 1.979976e-03	ci right 2.175864e-03	k: 1744	n:840000
KS ci ratio: 1.047655e+00	ci left: 8.240445e-06	ci right 2.646461e-05	k: 13	n:840000
TP53   840000 perm   539 sec   (1560 perm/sec)   p_kst 1.547619e-05   p_cons 2.076190e-03   p_joint 8.095238e-05

Joint ci ratio: 4.753505e-01	ci left: 6.108766e-05	ci right 1.001020e-04	k: 67	n:850000
Cons ci ratio: 9.313063e-02	ci left: 1.983109e-03	ci right 2.177956e-03	k: 1767	n:850000
KS ci ratio: 1.047655e+00	ci left: 8.143498e-06	ci right 2.615326e-05	k: 13	n:850000
TP53   850000 perm   549 sec   (1550 perm/sec)   p_kst 1.529412e-05   p_cons 2.078824e-03   p_joint 7.882353e-05

Joint ci ratio: 4.718933e-01	ci left: 6.140128e-05	ci right 1.002387e-04	k: 68	n:860000
Cons ci ratio: 9.263431e-02	ci left: 1.981629e-03	ci right 2.175237e-03	k: 1786	n:860000
KS ci ratio: 1.047655e+00	ci left: 8.048806e-06	ci right 2.584916e-05	k: 13	n:860000
TP53   860000 perm   559 sec   (1538 perm/sec)   p_kst 1.511628e-05   p_cons 2.076744e-03   p_joint 7.906977e-05

Joint ci ratio: 4.685105e-01	ci left: 6.170869e-05	ci right 1.003713e-04	k: 69	n:870000
Cons ci ratio: 9.219701e-02	ci left: 1.977940e-03	ci right 2.170227e-03	k: 1803	n:870000
KS ci ratio: 1.047655e+00	ci left: 7.956290e-06	ci right 2.555204e-05	k: 13	n:870000
TP53   870000 perm   570 sec   (1526 perm/sec)   p_kst 1.494253e-05   p_cons 2.072414e-03   p_joint 7.931034e-05

Joint ci ratio: 4.619573e-01	ci left: 6.301369e-05	ci right 1.017681e-04	k: 71	n:880000
Cons ci ratio: 9.133959e-02	ci left: 1.993214e-03	ci right 2.185087e-03	k: 1837	n:880000
KS ci ratio: 1.047655e+00	ci left: 7.865878e-06	ci right 2.526168e-05	k: 13	n:880000
TP53   880000 perm   581 sec   (1516 perm/sec)   p_kst 1.477273e-05   p_cons 2.087500e-03   p_joint 8.068182e-05

Joint ci ratio: 4.587822e-01	ci left: 6.329891e-05	ci right 1.018777e-04	k: 72	n:890000
Cons ci ratio: 9.096944e-02	ci left: 1.987288e-03	ci right 2.177774e-03	k: 1852	n:890000
KS ci ratio: 1.047655e+00	ci left: 7.777497e-06	ci right 2.497784e-05	k: 13	n:890000
TP53   890000 perm   591 sec   (1506 perm/sec)   p_kst 1.460674e-05   p_cons 2.080899e-03   p_joint 8.089888e-05

Joint ci ratio: 4.587824e-01	ci left: 6.259558e-05	ci right 1.007457e-04	k: 72	n:900000
Cons ci ratio: 9.055520e-02	ci left: 1.983667e-03	ci right 2.172894e-03	k: 1869	n:900000
KS ci ratio: 1.047655e+00	ci left: 7.691080e-06	ci right 2.470031e-05	k: 13	n:900000
TP53   900000 perm   601 sec   (1497 perm/sec)   p_kst 1.444444e-05   p_cons 2.076667e-03   p_joint 8.000000e-05

Joint ci ratio: 4.556720e-01	ci left: 6.288001e-05	ci right 1.008633e-04	k: 73	n:910000
Cons ci ratio: 9.009872e-02	ci left: 1.982276e-03	ci right 2.170367e-03	k: 1888	n:910000
KS ci ratio: 1.047655e+00	ci left: 7.606562e-06	ci right 2.442888e-05	k: 13	n:910000
TP53   910000 perm   612 sec   (1487 perm/sec)   p_kst 1.428571e-05   p_cons 2.074725e-03   p_joint 8.021978e-05

Joint ci ratio: 4.526239e-01	ci left: 6.315912e-05	ci right 1.009775e-04	k: 74	n:920000
Cons ci ratio: 8.967263e-02	ci left: 1.979855e-03	ci right 2.166781e-03	k: 1906	n:920000
KS ci ratio: 1.047656e+00	ci left: 7.523882e-06	ci right 2.416335e-05	k: 13	n:920000
TP53   920000 perm   623 sec   (1478 perm/sec)   p_kst 1.413043e-05   p_cons 2.071739e-03   p_joint 8.043478e-05

Joint ci ratio: 4.526241e-01	ci left: 6.247998e-05	ci right 9.989170e-05	k: 74	n:930000
Cons ci ratio: 8.927577e-02	ci left: 1.976436e-03	ci right 2.162171e-03	k: 1923	n:930000
KS ci ratio: 1.047656e+00	ci left: 7.442980e-06	ci right 2.390353e-05	k: 13	n:930000
TP53   930000 perm   633 sec   (1469 perm/sec)   p_kst 1.397849e-05   p_cons 2.067742e-03   p_joint 7.956989e-05

Joint ci ratio: 4.496364e-01	ci left: 6.275822e-05	ci right 1.000130e-04	k: 75	n:940000
Cons ci ratio: 8.879249e-02	ci left: 1.977253e-03	ci right 2.162007e-03	k: 1944	n:940000
KS ci ratio: 1.047656e+00	ci left: 7.363799e-06	ci right 2.364924e-05	k: 13	n:940000
TP53   940000 perm   643 sec   (1461 perm/sec)   p_kst 1.382979e-05   p_cons 2.068085e-03   p_joint 7.978723e-05

Joint ci ratio: 4.467071e-01	ci left: 6.303140e-05	ci right 1.001309e-04	k: 76	n:950000
Cons ci ratio: 8.802583e-02	ci left: 1.991439e-03	ci right 2.175829e-03	k: 1978	n:950000
KS ci ratio: 1.047656e+00	ci left: 7.286285e-06	ci right 2.340030e-05	k: 13	n:950000
TP53   950000 perm   654 sec   (1452 perm/sec)   p_kst 1.368421e-05   p_cons 2.082105e-03   p_joint 8.000000e-05

Joint ci ratio: 4.410161e-01	ci left: 6.422527e-05	ci right 1.014027e-04	k: 78	n:960000
Cons ci ratio: 8.760637e-02	ci left: 1.990052e-03	ci right 2.173390e-03	k: 1997	n:960000
KS ci ratio: 1.012131e+00	ci left: 7.972866e-06	ci right 2.446823e-05	k: 14	n:960000
TP53   960000 perm   665 sec   (1444 perm/sec)   p_kst 1.458333e-05   p_cons 2.080208e-03   p_joint 8.125000e-05

Joint ci ratio: 4.410163e-01	ci left: 6.356315e-05	ci right 1.003573e-04	k: 78	n:970000
Cons ci ratio: 8.708476e-02	ci left: 1.993738e-03	ci right 2.176266e-03	k: 2021	n:970000
KS ci ratio: 1.012131e+00	ci left: 7.890672e-06	ci right 2.421599e-05	k: 14	n:970000
TP53   970000 perm   676 sec   (1435 perm/sec)   p_kst 1.443299e-05   p_cons 2.083505e-03   p_joint 8.041237e-05

Joint ci ratio: 4.410165e-01	ci left: 6.291454e-05	ci right 9.933323e-05	k: 78	n:980000
Cons ci ratio: 8.667855e-02	ci left: 1.992360e-03	ci right 2.173868e-03	k: 2040	n:980000
KS ci ratio: 1.012131e+00	ci left: 7.810154e-06	ci right 2.396889e-05	k: 14	n:980000
TP53   980000 perm   688 sec   (1425 perm/sec)   p_kst 1.428571e-05   p_cons 2.081633e-03   p_joint 7.959184e-05

Joint ci ratio: 4.410166e-01	ci left: 6.227903e-05	ci right 9.832988e-05	k: 78	n:990000
Cons ci ratio: 8.606888e-02	ci left: 2.000896e-03	ci right 2.181835e-03	k: 2069	n:990000
KS ci ratio: 1.012131e+00	ci left: 7.731264e-06	ci right 2.372678e-05	k: 14	n:990000
TP53   990000 perm   699 sec   (1417 perm/sec)   p_kst 1.414141e-05   p_cons 2.089899e-03   p_joint 7.878788e-05

Joint ci ratio: 4.382516e-01	ci left: 6.254553e-05	ci right 9.845661e-05	k: 79	n:1000000
Cons ci ratio: 8.557410e-02	ci left: 2.004372e-03	ci right 2.184532e-03	k: 2093	n:1000000
KS ci ratio: 1.012132e+00	ci left: 7.653951e-06	ci right 2.348951e-05	k: 14	n:1000000
TP53   1000000 perm   710 sec   (1409 perm/sec)   p_kst 1.400000e-05   p_cons 2.093000e-03   p_joint 7.900000e-05

Joint ci ratio: 4.382517e-01	ci left: 6.192626e-05	ci right 9.748180e-05	k: 79	n:1010000
Cons ci ratio: 8.506763e-02	ci left: 2.008751e-03	ci right 2.188183e-03	k: 2118	n:1010000
KS ci ratio: 1.012132e+00	ci left: 7.578169e-06	ci right 2.325694e-05	k: 14	n:1010000
TP53   1010000 perm   721 sec   (1401 perm/sec)   p_kst 1.386139e-05   p_cons 2.097030e-03   p_joint 7.821782e-05

Joint ci ratio: 4.382519e-01	ci left: 6.131914e-05	ci right 9.652611e-05	k: 79	n:1020000
Cons ci ratio: 8.457004e-02	ci left: 2.013048e-03	ci right 2.191759e-03	k: 2143	n:1020000
KS ci ratio: 1.012132e+00	ci left: 7.503873e-06	ci right 2.302893e-05	k: 14	n:1020000
TP53   1020000 perm   732 sec   (1393 perm/sec)   p_kst 1.372549e-05   p_cons 2.100980e-03   p_joint 7.745098e-05

Joint ci ratio: 4.382521e-01	ci left: 6.072380e-05	ci right 9.558897e-05	k: 79	n:1030000
Cons ci ratio: 8.398414e-02	ci left: 2.022016e-03	ci right 2.200220e-03	k: 2173	n:1030000
KS ci ratio: 1.012132e+00	ci left: 7.431020e-06	ci right 2.280535e-05	k: 14	n:1030000
TP53   1030000 perm   743 sec   (1386 perm/sec)   p_kst 1.359223e-05   p_cons 2.109709e-03   p_joint 7.669903e-05

Joint ci ratio: 4.382523e-01	ci left: 6.013991e-05	ci right 9.466986e-05	k: 79	n:1040000
Cons ci ratio: 8.356236e-02	ci left: 2.023284e-03	ci right 2.200661e-03	k: 2195	n:1040000
KS ci ratio: 1.012132e+00	ci left: 7.359567e-06	ci right 2.258607e-05	k: 14	n:1040000
TP53   1040000 perm   755 sec   (1378 perm/sec)   p_kst 1.346154e-05   p_cons 2.110577e-03   p_joint 7.596154e-05

Joint ci ratio: 4.355385e-01	ci left: 6.041476e-05	ci right 9.482476e-05	k: 80	n:1050000
Cons ci ratio: 8.309058e-02	ci left: 2.027329e-03	ci right 2.204007e-03	k: 2220	n:1050000
KS ci ratio: 1.012132e+00	ci left: 7.289476e-06	ci right 2.237097e-05	k: 14	n:1050000
TP53   1050000 perm   766 sec   (1371 perm/sec)   p_kst 1.333333e-05   p_cons 2.114286e-03   p_joint 7.619048e-05

Joint ci ratio: 4.302589e-01	ci left: 6.152596e-05	ci right 9.602139e-05	k: 82	n:1060000
Cons ci ratio: 8.255306e-02	ci left: 2.034995e-03	ci right 2.211139e-03	k: 2249	n:1060000
KS ci ratio: 1.012132e+00	ci left: 7.220707e-06	ci right 2.215992e-05	k: 14	n:1060000
TP53   1060000 perm   778 sec   (1363 perm/sec)   p_kst 1.320755e-05   p_cons 2.121698e-03   p_joint 7.735849e-05

Joint ci ratio: 4.302590e-01	ci left: 6.095095e-05	ci right 9.512400e-05	k: 82	n:1070000
Cons ci ratio: 8.209808e-02	ci left: 2.038860e-03	ci right 2.214320e-03	k: 2274	n:1070000
KS ci ratio: 1.012132e+00	ci left: 7.153224e-06	ci right 2.195282e-05	k: 14	n:1070000
TP53   1070000 perm   789 sec   (1356 perm/sec)   p_kst 1.308411e-05   p_cons 2.125234e-03   p_joint 7.663551e-05

Joint ci ratio: 4.226874e-01	ci left: 6.286619e-05	ci right 9.731744e-05	k: 85	n:1080000
Cons ci ratio: 8.181109e-02	ci left: 2.034493e-03	ci right 2.208935e-03	k: 2290	n:1080000
KS ci ratio: 1.012132e+00	ci left: 7.086990e-06	ci right 2.174955e-05	k: 14	n:1080000
TP53   1080000 perm   802 sec   (1347 perm/sec)   p_kst 1.296296e-05   p_cons 2.120370e-03   p_joint 7.870370e-05

Joint ci ratio: 4.226876e-01	ci left: 6.228943e-05	ci right 9.642463e-05	k: 85	n:1090000
Cons ci ratio: 8.136820e-02	ci left: 2.038296e-03	ci right 2.212073e-03	k: 2315	n:1090000
KS ci ratio: 1.012132e+00	ci left: 7.021972e-06	ci right 2.155002e-05	k: 14	n:1090000
TP53   1090000 perm   814 sec   (1339 perm/sec)   p_kst 1.284404e-05   p_cons 2.123853e-03   p_joint 7.798165e-05

Joint ci ratio: 4.178565e-01	ci left: 6.334905e-05	ci right 9.755744e-05	k: 87	n:1100000
Cons ci ratio: 8.100180e-02	ci left: 2.038469e-03	ci right 2.211442e-03	k: 2336	n:1100000
KS ci ratio: 1.012132e+00	ci left: 6.958135e-06	ci right 2.135411e-05	k: 14	n:1100000
TP53   1100000 perm   826 sec   (1332 perm/sec)   p_kst 1.272727e-05   p_cons 2.123636e-03   p_joint 7.909091e-05

Joint ci ratio: 4.155023e-01	ci left: 6.358477e-05	ci right 9.767339e-05	k: 88	n:1110000
Cons ci ratio: 8.058895e-02	ci left: 2.041289e-03	ci right 2.213577e-03	k: 2360	n:1110000
KS ci ratio: 1.012132e+00	ci left: 6.895449e-06	ci right 2.116173e-05	k: 14	n:1110000
TP53   1110000 perm   838 sec   (1325 perm/sec)   p_kst 1.261261e-05   p_cons 2.126126e-03   p_joint 7.927928e-05

Joint ci ratio: 4.155025e-01	ci left: 6.301705e-05	ci right 9.680132e-05	k: 88	n:1120000
Cons ci ratio: 8.019920e-02	ci left: 2.043187e-03	ci right 2.214762e-03	k: 2383	n:1120000
KS ci ratio: 1.012132e+00	ci left: 6.833883e-06	ci right 2.097279e-05	k: 14	n:1120000
TP53   1120000 perm   851 sec   (1316 perm/sec)   p_kst 1.250000e-05   p_cons 2.127679e-03   p_joint 7.857143e-05

Joint ci ratio: 4.155026e-01	ci left: 6.245937e-05	ci right 9.594467e-05	k: 88	n:1130000
Cons ci ratio: 7.986494e-02	ci left: 2.042450e-03	ci right 2.213215e-03	k: 2403	n:1130000
KS ci ratio: 1.012132e+00	ci left: 6.773406e-06	ci right 2.078719e-05	k: 14	n:1130000
TP53   1130000 perm   863 sec   (1309 perm/sec)   p_kst 1.238938e-05   p_cons 2.126549e-03   p_joint 7.787611e-05

Joint ci ratio: 4.131878e-01	ci left: 6.269722e-05	ci right 9.607120e-05	k: 89	n:1140000
Cons ci ratio: 7.943637e-02	ci left: 2.046887e-03	ci right 2.217062e-03	k: 2429	n:1140000
KS ci ratio: 9.799927e-01	ci left: 7.364392e-06	ci right 2.170185e-05	k: 15	n:1140000
TP53   1140000 perm   876 sec   (1302 perm/sec)   p_kst 1.315789e-05   p_cons 2.130702e-03   p_joint 7.807018e-05

Joint ci ratio: 4.131879e-01	ci left: 6.215202e-05	ci right 9.523581e-05	k: 89	n:1150000
Cons ci ratio: 7.911152e-02	ci left: 2.046134e-03	ci right 2.215519e-03	k: 2449	n:1150000
KS ci ratio: 9.799928e-01	ci left: 7.300354e-06	ci right 2.151314e-05	k: 15	n:1150000
TP53   1150000 perm   889 sec   (1294 perm/sec)   p_kst 1.304348e-05   p_cons 2.129565e-03   p_joint 7.739130e-05

Joint ci ratio: 4.086719e-01	ci left: 6.316211e-05	ci right 9.631624e-05	k: 91	n:1160000
Cons ci ratio: 7.890275e-02	ci left: 2.039480e-03	ci right 2.207849e-03	k: 2462	n:1160000
KS ci ratio: 9.799928e-01	ci left: 7.237419e-06	ci right 2.132769e-05	k: 15	n:1160000
TP53   1160000 perm   901 sec   (1287 perm/sec)   p_kst 1.293103e-05   p_cons 2.122414e-03   p_joint 7.844828e-05

Joint ci ratio: 4.043007e-01	ci left: 6.415688e-05	ci right 9.737629e-05	k: 93	n:1170000
Cons ci ratio: 7.853684e-02	ci left: 2.041320e-03	ci right 2.209023e-03	k: 2485	n:1170000
KS ci ratio: 9.799929e-01	ci left: 7.175561e-06	ci right 2.114540e-05	k: 15	n:1170000
TP53   1170000 perm   914 sec   (1280 perm/sec)   p_kst 1.282051e-05   p_cons 2.123932e-03   p_joint 7.948718e-05

Joint ci ratio: 4.000669e-01	ci left: 6.513664e-05	ci right 9.841655e-05	k: 95	n:1180000
Cons ci ratio: 7.831687e-02	ci left: 2.035652e-03	ci right 2.202400e-03	k: 2499	n:1180000
KS ci ratio: 9.799929e-01	ci left: 7.114751e-06	ci right 2.096620e-05	k: 15	n:1180000
TP53   1180000 perm   927 sec   (1273 perm/sec)   p_kst 1.271186e-05   p_cons 2.117797e-03   p_joint 8.050847e-05

Joint ci ratio: 4.000670e-01	ci left: 6.458927e-05	ci right 9.758953e-05	k: 95	n:1190000
Cons ci ratio: 7.795902e-02	ci left: 2.037496e-03	ci right 2.203597e-03	k: 2522	n:1190000
KS ci ratio: 9.799930e-01	ci left: 7.054963e-06	ci right 2.079001e-05	k: 15	n:1190000
TP53   1190000 perm   939 sec   (1267 perm/sec)   p_kst 1.260504e-05   p_cons 2.119328e-03   p_joint 7.983193e-05

Joint ci ratio: 4.000672e-01	ci left: 6.405102e-05	ci right 9.677629e-05	k: 95	n:1200000
Cons ci ratio: 7.769783e-02	ci left: 2.034408e-03	ci right 2.199677e-03	k: 2539	n:1200000
KS ci ratio: 9.799931e-01	ci left: 6.996171e-06	ci right 2.061677e-05	k: 15	n:1200000
TP53   1200000 perm   952 sec   (1260 perm/sec)   p_kst 1.250000e-05   p_cons 2.115833e-03   p_joint 7.916667e-05

Joint ci ratio: 3.959636e-01	ci left: 6.500912e-05	ci right 9.779399e-05	k: 97	n:1210000
Cons ci ratio: 7.736349e-02	ci left: 2.035424e-03	ci right 2.200032e-03	k: 2561	n:1210000
KS ci ratio: 9.799931e-01	ci left: 6.938352e-06	ci right 2.044638e-05	k: 15	n:1210000
TP53   1210000 perm   965 sec   (1254 perm/sec)   p_kst 1.239669e-05   p_cons 2.116529e-03   p_joint 8.016529e-05

Joint ci ratio: 3.939587e-01	ci left: 6.521451e-05	ci right 9.789308e-05	k: 98	n:1220000
Cons ci ratio: 7.700357e-02	ci left: 2.038033e-03	ci right 2.202050e-03	k: 2585	n:1220000
KS ci ratio: 9.799932e-01	ci left: 6.881480e-06	ci right 2.027879e-05	k: 15	n:1220000
TP53   1220000 perm   978 sec   (1248 perm/sec)   p_kst 1.229508e-05   p_cons 2.118852e-03   p_joint 8.032787e-05

Joint ci ratio: 3.900384e-01	ci left: 6.615006e-05	ci right 9.888270e-05	k: 100	n:1230000
Cons ci ratio: 7.654583e-02	ci left: 2.046183e-03	ci right 2.209834e-03	k: 2616	n:1230000
KS ci ratio: 9.799932e-01	ci left: 6.825533e-06	ci right 2.011392e-05	k: 15	n:1230000
TP53   1230000 perm   991 sec   (1242 perm/sec)   p_kst 1.219512e-05   p_cons 2.126829e-03   p_joint 8.130081e-05

Joint ci ratio: 3.843714e-01	ci left: 6.780044e-05	ci right 1.007390e-04	k: 103	n:1240000
Cons ci ratio: 7.621161e-02	ci left: 2.047876e-03	ci right 2.210915e-03	k: 2639	n:1240000
KS ci ratio: 9.239458e-01	ci left: 7.986412e-06	ci right 2.195043e-05	k: 17	n:1240000
TP53   1240000 perm   1004 sec   (1235 perm/sec)   p_kst 1.370968e-05   p_cons 2.128226e-03   p_joint 8.306452e-05

Joint ci ratio: 3.843715e-01	ci left: 6.725803e-05	ci right 9.993309e-05	k: 103	n:1250000
Cons ci ratio: 7.588173e-02	ci left: 2.049543e-03	ci right 2.211978e-03	k: 2662	n:1250000
KS ci ratio: 9.239458e-01	ci left: 7.922520e-06	ci right 2.177483e-05	k: 17	n:1250000
TP53   1250000 perm   1017 sec   (1229 perm/sec)   p_kst 1.360000e-05   p_cons 2.129600e-03   p_joint 8.240000e-05

Joint ci ratio: 3.881220e-01	ci left: 6.529106e-05	ci right 9.739928e-05	k: 101	n:1260000
Cons ci ratio: 7.557019e-02	ci left: 2.050406e-03	ci right 2.212213e-03	k: 2684	n:1260000
KS ci ratio: 9.239459e-01	ci left: 7.859643e-06	ci right 2.160201e-05	k: 17	n:1260000
TP53   1260000 perm   1030 sec   (1223 perm/sec)   p_kst 1.349206e-05   p_cons 2.130159e-03   p_joint 8.015873e-05

Joint ci ratio: 3.862333e-01	ci left: 6.548771e-05	ci right 9.749604e-05	k: 102	n:1270000
Cons ci ratio: 7.531825e-02	ci left: 2.048167e-03	ci right 2.209235e-03	k: 2702	n:1270000
KS ci ratio: 9.239459e-01	ci left: 7.797756e-06	ci right 2.143192e-05	k: 17	n:1270000
TP53   1270000 perm   1044 sec   (1216 perm/sec)   p_kst 1.338583e-05   p_cons 2.127559e-03   p_joint 8.031496e-05

Joint ci ratio: 3.980005e-01	ci left: 6.075065e-05	ci right 9.158708e-05	k: 96	n:1280000
Cons ci ratio: 7.509647e-02	ci left: 2.044431e-03	ci right 2.204710e-03	k: 2718	n:1280000
KS ci ratio: 9.239460e-01	ci left: 7.736836e-06	ci right 2.126448e-05	k: 17	n:1280000
TP53   1280000 perm   1058 sec   (1210 perm/sec)   p_kst 1.328125e-05   p_cons 2.123437e-03   p_joint 7.500000e-05

Joint ci ratio: 3.980006e-01	ci left: 6.027971e-05	ci right 9.087711e-05	k: 96	n:1290000
Cons ci ratio: 7.486293e-02	ci left: 2.041514e-03	ci right 2.201045e-03	k: 2735	n:1290000
KS ci ratio: 9.239461e-01	ci left: 7.676860e-06	ci right 2.109964e-05	k: 17	n:1290000
TP53   1290000 perm   1071 sec   (1204 perm/sec)   p_kst 1.317829e-05   p_cons 2.120155e-03   p_joint 7.441860e-05

Joint ci ratio: 3.980007e-01	ci left: 5.981602e-05	ci right 9.017806e-05	k: 96	n:1300000
Cons ci ratio: 7.450960e-02	ci left: 2.045436e-03	ci right 2.204487e-03	k: 2761	n:1300000
KS ci ratio: 9.239461e-01	ci left: 7.617807e-06	ci right 2.093734e-05	k: 17	n:1300000
TP53   1300000 perm   1085 sec   (1198 perm/sec)   p_kst 1.307692e-05   p_cons 2.123846e-03   p_joint 7.384615e-05

Joint ci ratio: 3.959648e-01	ci left: 6.004655e-05	ci right 9.032886e-05	k: 97	n:1310000
Cons ci ratio: 7.418789e-02	ci left: 2.047802e-03	ci right 2.206320e-03	k: 2785	n:1310000
KS ci ratio: 9.239462e-01	ci left: 7.559656e-06	ci right 2.077751e-05	k: 17	n:1310000
TP53   1310000 perm   1099 sec   (1192 perm/sec)   p_kst 1.297710e-05   p_cons 2.125954e-03   p_joint 7.404580e-05

Joint ci ratio: 3.959649e-01	ci left: 5.959165e-05	ci right 8.964456e-05	k: 97	n:1320000
Cons ci ratio: 7.384399e-02	ci left: 2.051621e-03	ci right 2.209667e-03	k: 2811	n:1320000
KS ci ratio: 9.239462e-01	ci left: 7.502386e-06	ci right 2.062011e-05	k: 17	n:1320000
TP53   1320000 perm   1113 sec   (1186 perm/sec)   p_kst 1.287879e-05   p_cons 2.129545e-03   p_joint 7.348485e-05

Joint ci ratio: 3.939600e-01	ci left: 5.982080e-05	ci right 8.979673e-05	k: 98	n:1330000
Cons ci ratio: 7.355679e-02	ci left: 2.052432e-03	ci right 2.209899e-03	k: 2833	n:1330000
KS ci ratio: 8.993029e-01	ci left: 8.021027e-06	ci right 2.138921e-05	k: 18	n:1330000
TP53   1330000 perm   1127 sec   (1180 perm/sec)   p_kst 1.353383e-05   p_cons 2.130075e-03   p_joint 7.368421e-05

Joint ci ratio: 3.919852e-01	ci left: 6.004690e-05	ci right 8.994625e-05	k: 99	n:1340000
Cons ci ratio: 7.332439e-02	ci left: 2.050301e-03	ci right 2.207087e-03	k: 2851	n:1340000
KS ci ratio: 8.993030e-01	ci left: 7.961169e-06	ci right 2.122959e-05	k: 18	n:1340000
TP53   1340000 perm   1142 sec   (1173 perm/sec)   p_kst 1.343284e-05   p_cons 2.127612e-03   p_joint 7.388060e-05

Joint ci ratio: 3.900398e-01	ci left: 6.027002e-05	ci right 9.009320e-05	k: 100	n:1350000
Cons ci ratio: 7.308143e-02	ci left: 2.048930e-03	ci right 2.205070e-03	k: 2870	n:1350000
KS ci ratio: 8.765318e-01	ci left: 8.473533e-06	ci right 2.197832e-05	k: 19	n:1350000
TP53   1350000 perm   1157 sec   (1167 perm/sec)   p_kst 1.407407e-05   p_cons 2.125926e-03   p_joint 7.407407e-05

Joint ci ratio: 3.919854e-01	ci left: 5.916385e-05	ci right 8.862352e-05	k: 99	n:1360000
Cons ci ratio: 7.287878e-02	ci left: 2.045415e-03	ci right 2.200836e-03	k: 2886	n:1360000
KS ci ratio: 8.765319e-01	ci left: 8.411227e-06	ci right 2.181672e-05	k: 19	n:1360000
TP53   1360000 perm   1172 sec   (1161 perm/sec)   p_kst 1.397059e-05   p_cons 2.122059e-03   p_joint 7.279412e-05

Joint ci ratio: 3.900401e-01	ci left: 5.939016e-05	ci right 8.877798e-05	k: 100	n:1370000
Cons ci ratio: 7.264020e-02	ci left: 2.044101e-03	ci right 2.198892e-03	k: 2905	n:1370000
KS ci ratio: 8.765319e-01	ci left: 8.349831e-06	ci right 2.165747e-05	k: 19	n:1370000
TP53   1370000 perm   1187 sec   (1154 perm/sec)   p_kst 1.386861e-05   p_cons 2.120438e-03   p_joint 7.299270e-05

Joint ci ratio: 3.881234e-01	ci left: 5.961354e-05	ci right 8.892985e-05	k: 101	n:1380000
Cons ci ratio: 7.234201e-02	ci left: 2.046365e-03	ci right 2.200664e-03	k: 2929	n:1380000
KS ci ratio: 8.765320e-01	ci left: 8.289325e-06	ci right 2.150054e-05	k: 19	n:1380000
TP53   1380000 perm   1202 sec   (1148 perm/sec)   p_kst 1.376812e-05   p_cons 2.122464e-03   p_joint 7.318841e-05

Joint ci ratio: 3.881235e-01	ci left: 5.918466e-05	ci right 8.829007e-05	k: 101	n:1390000
Cons ci ratio: 7.210865e-02	ci left: 2.045065e-03	ci right 2.198748e-03	k: 2948	n:1390000
KS ci ratio: 8.765320e-01	ci left: 8.229689e-06	ci right 2.134586e-05	k: 19	n:1390000
TP53   1390000 perm   1217 sec   (1142 perm/sec)   p_kst 1.366906e-05   p_cons 2.120863e-03   p_joint 7.266187e-05

Joint ci ratio: 3.881236e-01	ci left: 5.876191e-05	ci right 8.765943e-05	k: 101	n:1400000
Cons ci ratio: 7.187753e-02	ci left: 2.043784e-03	ci right 2.196859e-03	k: 2967	n:1400000
KS ci ratio: 8.765321e-01	ci left: 8.170906e-06	ci right 2.119339e-05	k: 19	n:1400000
TP53   1400000 perm   1233 sec   (1136 perm/sec)   p_kst 1.357143e-05   p_cons 2.119286e-03   p_joint 7.214286e-05

Joint ci ratio: 3.862348e-01	ci left: 5.898534e-05	ci right 8.781566e-05	k: 102	n:1410000
Cons ci ratio: 7.170879e-02	ci left: 2.039040e-03	ci right 2.191386e-03	k: 2981	n:1410000
KS ci ratio: 8.765321e-01	ci left: 8.112956e-06	ci right 2.104308e-05	k: 19	n:1410000
TP53   1410000 perm   1247 sec   (1131 perm/sec)   p_kst 1.347518e-05   p_cons 2.114184e-03   p_joint 7.234043e-05

Joint ci ratio: 3.862349e-01	ci left: 5.856995e-05	ci right 8.719725e-05	k: 102	n:1420000
Cons ci ratio: 7.143379e-02	ci left: 2.040588e-03	ci right 2.192440e-03	k: 3004	n:1420000
KS ci ratio: 8.765322e-01	ci left: 8.055822e-06	ci right 2.089489e-05	k: 19	n:1420000
TP53   1420000 perm   1262 sec   (1125 perm/sec)   p_kst 1.338028e-05   p_cons 2.115493e-03   p_joint 7.183099e-05

Joint ci ratio: 3.862350e-01	ci left: 5.816037e-05	ci right 8.658748e-05	k: 102	n:1430000
Cons ci ratio: 7.115015e-02	ci left: 2.042802e-03	ci right 2.194191e-03	k: 3028	n:1430000
KS ci ratio: 8.765322e-01	ci left: 7.999488e-06	ci right 2.074877e-05	k: 19	n:1430000
TP53   1430000 perm   1277 sec   (1120 perm/sec)   p_kst 1.328671e-05   p_cons 2.117483e-03   p_joint 7.132867e-05

Joint ci ratio: 3.862351e-01	ci left: 5.775648e-05	ci right 8.598618e-05	k: 102	n:1440000
Cons ci ratio: 7.096310e-02	ci left: 2.039530e-03	ci right 2.190262e-03	k: 3044	n:1440000
KS ci ratio: 8.765323e-01	ci left: 7.943936e-06	ci right 2.060468e-05	k: 19	n:1440000
TP53   1440000 perm   1292 sec   (1115 perm/sec)   p_kst 1.319444e-05   p_cons 2.113889e-03   p_joint 7.083333e-05

Joint ci ratio: 3.862352e-01	ci left: 5.735815e-05	ci right 8.539318e-05	k: 102	n:1450000
Cons ci ratio: 7.069656e-02	ci left: 2.041045e-03	ci right 2.191300e-03	k: 3067	n:1450000
KS ci ratio: 8.765323e-01	ci left: 7.889150e-06	ci right 2.046258e-05	k: 19	n:1450000
TP53   1450000 perm   1307 sec   (1109 perm/sec)   p_kst 1.310345e-05   p_cons 2.115172e-03   p_joint 7.034483e-05

Joint ci ratio: 3.862353e-01	ci left: 5.696529e-05	ci right 8.480830e-05	k: 102	n:1460000
Cons ci ratio: 7.042159e-02	ci left: 2.043214e-03	ci right 2.193019e-03	k: 3091	n:1460000
KS ci ratio: 8.765323e-01	ci left: 7.835114e-06	ci right 2.032243e-05	k: 19	n:1460000
TP53   1460000 perm   1324 sec   (1102 perm/sec)   p_kst 1.301370e-05   p_cons 2.117123e-03   p_joint 6.986301e-05

Joint ci ratio: 3.825390e-01	ci left: 5.780684e-05	ci right 8.572276e-05	k: 104	n:1470000
Cons ci ratio: 7.016108e-02	ci left: 2.044686e-03	ci right 2.194022e-03	k: 3114	n:1470000
KS ci ratio: 8.554077e-01	ci left: 8.310577e-06	ci right 2.101242e-05	k: 20	n:1470000
TP53   1470000 perm   1340 sec   (1097 perm/sec)   p_kst 1.360544e-05   p_cons 2.118367e-03   p_joint 7.074830e-05

Joint ci ratio: 3.789469e-01	ci left: 5.863828e-05	ci right 8.662364e-05	k: 106	n:1480000
Cons ci ratio: 6.986998e-02	ci left: 2.048130e-03	ci right 2.197072e-03	k: 3140	n:1480000
KS ci ratio: 8.357403e-01	ci left: 8.783353e-06	ci right 2.168960e-05	k: 21	n:1480000
TP53   1480000 perm   1355 sec   (1092 perm/sec)   p_kst 1.418919e-05   p_cons 2.121622e-03   p_joint 7.162162e-05

Joint ci ratio: 3.789470e-01	ci left: 5.824473e-05	ci right 8.604228e-05	k: 106	n:1490000
Cons ci ratio: 6.968176e-02	ci left: 2.045595e-03	ci right 2.193935e-03	k: 3157	n:1490000
KS ci ratio: 8.357404e-01	ci left: 8.724404e-06	ci right 2.154403e-05	k: 21	n:1490000
TP53   1490000 perm   1371 sec   (1087 perm/sec)   p_kst 1.409396e-05   p_cons 2.118792e-03   p_joint 7.114094e-05

Joint ci ratio: 3.789471e-01	ci left: 5.785643e-05	ci right 8.546867e-05	k: 106	n:1500000
Cons ci ratio: 6.940749e-02	ci left: 2.048334e-03	ci right 2.196265e-03	k: 3182	n:1500000
KS ci ratio: 8.357404e-01	ci left: 8.666241e-06	ci right 2.140041e-05	k: 21	n:1500000
TP53   1500000 perm   1387 sec   (1082 perm/sec)   p_kst 1.400000e-05   p_cons 2.121333e-03   p_joint 7.066667e-05

Joint ci ratio: 3.754542e-01	ci left: 5.867221e-05	ci right 8.635215e-05	k: 108	n:1510000
Cons ci ratio: 6.920131e-02	ci left: 2.047134e-03	ci right 2.194521e-03	k: 3201	n:1510000
KS ci ratio: 8.357404e-01	ci left: 8.608848e-06	ci right 2.125868e-05	k: 21	n:1510000
TP53   1510000 perm   1402 sec   (1077 perm/sec)   p_kst 1.390728e-05   p_cons 2.119868e-03   p_joint 7.152318e-05

Joint ci ratio: 3.703914e-01	ci left: 6.007493e-05	ci right 8.794187e-05	k: 111	n:1520000
Cons ci ratio: 6.897550e-02	ci left: 2.047243e-03	ci right 2.194138e-03	k: 3222	n:1520000
KS ci ratio: 8.357405e-01	ci left: 8.552211e-06	ci right 2.111882e-05	k: 21	n:1520000
TP53   1520000 perm   1418 sec   (1072 perm/sec)   p_kst 1.381579e-05   p_cons 2.119737e-03   p_joint 7.302632e-05

Joint ci ratio: 3.687488e-01	ci left: 6.027518e-05	ci right 8.808111e-05	k: 112	n:1530000
Cons ci ratio: 6.881569e-02	ci left: 2.043497e-03	ci right 2.189770e-03	k: 3237	n:1530000
KS ci ratio: 8.357405e-01	ci left: 8.496314e-06	ci right 2.098079e-05	k: 21	n:1530000
TP53   1530000 perm   1433 sec   (1067 perm/sec)   p_kst 1.372549e-05   p_cons 2.115686e-03   p_joint 7.320261e-05

Joint ci ratio: 3.655281e-01	ci left: 6.106268e-05	ci right 8.892714e-05	k: 114	n:1540000
Cons ci ratio: 6.861472e-02	ci left: 2.042353e-03	ci right 2.188101e-03	k: 3256	n:1540000
KS ci ratio: 8.173701e-01	ci left: 8.952802e-06	ci right 2.162866e-05	k: 22	n:1540000
TP53   1540000 perm   1449 sec   (1063 perm/sec)   p_kst 1.428571e-05   p_cons 2.114286e-03   p_joint 7.402597e-05

Joint ci ratio: 3.608514e-01	ci left: 6.242761e-05	ci right 9.046476e-05	k: 117	n:1550000
Cons ci ratio: 6.837369e-02	ci left: 2.043762e-03	ci right 2.189077e-03	k: 3279	n:1550000
KS ci ratio: 8.173702e-01	ci left: 8.895042e-06	ci right 2.148912e-05	k: 22	n:1550000
TP53   1550000 perm   1465 sec   (1058 perm/sec)   p_kst 1.419355e-05   p_cons 2.115484e-03   p_joint 7.548387e-05

Joint ci ratio: 3.608515e-01	ci left: 6.202743e-05	ci right 8.988486e-05	k: 117	n:1560000
Cons ci ratio: 6.817656e-02	ci left: 2.042632e-03	ci right 2.187431e-03	k: 3298	n:1560000
KS ci ratio: 8.173702e-01	ci left: 8.838022e-06	ci right 2.135137e-05	k: 22	n:1560000
TP53   1560000 perm   1484 sec   (1051 perm/sec)   p_kst 1.410256e-05   p_cons 2.114103e-03   p_joint 7.500000e-05

Joint ci ratio: 3.593321e-01	ci left: 6.221167e-05	ci right 9.000667e-05	k: 118	n:1570000
Cons ci ratio: 6.797086e-02	ci left: 2.042144e-03	ci right 2.186454e-03	k: 3318	n:1570000
KS ci ratio: 8.001603e-01	ci left: 9.286663e-06	ci right 2.198163e-05	k: 23	n:1570000
TP53   1570000 perm   1502 sec   (1045 perm/sec)   p_kst 1.464968e-05   p_cons 2.113376e-03   p_joint 7.515924e-05

Joint ci ratio: 3.563499e-01	ci left: 6.296996e-05	ci right 9.081615e-05	k: 120	n:1580000
Cons ci ratio: 6.780773e-02	ci left: 2.039173e-03	ci right 2.182915e-03	k: 3334	n:1580000
KS ci ratio: 8.001603e-01	ci left: 9.227887e-06	ci right 2.184251e-05	k: 23	n:1580000
TP53   1580000 perm   1519 sec   (1040 perm/sec)   p_kst 1.455696e-05   p_cons 2.110127e-03   p_joint 7.594937e-05

Joint ci ratio: 3.548864e-01	ci left: 6.314667e-05	ci right 9.092987e-05	k: 121	n:1590000
Cons ci ratio: 6.755491e-02	ci left: 2.041805e-03	ci right 2.185175e-03	k: 3359	n:1590000
KS ci ratio: 8.001604e-01	ci left: 9.169850e-06	ci right 2.170514e-05	k: 23	n:1590000
TP53   1590000 perm   1535 sec   (1036 perm/sec)   p_kst 1.446541e-05   p_cons 2.112579e-03   p_joint 7.610063e-05

Joint ci ratio: 3.520126e-01	ci left: 6.389104e-05	ci right 9.172208e-05	k: 123	n:1600000
Cons ci ratio: 6.734479e-02	ci left: 2.041948e-03	ci right 2.184864e-03	k: 3380	n:1600000
KS ci ratio: 8.001604e-01	ci left: 9.112538e-06	ci right 2.156948e-05	k: 23	n:1600000
TP53   1600000 perm   1551 sec   (1032 perm/sec)   p_kst 1.437500e-05   p_cons 2.112500e-03   p_joint 7.687500e-05

Joint ci ratio: 3.506017e-01	ci left: 6.406051e-05	ci right 9.182809e-05	k: 124	n:1610000
Cons ci ratio: 6.714651e-02	ci left: 2.041478e-03	ci right 2.183925e-03	k: 3400	n:1610000
KS ci ratio: 8.001604e-01	ci left: 9.055938e-06	ci right 2.143551e-05	k: 23	n:1610000
TP53   1610000 perm   1568 sec   (1027 perm/sec)   p_kst 1.428571e-05   p_cons 2.111801e-03   p_joint 7.701863e-05

Joint ci ratio: 3.492077e-01	ci left: 6.422811e-05	ci right 9.193257e-05	k: 125	n:1620000
Cons ci ratio: 6.690099e-02	ci left: 2.044050e-03	ci right 2.186134e-03	k: 3425	n:1620000
KS ci ratio: 8.001605e-01	ci left: 9.000037e-06	ci right 2.130319e-05	k: 23	n:1620000
TP53   1620000 perm   1585 sec   (1022 perm/sec)   p_kst 1.419753e-05   p_cons 2.114198e-03   p_joint 7.716049e-05

Joint ci ratio: 3.478301e-01	ci left: 6.439387e-05	ci right 9.203555e-05	k: 126	n:1630000
Cons ci ratio: 6.667751e-02	ci left: 2.045385e-03	ci right 2.187068e-03	k: 3448	n:1630000
KS ci ratio: 7.839937e-01	ci left: 9.433920e-06	ci right 2.190796e-05	k: 24	n:1630000
TP53   1630000 perm   1602 sec   (1018 perm/sec)   p_kst 1.472393e-05   p_cons 2.115337e-03   p_joint 7.730061e-05

Joint ci ratio: 3.478302e-01	ci left: 6.400122e-05	ci right 9.147436e-05	k: 126	n:1640000
Cons ci ratio: 6.648505e-02	ci left: 2.044905e-03	ci right 2.186131e-03	k: 3468	n:1640000
KS ci ratio: 7.839938e-01	ci left: 9.376395e-06	ci right 2.177437e-05	k: 24	n:1640000
TP53   1640000 perm   1622 sec   (1011 perm/sec)   p_kst 1.463415e-05   p_cons 2.114634e-03   p_joint 7.682927e-05

Joint ci ratio: 3.478303e-01	ci left: 6.361333e-05	ci right 9.091998e-05	k: 126	n:1650000
Cons ci ratio: 6.625619e-02	ci left: 2.046816e-03	ci right 2.187668e-03	k: 3492	n:1650000
KS ci ratio: 7.839938e-01	ci left: 9.319569e-06	ci right 2.164241e-05	k: 24	n:1650000
TP53   1650000 perm   1639 sec   (1007 perm/sec)   p_kst 1.454545e-05   p_cons 2.116364e-03   p_joint 7.636364e-05

Joint ci ratio: 3.478303e-01	ci left: 6.323012e-05	ci right 9.037227e-05	k: 126	n:1660000
Cons ci ratio: 6.602028e-02	ci left: 2.049297e-03	ci right 2.189799e-03	k: 3517	n:1660000
KS ci ratio: 7.839939e-01	ci left: 9.263427e-06	ci right 2.151203e-05	k: 24	n:1660000
TP53   1660000 perm   1656 sec   (1003 perm/sec)   p_kst 1.445783e-05   p_cons 2.118675e-03   p_joint 7.590361e-05

Joint ci ratio: 3.478304e-01	ci left: 6.285149e-05	ci right 8.983112e-05	k: 126	n:1670000
Cons ci ratio: 6.586142e-02	ci left: 2.047037e-03	ci right 2.187034e-03	k: 3534	n:1670000
KS ci ratio: 7.839939e-01	ci left: 9.207957e-06	ci right 2.138322e-05	k: 24	n:1670000
TP53   1670000 perm   1673 sec   (998 perm/sec)   p_kst 1.437126e-05   p_cons 2.116168e-03   p_joint 7.544910e-05

Joint ci ratio: 3.563507e-01	ci left: 5.922173e-05	ci right 8.541047e-05	k: 120	n:1680000
Cons ci ratio: 6.571298e-02	ci left: 2.044220e-03	ci right 2.183696e-03	k: 3550	n:1680000
KS ci ratio: 7.839939e-01	ci left: 9.153147e-06	ci right 2.125594e-05	k: 24	n:1680000
TP53   1680000 perm   1690 sec   (994 perm/sec)   p_kst 1.428571e-05   p_cons 2.113095e-03   p_joint 7.142857e-05

Joint ci ratio: 4.251729e-01	ci left: 3.964616e-05	ci right 6.153675e-05	k: 84	n:1690000
Cons ci ratio: 6.547362e-02	ci left: 2.047256e-03	ci right 2.186412e-03	k: 3576	n:1690000
KS ci ratio: 7.543981e-01	ci left: 1.004977e-05	ci right 2.254195e-05	k: 26	n:1690000
TP53   1690000 perm   1707 sec   (990 perm/sec)   p_kst 1.538462e-05   p_cons 2.115976e-03   p_joint 4.970414e-05

Joint ci ratio: 4.251729e-01	ci left: 3.941294e-05	ci right 6.117477e-05	k: 84	n:1700000
Cons ci ratio: 6.523687e-02	ci left: 2.050258e-03	ci right 2.189094e-03	k: 3602	n:1700000
KS ci ratio: 7.543981e-01	ci left: 9.990649e-06	ci right 2.240935e-05	k: 26	n:1700000
TP53   1700000 perm   1726 sec   (985 perm/sec)   p_kst 1.529412e-05   p_cons 2.118824e-03   p_joint 4.941176e-05

Joint ci ratio: 4.251730e-01	ci left: 3.918246e-05	ci right 6.081702e-05	k: 84	n:1710000
Cons ci ratio: 6.508359e-02	ci left: 2.048047e-03	ci right 2.186396e-03	k: 3619	n:1710000
KS ci ratio: 7.543982e-01	ci left: 9.932224e-06	ci right 2.227830e-05	k: 26	n:1710000
TP53   1710000 perm   1744 sec   (981 perm/sec)   p_kst 1.520468e-05   p_cons 2.116374e-03   p_joint 4.912281e-05

Joint ci ratio: 4.226938e-01	ci left: 3.947401e-05	ci right 6.110651e-05	k: 85	n:1720000
Cons ci ratio: 6.488670e-02	ci left: 2.048723e-03	ci right 2.186683e-03	k: 3641	n:1720000
KS ci ratio: 7.408041e-01	ci left: 1.034489e-05	ci right 2.283921e-05	k: 27	n:1720000
TP53   1720000 perm   1761 sec   (977 perm/sec)   p_kst 1.569767e-05   p_cons 2.116860e-03   p_joint 4.941860e-05

Joint ci ratio: 4.202574e-01	ci left: 3.976256e-05	ci right 6.139230e-05	k: 86	n:1730000
Cons ci ratio: 6.466507e-02	ci left: 2.051098e-03	ci right 2.188728e-03	k: 3666	n:1730000
KS ci ratio: 7.408042e-01	ci left: 1.028509e-05	ci right 2.270719e-05	k: 27	n:1730000
TP53   1730000 perm   1780 sec   (972 perm/sec)   p_kst 1.560694e-05   p_cons 2.119075e-03   p_joint 4.971098e-05

Joint ci ratio: 4.202575e-01	ci left: 3.953403e-05	ci right 6.103947e-05	k: 86	n:1740000
Cons ci ratio: 6.445443e-02	ci left: 2.052880e-03	ci right 2.190165e-03	k: 3690	n:1740000
KS ci ratio: 7.408042e-01	ci left: 1.022598e-05	ci right 2.257669e-05	k: 27	n:1740000
TP53   1740000 perm   1799 sec   (967 perm/sec)   p_kst 1.551724e-05   p_cons 2.120690e-03   p_joint 4.942529e-05

Joint ci ratio: 4.178628e-01	ci left: 3.981929e-05	ci right 6.132203e-05	k: 87	n:1750000
Cons ci ratio: 6.427186e-02	ci left: 2.052956e-03	ci right 2.189843e-03	k: 3711	n:1750000
KS ci ratio: 7.408042e-01	ci left: 1.016755e-05	ci right 2.244768e-05	k: 27	n:1750000
TP53   1750000 perm   1817 sec   (963 perm/sec)   p_kst 1.542857e-05   p_cons 2.120571e-03   p_joint 4.971429e-05

Joint ci ratio: 4.178628e-01	ci left: 3.959304e-05	ci right 6.097361e-05	k: 87	n:1760000
Cons ci ratio: 6.412527e-02	ci left: 2.050796e-03	ci right 2.187214e-03	k: 3728	n:1760000
KS ci ratio: 7.408043e-01	ci left: 1.010978e-05	ci right 2.232014e-05	k: 27	n:1760000
TP53   1760000 perm   1835 sec   (959 perm/sec)   p_kst 1.534091e-05   p_cons 2.118182e-03   p_joint 4.943182e-05

Joint ci ratio: 4.178629e-01	ci left: 3.936935e-05	ci right 6.062913e-05	k: 87	n:1770000
Cons ci ratio: 6.397967e-02	ci left: 2.048660e-03	ci right 2.184616e-03	k: 3745	n:1770000
KS ci ratio: 7.408043e-01	ci left: 1.005266e-05	ci right 2.219404e-05	k: 27	n:1770000
TP53   1770000 perm   1854 sec   (955 perm/sec)   p_kst 1.525424e-05   p_cons 2.115819e-03   p_joint 4.915254e-05

Joint ci ratio: 4.155087e-01	ci left: 3.965107e-05	ci right 6.090890e-05	k: 88	n:1780000
Cons ci ratio: 6.382656e-02	ci left: 2.047101e-03	ci right 2.182617e-03	k: 3763	n:1780000
KS ci ratio: 7.408043e-01	ci left: 9.996186e-06	ci right 2.206935e-05	k: 27	n:1780000
TP53   1780000 perm   1874 sec   (950 perm/sec)   p_kst 1.516854e-05   p_cons 2.114045e-03   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: 6.367455e-02	ci left: 2.045561e-03	ci right 2.180639e-03	k: 3781	n:1790000
KS ci ratio: 7.408044e-01	ci left: 9.940341e-06	ci right 2.194606e-05	k: 27	n:1790000
TP53   1790000 perm   1894 sec   (945 perm/sec)   p_kst 1.508380e-05   p_cons 2.112291e-03   p_joint 4.916201e-05

Joint ci ratio: 4.109172e-01	ci left: 4.020609e-05	ci right 6.145814e-05	k: 90	n:1800000
Cons ci ratio: 6.351525e-02	ci left: 2.044584e-03	ci right 2.179248e-03	k: 3800	n:1800000
KS ci ratio: 7.279197e-01	ci left: 1.033658e-05	ci right 2.248203e-05	k: 28	n:1800000
TP53   1800000 perm   1913 sec   (941 perm/sec)   p_kst 1.555556e-05   p_cons 2.111111e-03   p_joint 5.000000e-05

Joint ci ratio: 4.109172e-01	ci left: 3.998396e-05	ci right 6.111859e-05	k: 90	n:1810000
Cons ci ratio: 6.344040e-02	ci left: 2.038181e-03	ci right 2.172260e-03	k: 3809	n:1810000
KS ci ratio: 7.279197e-01	ci left: 1.027947e-05	ci right 2.235782e-05	k: 28	n:1810000
TP53   1810000 perm   1931 sec   (937 perm/sec)   p_kst 1.546961e-05   p_cons 2.104420e-03   p_joint 4.972376e-05

Joint ci ratio: 4.109173e-01	ci left: 3.976426e-05	ci right 6.078278e-05	k: 90	n:1820000
Cons ci ratio: 6.328284e-02	ci left: 2.037257e-03	ci right 2.170929e-03	k: 3828	n:1820000
KS ci ratio: 7.279197e-01	ci left: 1.022299e-05	ci right 2.223498e-05	k: 28	n:1820000
TP53   1820000 perm   1949 sec   (934 perm/sec)   p_kst 1.538462e-05   p_cons 2.103297e-03   p_joint 4.945055e-05

Joint ci ratio: 3.789495e-01	ci left: 4.742325e-05	ci right 7.005638e-05	k: 106	n:1830000
Cons ci ratio: 6.999590e-02	ci left: 1.651031e-03	ci right 1.771320e-03	k: 3130	n:1830000
KS ci ratio: 7.279198e-01	ci left: 1.016713e-05	ci right 2.211347e-05	k: 28	n:1830000
TP53   1830000 perm   1969 sec   (930 perm/sec)   p_kst 1.530055e-05   p_cons 1.710383e-03   p_joint 5.792350e-05

Joint ci ratio: 3.789496e-01	ci left: 4.716551e-05	ci right 6.967564e-05	k: 106	n:1840000
Cons ci ratio: 6.988452e-02	ci left: 1.647397e-03	ci right 1.767223e-03	k: 3140	n:1840000
KS ci ratio: 7.279198e-01	ci left: 1.011187e-05	ci right 2.199329e-05	k: 28	n:1840000
TP53   1840000 perm   1988 sec   (926 perm/sec)   p_kst 1.521739e-05   p_cons 1.706522e-03   p_joint 5.760870e-05

Joint ci ratio: 3.789496e-01	ci left: 4.691056e-05	ci right 6.929901e-05	k: 106	n:1850000
Cons ci ratio: 6.970722e-02	ci left: 1.646990e-03	ci right 1.766470e-03	k: 3156	n:1850000
KS ci ratio: 7.279198e-01	ci left: 1.005721e-05	ci right 2.187441e-05	k: 28	n:1850000
TP53   1850000 perm   2008 sec   (921 perm/sec)   p_kst 1.513514e-05   p_cons 1.705946e-03   p_joint 5.729730e-05

Joint ci ratio: 3.771911e-01	ci left: 4.714490e-05	ci right 6.951493e-05	k: 107	n:1860000
Cons ci ratio: 6.955323e-02	ci left: 1.645531e-03	ci right 1.764631e-03	k: 3170	n:1860000
KS ci ratio: 7.279199e-01	ci left: 1.000314e-05	ci right 2.175681e-05	k: 28	n:1860000
TP53   1860000 perm   2027 sec   (918 perm/sec)   p_kst 1.505376e-05   p_cons 1.704301e-03   p_joint 5.752688e-05

Joint ci ratio: 3.754569e-01	ci left: 4.737697e-05	ci right 6.972830e-05	k: 108	n:1870000
Cons ci ratio: 6.941117e-02	ci left: 1.643563e-03	ci right 1.762267e-03	k: 3183	n:1870000
KS ci ratio: 7.279199e-01	ci left: 9.949646e-06	ci right 2.164046e-05	k: 28	n:1870000
TP53   1870000 perm   2046 sec   (914 perm/sec)   p_kst 1.497326e-05   p_cons 1.702139e-03   p_joint 5.775401e-05

Joint ci ratio: 3.754569e-01	ci left: 4.712496e-05	ci right 6.935741e-05	k: 108	n:1880000
Cons ci ratio: 6.924828e-02	ci left: 1.642661e-03	ci right 1.761010e-03	k: 3198	n:1880000
KS ci ratio: 7.279199e-01	ci left: 9.896722e-06	ci right 2.152535e-05	k: 28	n:1880000
TP53   1880000 perm   2066 sec   (910 perm/sec)   p_kst 1.489362e-05   p_cons 1.701064e-03   p_joint 5.744681e-05

Joint ci ratio: 3.754570e-01	ci left: 4.687562e-05	ci right 6.899044e-05	k: 108	n:1890000
Cons ci ratio: 6.910808e-02	ci left: 1.640729e-03	ci right 1.758690e-03	k: 3211	n:1890000
KS ci ratio: 7.279199e-01	ci left: 9.844359e-06	ci right 2.141146e-05	k: 28	n:1890000
TP53   1890000 perm   2086 sec   (906 perm/sec)   p_kst 1.481481e-05   p_cons 1.698942e-03   p_joint 5.714286e-05

Joint ci ratio: 3.789499e-01	ci left: 4.567607e-05	ci right 6.747537e-05	k: 106	n:1900000
Cons ci ratio: 6.891523e-02	ci left: 1.641403e-03	ci right 1.759071e-03	k: 3229	n:1900000
KS ci ratio: 7.279200e-01	ci left: 9.792546e-06	ci right 2.129877e-05	k: 28	n:1900000
TP53   1900000 perm   2105 sec   (903 perm/sec)   p_kst 1.473684e-05   p_cons 1.699474e-03   p_joint 5.578947e-05

Joint ci ratio: 3.771914e-01	ci left: 4.591073e-05	ci right 6.769518e-05	k: 107	n:1910000
Cons ci ratio: 6.876642e-02	ci left: 1.640013e-03	ci right 1.757317e-03	k: 3243	n:1910000
KS ci ratio: 7.279200e-01	ci left: 9.741276e-06	ci right 2.118726e-05	k: 28	n:1910000
TP53   1910000 perm   2124 sec   (899 perm/sec)   p_kst 1.465969e-05   p_cons 1.697906e-03   p_joint 5.602094e-05

Joint ci ratio: 3.737465e-01	ci left: 4.661499e-05	ci right 6.848212e-05	k: 109	n:1920000
Cons ci ratio: 6.858694e-02	ci left: 1.640174e-03	ci right 1.757171e-03	k: 3260	n:1920000
KS ci ratio: 7.040469e-01	ci left: 1.054215e-05	ci right 2.230558e-05	k: 30	n:1920000
TP53   1920000 perm   2144 sec   (896 perm/sec)   p_kst 1.562500e-05   p_cons 1.697917e-03   p_joint 5.677083e-05

Joint ci ratio: 3.720591e-01	ci left: 4.684304e-05	ci right 6.869377e-05	k: 110	n:1930000
Cons ci ratio: 6.837752e-02	ci left: 1.641861e-03	ci right 1.758606e-03	k: 3280	n:1930000
KS ci ratio: 7.040469e-01	ci left: 1.048752e-05	ci right 2.219001e-05	k: 30	n:1930000
TP53   1930000 perm   2163 sec   (892 perm/sec)   p_kst 1.554404e-05   p_cons 1.699482e-03   p_joint 5.699482e-05

Joint ci ratio: 3.720592e-01	ci left: 4.660157e-05	ci right 6.833968e-05	k: 110	n:1940000
Cons ci ratio: 6.821143e-02	ci left: 1.641504e-03	ci right 1.757930e-03	k: 3296	n:1940000
KS ci ratio: 7.040470e-01	ci left: 1.043346e-05	ci right 2.207563e-05	k: 30	n:1940000
TP53   1940000 perm   2182 sec   (889 perm/sec)   p_kst 1.546392e-05   p_cons 1.698969e-03   p_joint 5.670103e-05

Joint ci ratio: 3.737467e-01	ci left: 4.589783e-05	ci right 6.742856e-05	k: 109	n:1950000
Cons ci ratio: 6.803625e-02	ci left: 1.641656e-03	ci right 1.757781e-03	k: 3313	n:1950000
KS ci ratio: 7.040470e-01	ci left: 1.037996e-05	ci right 2.196242e-05	k: 30	n:1950000
TP53   1950000 perm   2202 sec   (885 perm/sec)   p_kst 1.538462e-05   p_cons 1.698974e-03   p_joint 5.589744e-05

Joint ci ratio: 3.737468e-01	ci left: 4.566366e-05	ci right 6.708453e-05	k: 109	n:1960000
Cons ci ratio: 6.780127e-02	ci left: 1.644815e-03	ci right 1.760747e-03	k: 3336	n:1960000
KS ci ratio: 6.929588e-01	ci left: 1.074645e-05	ci right 2.244994e-05	k: 31	n:1960000
TP53   1960000 perm   2222 sec   (882 perm/sec)   p_kst 1.581633e-05   p_cons 1.702041e-03   p_joint 5.561224e-05

Joint ci ratio: 3.737468e-01	ci left: 4.543186e-05	ci right 6.674401e-05	k: 109	n:1970000
Cons ci ratio: 6.766966e-02	ci left: 1.642953e-03	ci right 1.758520e-03	k: 3349	n:1970000
KS ci ratio: 6.929588e-01	ci left: 1.069190e-05	ci right 2.233598e-05	k: 31	n:1970000
TP53   1970000 perm   2242 sec   (879 perm/sec)   p_kst 1.573604e-05   p_cons 1.700000e-03   p_joint 5.532995e-05

Joint ci ratio: 3.737469e-01	ci left: 4.520240e-05	ci right 6.640692e-05	k: 109	n:1980000
Cons ci ratio: 6.749861e-02	ci left: 1.643096e-03	ci right 1.758369e-03	k: 3366	n:1980000
KS ci ratio: 6.929589e-01	ci left: 1.063790e-05	ci right 2.222317e-05	k: 31	n:1980000
TP53   1980000 perm   2261 sec   (876 perm/sec)   p_kst 1.565657e-05   p_cons 1.700000e-03   p_joint 5.505051e-05

Joint ci ratio: 3.737469e-01	ci left: 4.497526e-05	ci right 6.607322e-05	k: 109	n:1990000
Cons ci ratio: 6.736875e-02	ci left: 1.641262e-03	ci right 1.756176e-03	k: 3379	n:1990000
KS ci ratio: 6.929589e-01	ci left: 1.058444e-05	ci right 2.211150e-05	k: 31	n:1990000
TP53   1990000 perm   2281 sec   (872 perm/sec)   p_kst 1.557789e-05   p_cons 1.697990e-03   p_joint 5.477387e-05

Joint ci ratio: 3.807339e-01	ci left: 4.293999e-05	ci right 6.355410e-05	k: 105	n:2000000
Cons ci ratio: 6.722971e-02	ci left: 1.639938e-03	ci right 1.754513e-03	k: 3393	n:2000000
KS ci ratio: 6.929589e-01	ci left: 1.053152e-05	ci right 2.200094e-05	k: 31	n:2000000
TP53   2000000 perm   2301 sec   (869 perm/sec)   p_kst 1.550000e-05   p_cons 1.696500e-03   p_joint 5.250000e-05

Joint ci ratio: 3.881279e-01	ci left: 4.092862e-05	ci right 6.105646e-05	k: 101	n:2010000
Cons ci ratio: 6.708167e-02	ci left: 1.639116e-03	ci right 1.753372e-03	k: 3408	n:2010000
KS ci ratio: 6.929590e-01	ci left: 1.047913e-05	ci right 2.189148e-05	k: 31	n:2010000
TP53   2010000 perm   2321 sec   (866 perm/sec)   p_kst 1.542289e-05   p_cons 1.695522e-03   p_joint 5.024876e-05

Joint ci ratio: 3.862391e-01	ci left: 4.117286e-05	ci right 6.129721e-05	k: 102	n:2020000
Cons ci ratio: 6.697380e-02	ci left: 1.636356e-03	ci right 1.750229e-03	k: 3419	n:2020000
KS ci ratio: 6.929590e-01	ci left: 1.042725e-05	ci right 2.178311e-05	k: 31	n:2020000
TP53   2020000 perm   2341 sec   (863 perm/sec)   p_kst 1.534653e-05   p_cons 1.692574e-03   p_joint 5.049505e-05

Joint ci ratio: 3.843777e-01	ci left: 4.141493e-05	ci right 6.153536e-05	k: 103	n:2030000
Cons ci ratio: 6.680796e-02	ci left: 1.636529e-03	ci right 1.750121e-03	k: 3436	n:2030000
KS ci ratio: 6.823787e-01	ci left: 1.078228e-05	ci right 2.225335e-05	k: 32	n:2030000
TP53   2030000 perm   2361 sec   (860 perm/sec)   p_kst 1.576355e-05   p_cons 1.692611e-03   p_joint 5.073892e-05

Joint ci ratio: 3.843777e-01	ci left: 4.121192e-05	ci right 6.123372e-05	k: 103	n:2040000
Cons ci ratio: 6.667236e-02	ci left: 1.635255e-03	ci right 1.748520e-03	k: 3450	n:2040000
KS ci ratio: 6.823787e-01	ci left: 1.072942e-05	ci right 2.214427e-05	k: 32	n:2040000
TP53   2040000 perm   2382 sec   (856 perm/sec)   p_kst 1.568627e-05   p_cons 1.691176e-03   p_joint 5.049020e-05

Joint ci ratio: 3.843778e-01	ci left: 4.101088e-05	ci right 6.093502e-05	k: 103	n:2050000
Cons ci ratio: 6.654720e-02	ci left: 1.633514e-03	ci right 1.746438e-03	k: 3463	n:2050000
KS ci ratio: 6.722687e-01	ci left: 1.108085e-05	ci right 2.260689e-05	k: 33	n:2050000
TP53   2050000 perm   2402 sec   (853 perm/sec)   p_kst 1.609756e-05   p_cons 1.689268e-03   p_joint 5.024390e-05

Joint ci ratio: 3.843778e-01	ci left: 4.081180e-05	ci right 6.063922e-05	k: 103	n:2060000
Cons ci ratio: 6.643231e-02	ci left: 1.631313e-03	ci right 1.743882e-03	k: 3475	n:2060000
KS ci ratio: 6.722687e-01	ci left: 1.102705e-05	ci right 2.249715e-05	k: 33	n:2060000
TP53   2060000 perm   2422 sec   (850 perm/sec)   p_kst 1.601942e-05   p_cons 1.686893e-03   p_joint 5.000000e-05

Joint ci ratio: 3.825430e-01	ci left: 4.105116e-05	ci right 6.087572e-05	k: 104	n:2070000
Cons ci ratio: 6.630849e-02	ci left: 1.629608e-03	ci right 1.741842e-03	k: 3488	n:2070000
KS ci ratio: 6.722688e-01	ci left: 1.097378e-05	ci right 2.238846e-05	k: 33	n:2070000
TP53   2070000 perm   2443 sec   (847 perm/sec)   p_kst 1.594203e-05   p_cons 1.685024e-03   p_joint 5.024155e-05

Joint ci ratio: 3.825431e-01	ci left: 4.085380e-05	ci right 6.058305e-05	k: 104	n:2080000
Cons ci ratio: 6.619483e-02	ci left: 1.627447e-03	ci right 1.739332e-03	k: 3500	n:2080000
KS ci ratio: 6.625952e-01	ci left: 1.132021e-05	ci right 2.284204e-05	k: 34	n:2080000
TP53   2080000 perm   2464 sec   (844 perm/sec)   p_kst 1.634615e-05   p_cons 1.682692e-03   p_joint 5.000000e-05

Joint ci ratio: 3.825431e-01	ci left: 4.065833e-05	ci right 6.029318e-05	k: 104	n:2090000
Cons ci ratio: 6.611004e-02	ci left: 1.623895e-03	ci right 1.735388e-03	k: 3509	n:2090000
KS ci ratio: 6.625952e-01	ci left: 1.126605e-05	ci right 2.273275e-05	k: 34	n:2090000
TP53   2090000 perm   2485 sec   (841 perm/sec)   p_kst 1.626794e-05   p_cons 1.678947e-03   p_joint 4.976077e-05

Joint ci ratio: 3.807344e-01	ci left: 4.089522e-05	ci right 6.052773e-05	k: 105	n:2100000
Cons ci ratio: 6.593180e-02	ci left: 1.625061e-03	ci right 1.736321e-03	k: 3528	n:2100000
KS ci ratio: 6.625953e-01	ci left: 1.121240e-05	ci right 2.262449e-05	k: 34	n:2100000
TP53   2100000 perm   2505 sec   (838 perm/sec)   p_kst 1.619048e-05   p_cons 1.680000e-03   p_joint 5.000000e-05

Joint ci ratio: 3.789510e-01	ci left: 4.113009e-05	ci right 6.075984e-05	k: 106	n:2110000
Cons ci ratio: 6.582937e-02	ci left: 1.622486e-03	ci right 1.733391e-03	k: 3539	n:2110000
KS ci ratio: 6.533276e-01	ci left: 1.155395e-05	ci right 2.306937e-05	k: 35	n:2110000
TP53   2110000 perm   2525 sec   (836 perm/sec)   p_kst 1.658768e-05   p_cons 1.677251e-03   p_joint 5.023697e-05

Joint ci ratio: 3.789511e-01	ci left: 4.093608e-05	ci right 6.047324e-05	k: 106	n:2120000
Cons ci ratio: 6.568112e-02	ci left: 1.622256e-03	ci right 1.732886e-03	k: 3555	n:2120000
KS ci ratio: 6.533276e-01	ci left: 1.149945e-05	ci right 2.296055e-05	k: 35	n:2120000
TP53   2120000 perm   2546 sec   (833 perm/sec)   p_kst 1.650943e-05   p_cons 1.676887e-03   p_joint 5.000000e-05

Joint ci ratio: 3.789511e-01	ci left: 4.074389e-05	ci right 6.018933e-05	k: 106	n:2130000
Cons ci ratio: 6.553386e-02	ci left: 1.622028e-03	ci right 1.732385e-03	k: 3571	n:2130000
KS ci ratio: 6.533277e-01	ci left: 1.144546e-05	ci right 2.285276e-05	k: 35	n:2130000
TP53   2130000 perm   2566 sec   (830 perm/sec)   p_kst 1.643192e-05   p_cons 1.676526e-03   p_joint 4.976526e-05

Joint ci ratio: 4.021745e-01	ci left: 3.549620e-05	ci right 5.375310e-05	k: 94	n:2140000
Cons ci ratio: 6.533290e-02	ci left: 1.624561e-03	ci right 1.734739e-03	k: 3593	n:2140000
KS ci ratio: 6.533277e-01	ci left: 1.139198e-05	ci right 2.274597e-05	k: 35	n:2140000
TP53   2140000 perm   2587 sec   (827 perm/sec)   p_kst 1.635514e-05   p_cons 1.678972e-03   p_joint 4.392523e-05

Joint ci ratio: 4.021745e-01	ci left: 3.533110e-05	ci right 5.350308e-05	k: 94	n:2150000
Cons ci ratio: 6.516989e-02	ci left: 1.625240e-03	ci right 1.735179e-03	k: 3611	n:2150000
KS ci ratio: 6.533277e-01	ci left: 1.133899e-05	ci right 2.264017e-05	k: 35	n:2150000
TP53   2150000 perm   2608 sec   (825 perm/sec)   p_kst 1.627907e-05   p_cons 1.679535e-03   p_joint 4.372093e-05

Joint ci ratio: 4.000743e-01	ci left: 3.558379e-05	ci right 5.376482e-05	k: 95	n:2160000
Cons ci ratio: 6.505299e-02	ci left: 1.623637e-03	ci right 1.733262e-03	k: 3624	n:2160000
KS ci ratio: 6.533277e-01	ci left: 1.128650e-05	ci right 2.253536e-05	k: 35	n:2160000
TP53   2160000 perm   2628 sec   (822 perm/sec)   p_kst 1.620370e-05   p_cons 1.677778e-03   p_joint 4.398148e-05

Joint ci ratio: 4.000744e-01	ci left: 3.541980e-05	ci right 5.351705e-05	k: 95	n:2170000
Cons ci ratio: 6.483859e-02	ci left: 1.627035e-03	ci right 1.736514e-03	k: 3648	n:2170000
KS ci ratio: 6.533278e-01	ci left: 1.123449e-05	ci right 2.243151e-05	k: 35	n:2170000
TP53   2170000 perm   2649 sec   (819 perm/sec)   p_kst 1.612903e-05   p_cons 1.681106e-03   p_joint 4.377880e-05

Joint ci ratio: 4.064763e-01	ci left: 3.402077e-05	ci right 5.175656e-05	k: 92	n:2180000
Cons ci ratio: 6.461750e-02	ci left: 1.630854e-03	ci right 1.740202e-03	k: 3673	n:2180000
KS ci ratio: 6.359023e-01	ci left: 1.195022e-05	ci right 2.339425e-05	k: 37	n:2180000
TP53   2180000 perm   2670 sec   (816 perm/sec)   p_kst 1.697248e-05   p_cons 1.684862e-03   p_joint 4.220183e-05

Joint ci ratio: 4.043084e-01	ci left: 3.427548e-05	ci right 5.202317e-05	k: 93	n:2190000
Cons ci ratio: 6.446851e-02	ci left: 1.631044e-03	ci right 1.740143e-03	k: 3690	n:2190000
KS ci ratio: 6.276966e-01	ci left: 1.227905e-05	ci right 2.381635e-05	k: 38	n:2190000
TP53   2190000 perm   2691 sec   (814 perm/sec)   p_kst 1.735160e-05   p_cons 1.684932e-03   p_joint 4.246575e-05

Joint ci ratio: 4.043084e-01	ci left: 3.411968e-05	ci right 5.178670e-05	k: 93	n:2200000
Cons ci ratio: 6.432056e-02	ci left: 1.631233e-03	ci right 1.740085e-03	k: 3707	n:2200000
KS ci ratio: 6.276967e-01	ci left: 1.222324e-05	ci right 2.370809e-05	k: 38	n:2200000
TP53   2200000 perm   2712 sec   (811 perm/sec)   p_kst 1.727273e-05   p_cons 1.685000e-03   p_joint 4.227273e-05

Joint ci ratio: 4.021748e-01	ci left: 3.437188e-05	ci right 5.205052e-05	k: 94	n:2210000
Cons ci ratio: 6.420816e-02	ci left: 1.629640e-03	ci right 1.738188e-03	k: 3720	n:2210000
KS ci ratio: 6.276967e-01	ci left: 1.216793e-05	ci right 2.360082e-05	k: 38	n:2210000
TP53   2210000 perm   2734 sec   (808 perm/sec)   p_kst 1.719457e-05   p_cons 1.683258e-03   p_joint 4.253394e-05

Joint ci ratio: 4.021748e-01	ci left: 3.421705e-05	ci right 5.181606e-05	k: 94	n:2220000
Cons ci ratio: 6.402768e-02	ci left: 1.631607e-03	ci right 1.739970e-03	k: 3741	n:2220000
KS ci ratio: 6.276967e-01	ci left: 1.211312e-05	ci right 2.349451e-05	k: 38	n:2220000
TP53   2220000 perm   2755 sec   (806 perm/sec)   p_kst 1.711712e-05   p_cons 1.685135e-03   p_joint 4.234234e-05

Joint ci ratio: 4.064765e-01	ci left: 3.325797e-05	ci right 5.059610e-05	k: 92	n:2230000
Cons ci ratio: 6.393386e-02	ci left: 1.629144e-03	ci right 1.737179e-03	k: 3752	n:2230000
KS ci ratio: 6.276967e-01	ci left: 1.205880e-05	ci right 2.338915e-05	k: 38	n:2230000
TP53   2230000 perm   2776 sec   (803 perm/sec)   p_kst 1.704036e-05   p_cons 1.682511e-03   p_joint 4.125561e-05

Joint ci ratio: 4.064765e-01	ci left: 3.310949e-05	ci right 5.037023e-05	k: 92	n:2240000
Cons ci ratio: 6.376414e-02	ci left: 1.630657e-03	ci right 1.738495e-03	k: 3772	n:2240000
KS ci ratio: 6.276968e-01	ci left: 1.200497e-05	ci right 2.328473e-05	k: 38	n:2240000
TP53   2240000 perm   2798 sec   (801 perm/sec)   p_kst 1.696429e-05   p_cons 1.683929e-03   p_joint 4.107143e-05

Joint ci ratio: 4.064766e-01	ci left: 3.296234e-05	ci right 5.014636e-05	k: 92	n:2250000
Cons ci ratio: 6.363779e-02	ci left: 1.629970e-03	ci right 1.737541e-03	k: 3787	n:2250000
KS ci ratio: 6.198008e-01	ci left: 1.232572e-05	ci right 2.369516e-05	k: 39	n:2250000
TP53   2250000 perm   2819 sec   (798 perm/sec)   p_kst 1.733333e-05   p_cons 1.683111e-03   p_joint 4.088889e-05

Joint ci ratio: 4.064766e-01	ci left: 3.281649e-05	ci right 4.992447e-05	k: 92	n:2260000
Cons ci ratio: 6.347041e-02	ci left: 1.631467e-03	ci right 1.738843e-03	k: 3807	n:2260000
KS ci ratio: 6.198008e-01	ci left: 1.227118e-05	ci right 2.359032e-05	k: 39	n:2260000
TP53   2260000 perm   2841 sec   (796 perm/sec)   p_kst 1.725664e-05   p_cons 1.684513e-03   p_joint 4.070796e-05

Joint ci ratio: 4.086799e-01	ci left: 3.227656e-05	ci right 4.921909e-05	k: 91	n:2270000
Cons ci ratio: 6.336240e-02	ci left: 1.629916e-03	ci right 1.737000e-03	k: 3820	n:2270000
KS ci ratio: 6.198008e-01	ci left: 1.221713e-05	ci right 2.348639e-05	k: 39	n:2270000
TP53   2270000 perm   2863 sec   (793 perm/sec)   p_kst 1.718062e-05   p_cons 1.682819e-03   p_joint 4.008811e-05

Joint ci ratio: 4.086799e-01	ci left: 3.213500e-05	ci right 4.900321e-05	k: 91	n:2280000
Cons ci ratio: 6.322192e-02	ci left: 1.630105e-03	ci right 1.736956e-03	k: 3837	n:2280000
KS ci ratio: 6.198008e-01	ci left: 1.216354e-05	ci right 2.338338e-05	k: 39	n:2280000
TP53   2280000 perm   2884 sec   (790 perm/sec)   p_kst 1.710526e-05   p_cons 1.682895e-03   p_joint 3.991228e-05

Joint ci ratio: 4.086800e-01	ci left: 3.199467e-05	ci right 4.878923e-05	k: 91	n:2290000
Cons ci ratio: 6.309056e-02	ci left: 1.629864e-03	ci right 1.736468e-03	k: 3853	n:2290000
KS ci ratio: 6.198009e-01	ci left: 1.211043e-05	ci right 2.328127e-05	k: 39	n:2290000
TP53   2290000 perm   2906 sec   (788 perm/sec)   p_kst 1.703057e-05   p_cons 1.682533e-03   p_joint 3.973799e-05

Joint ci ratio: 4.086800e-01	ci left: 3.185556e-05	ci right 4.857710e-05	k: 91	n:2300000
Cons ci ratio: 6.296001e-02	ci left: 1.629624e-03	ci right 1.735985e-03	k: 3869	n:2300000
KS ci ratio: 6.198009e-01	ci left: 1.205777e-05	ci right 2.318005e-05	k: 39	n:2300000
TP53   2300000 perm   2928 sec   (785 perm/sec)   p_kst 1.695652e-05   p_cons 1.682174e-03   p_joint 3.956522e-05

Joint ci ratio: 4.086800e-01	ci left: 3.171766e-05	ci right 4.836681e-05	k: 91	n:2310000
Cons ci ratio: 6.283028e-02	ci left: 1.629387e-03	ci right 1.735505e-03	k: 3885	n:2310000
KS ci ratio: 6.198009e-01	ci left: 1.200557e-05	ci right 2.307971e-05	k: 39	n:2310000
TP53   2310000 perm   2950 sec   (783 perm/sec)   p_kst 1.688312e-05   p_cons 1.681818e-03   p_joint 3.939394e-05

Joint ci ratio: 4.086801e-01	ci left: 3.158094e-05	ci right 4.815833e-05	k: 91	n:2320000
Cons ci ratio: 6.266917e-02	ci left: 1.630849e-03	ci right 1.736780e-03	k: 3905	n:2320000
KS ci ratio: 6.198009e-01	ci left: 1.195382e-05	ci right 2.298022e-05	k: 39	n:2320000
TP53   2320000 perm   2972 sec   (781 perm/sec)   p_kst 1.681034e-05   p_cons 1.683190e-03   p_joint 3.922414e-05

Joint ci ratio: 4.086801e-01	ci left: 3.144540e-05	ci right 4.795165e-05	k: 91	n:2330000
Cons ci ratio: 6.248539e-02	ci left: 1.633567e-03	ci right 1.739352e-03	k: 3928	n:2330000
KS ci ratio: 6.198010e-01	ci left: 1.190252e-05	ci right 2.288160e-05	k: 39	n:2330000
TP53   2330000 perm   2995 sec   (778 perm/sec)   p_kst 1.673820e-05   p_cons 1.685837e-03   p_joint 3.905579e-05

Joint ci ratio: 4.086801e-01	ci left: 3.131102e-05	ci right 4.774673e-05	k: 91	n:2340000
Cons ci ratio: 6.235856e-02	ci left: 1.633316e-03	ci right 1.738863e-03	k: 3944	n:2340000
KS ci ratio: 6.198010e-01	ci left: 1.185166e-05	ci right 2.278381e-05	k: 39	n:2340000
TP53   2340000 perm   3017 sec   (776 perm/sec)   p_kst 1.666667e-05   p_cons 1.685470e-03   p_joint 3.888889e-05

Joint ci ratio: 4.086802e-01	ci left: 3.117778e-05	ci right 4.754355e-05	k: 91	n:2350000
Cons ci ratio: 6.216180e-02	ci left: 1.636839e-03	ci right 1.742267e-03	k: 3969	n:2350000
KS ci ratio: 6.198010e-01	ci left: 1.180122e-05	ci right 2.268686e-05	k: 39	n:2350000
TP53   2350000 perm   3040 sec   (773 perm/sec)   p_kst 1.659574e-05   p_cons 1.688936e-03   p_joint 3.872340e-05

Joint ci ratio: 4.086802e-01	ci left: 3.104567e-05	ci right 4.734210e-05	k: 91	n:2360000
Cons ci ratio: 6.203692e-02	ci left: 1.636578e-03	ci right 1.741770e-03	k: 3985	n:2360000
KS ci ratio: 6.198010e-01	ci left: 1.175122e-05	ci right 2.259073e-05	k: 39	n:2360000
TP53   2360000 perm   3062 sec   (771 perm/sec)   p_kst 1.652542e-05   p_cons 1.688559e-03   p_joint 3.855932e-05

Joint ci ratio: 4.064770e-01	ci left: 3.129335e-05	ci right 4.760732e-05	k: 92	n:2370000
Cons ci ratio: 6.191280e-02	ci left: 1.636319e-03	ci right 1.741276e-03	k: 4001	n:2370000
KS ci ratio: 6.198011e-01	ci left: 1.170163e-05	ci right 2.249541e-05	k: 39	n:2370000
TP53   2370000 perm   3085 sec   (768 perm/sec)   p_kst 1.645570e-05   p_cons 1.688186e-03   p_joint 3.881857e-05

Joint ci ratio: 4.043091e-01	ci left: 3.153919e-05	ci right 4.787008e-05	k: 93	n:2380000
Cons ci ratio: 6.177402e-02	ci left: 1.636889e-03	ci right 1.741640e-03	k: 4019	n:2380000
KS ci ratio: 6.198011e-01	ci left: 1.165247e-05	ci right 2.240089e-05	k: 39	n:2380000
TP53   2380000 perm   3108 sec   (766 perm/sec)   p_kst 1.638655e-05   p_cons 1.688655e-03   p_joint 3.907563e-05

Joint ci ratio: 4.021754e-01	ci left: 3.178320e-05	ci right 4.813041e-05	k: 94	n:2390000
Cons ci ratio: 6.162088e-02	ci left: 1.638280e-03	ci right 1.742850e-03	k: 4039	n:2390000
KS ci ratio: 6.198011e-01	ci left: 1.160371e-05	ci right 2.230716e-05	k: 39	n:2390000
TP53   2390000 perm   3131 sec   (763 perm/sec)   p_kst 1.631799e-05   p_cons 1.689958e-03   p_joint 3.933054e-05

Joint ci ratio: 4.021755e-01	ci left: 3.165077e-05	ci right 4.792987e-05	k: 94	n:2400000
Cons ci ratio: 6.144615e-02	ci left: 1.640889e-03	ci right 1.745319e-03	k: 4062	n:2400000
KS ci ratio: 6.121958e-01	ci left: 1.190694e-05	ci right 2.269520e-05	k: 40	n:2400000
TP53   2400000 perm   3154 sec   (761 perm/sec)   p_kst 1.666667e-05   p_cons 1.692500e-03   p_joint 3.916667e-05

Joint ci ratio: 4.000753e-01	ci left: 3.189251e-05	ci right 4.818758e-05	k: 95	n:2410000
Cons ci ratio: 6.124286e-02	ci left: 1.645112e-03	ci right 1.749452e-03	k: 4089	n:2410000
KS ci ratio: 6.121958e-01	ci left: 1.185753e-05	ci right 2.260103e-05	k: 40	n:2410000
TP53   2410000 perm   3177 sec   (759 perm/sec)   p_kst 1.659751e-05   p_cons 1.696680e-03   p_joint 3.941909e-05

Joint ci ratio: 4.000753e-01	ci left: 3.176072e-05	ci right 4.798846e-05	k: 95	n:2420000
Cons ci ratio: 6.112344e-02	ci left: 1.644825e-03	ci right 1.748935e-03	k: 4105	n:2420000
KS ci ratio: 6.121958e-01	ci left: 1.180853e-05	ci right 2.250764e-05	k: 40	n:2420000
TP53   2420000 perm   3200 sec   (756 perm/sec)   p_kst 1.652893e-05   p_cons 1.696281e-03   p_joint 3.925620e-05

Joint ci ratio: 3.959717e-01	ci left: 3.237068e-05	ci right 4.869599e-05	k: 97	n:2430000
Cons ci ratio: 6.098988e-02	ci left: 1.645350e-03	ci right 1.749259e-03	k: 4123	n:2430000
KS ci ratio: 6.048638e-01	ci left: 1.210797e-05	ci right 2.288928e-05	k: 41	n:2430000
TP53   2430000 perm   3223 sec   (754 perm/sec)   p_kst 1.687243e-05   p_cons 1.696708e-03   p_joint 3.991770e-05

Joint ci ratio: 3.959718e-01	ci left: 3.223801e-05	ci right 4.849642e-05	k: 97	n:2440000
Cons ci ratio: 6.082779e-02	ci left: 1.647486e-03	ci right 1.751243e-03	k: 4145	n:2440000
KS ci ratio: 6.048638e-01	ci left: 1.205835e-05	ci right 2.279548e-05	k: 41	n:2440000
TP53   2440000 perm   3246 sec   (752 perm/sec)   p_kst 1.680328e-05   p_cons 1.698770e-03   p_joint 3.975410e-05

Joint ci ratio: 3.959718e-01	ci left: 3.210643e-05	ci right 4.829847e-05	k: 97	n:2450000
Cons ci ratio: 6.078396e-02	ci left: 1.643173e-03	ci right 1.746582e-03	k: 4151	n:2450000
KS ci ratio: 6.048638e-01	ci left: 1.200913e-05	ci right 2.270243e-05	k: 41	n:2450000
TP53   2450000 perm   3269 sec   (749 perm/sec)   p_kst 1.673469e-05   p_cons 1.694286e-03   p_joint 3.959184e-05

Joint ci ratio: 3.939668e-01	ci left: 3.234204e-05	ci right 4.854882e-05	k: 98	n:2460000
Cons ci ratio: 6.071098e-02	ci left: 1.640497e-03	ci right 1.743608e-03	k: 4161	n:2460000
KS ci ratio: 6.048638e-01	ci left: 1.196031e-05	ci right 2.261015e-05	k: 41	n:2460000
TP53   2460000 perm   3293 sec   (747 perm/sec)   p_kst 1.666667e-05   p_cons 1.691463e-03   p_joint 3.983740e-05

Joint ci ratio: 4.155116e-01	ci left: 2.857442e-05	ci right 4.389393e-05	k: 88	n:2470000
Cons ci ratio: 6.056560e-02	ci left: 1.641830e-03	ci right 1.744769e-03	k: 4181	n:2470000
KS ci ratio: 6.048639e-01	ci left: 1.191189e-05	ci right 2.251861e-05	k: 41	n:2470000
TP53   2470000 perm   3316 sec   (745 perm/sec)   p_kst 1.659919e-05   p_cons 1.692713e-03   p_joint 3.562753e-05

Joint ci ratio: 4.155116e-01	ci left: 2.845920e-05	ci right 4.371694e-05	k: 88	n:2480000
Cons ci ratio: 6.044287e-02	ci left: 1.641961e-03	ci right 1.744692e-03	k: 4198	n:2480000
KS ci ratio: 6.048639e-01	ci left: 1.186386e-05	ci right 2.242781e-05	k: 41	n:2480000
TP53   2480000 perm   3340 sec   (743 perm/sec)   p_kst 1.653226e-05   p_cons 1.692742e-03   p_joint 3.548387e-05

Joint ci ratio: 4.155117e-01	ci left: 2.834490e-05	ci right 4.354137e-05	k: 88	n:2490000
Cons ci ratio: 6.030656e-02	ci left: 1.642882e-03	ci right 1.745431e-03	k: 4217	n:2490000
KS ci ratio: 6.048639e-01	ci left: 1.181621e-05	ci right 2.233774e-05	k: 41	n:2490000
TP53   2490000 perm   3364 sec   (740 perm/sec)   p_kst 1.646586e-05   p_cons 1.693574e-03   p_joint 3.534137e-05

Joint ci ratio: 4.155117e-01	ci left: 2.823152e-05	ci right 4.336721e-05	k: 88	n:2500000
Cons ci ratio: 6.013563e-02	ci left: 1.645766e-03	ci right 1.748194e-03	k: 4241	n:2500000
KS ci ratio: 6.048639e-01	ci left: 1.176895e-05	ci right 2.224839e-05	k: 41	n:2500000
TP53   2500000 perm   3388 sec   (738 perm/sec)   p_kst 1.640000e-05   p_cons 1.696400e-03   p_joint 3.520000e-05

Joint ci ratio: 4.131968e-01	ci left: 2.847591e-05	ci right 4.363415e-05	k: 89	n:2510000
Cons ci ratio: 6.000844e-02	ci left: 1.646273e-03	ci right 1.748508e-03	k: 4259	n:2510000
KS ci ratio: 5.977892e-01	ci left: 1.205975e-05	ci right 2.261818e-05	k: 42	n:2510000
TP53   2510000 perm   3411 sec   (736 perm/sec)   p_kst 1.673307e-05   p_cons 1.696813e-03   p_joint 3.545817e-05

Joint ci ratio: 4.131968e-01	ci left: 2.836291e-05	ci right 4.346100e-05	k: 89	n:2520000
Cons ci ratio: 5.990309e-02	ci left: 1.645603e-03	ci right 1.747611e-03	k: 4274	n:2520000
KS ci ratio: 5.977892e-01	ci left: 1.201189e-05	ci right 2.252843e-05	k: 42	n:2520000
TP53   2520000 perm   3435 sec   (734 perm/sec)   p_kst 1.666667e-05   p_cons 1.696032e-03   p_joint 3.531746e-05

Joint ci ratio: 4.131968e-01	ci left: 2.825081e-05	ci right 4.328922e-05	k: 89	n:2530000
Cons ci ratio: 5.980528e-02	ci left: 1.644549e-03	ci right 1.746320e-03	k: 4288	n:2530000
KS ci ratio: 5.977892e-01	ci left: 1.196441e-05	ci right 2.243938e-05	k: 42	n:2530000
TP53   2530000 perm   3459 sec   (731 perm/sec)   p_kst 1.660079e-05   p_cons 1.694862e-03   p_joint 3.517787e-05

Joint ci ratio: 4.131969e-01	ci left: 2.813958e-05	ci right 4.311879e-05	k: 89	n:2540000
Cons ci ratio: 5.971490e-02	ci left: 1.643116e-03	ci right 1.744639e-03	k: 4301	n:2540000
KS ci ratio: 5.977892e-01	ci left: 1.191731e-05	ci right 2.235104e-05	k: 42	n:2540000
TP53   2540000 perm   3483 sec   (729 perm/sec)   p_kst 1.653543e-05   p_cons 1.693307e-03   p_joint 3.503937e-05

Joint ci ratio: 4.276999e-01	ci left: 2.592519e-05	ci right 4.034925e-05	k: 83	n:2550000
Cons ci ratio: 5.959035e-02	ci left: 1.643626e-03	ci right 1.744962e-03	k: 4319	n:2550000
KS ci ratio: 5.977892e-01	ci left: 1.187058e-05	ci right 2.226339e-05	k: 42	n:2550000
TP53   2550000 perm   3507 sec   (727 perm/sec)   p_kst 1.647059e-05   p_cons 1.693725e-03   p_joint 3.254902e-05

Joint ci ratio: 4.410276e-01	ci left: 2.408435e-05	ci right 3.802624e-05	k: 78	n:2560000
Cons ci ratio: 5.797299e-02	ci left: 1.731120e-03	ci right 1.834856e-03	k: 4563	n:2560000
KS ci ratio: 5.977893e-01	ci left: 1.182421e-05	ci right 2.217642e-05	k: 42	n:2560000
TP53   2560000 perm   3532 sec   (725 perm/sec)   p_kst 1.640625e-05   p_cons 1.782422e-03   p_joint 3.046875e-05

Joint ci ratio: 4.410276e-01	ci left: 2.399064e-05	ci right 3.787827e-05	k: 78	n:2570000
Cons ci ratio: 5.789699e-02	ci left: 1.728986e-03	ci right 1.832453e-03	k: 4575	n:2570000
KS ci ratio: 5.977893e-01	ci left: 1.177820e-05	ci right 2.209013e-05	k: 42	n:2570000
TP53   2570000 perm   3557 sec   (723 perm/sec)   p_kst 1.634241e-05   p_cons 1.780156e-03   p_joint 3.035019e-05

Joint ci ratio: 4.410276e-01	ci left: 2.389765e-05	ci right 3.773146e-05	k: 78	n:2580000
Cons ci ratio: 5.777086e-02	ci left: 1.729924e-03	ci right 1.833215e-03	k: 4595	n:2580000
KS ci ratio: 5.977893e-01	ci left: 1.173255e-05	ci right 2.200451e-05	k: 42	n:2580000
TP53   2580000 perm   3581 sec   (720 perm/sec)   p_kst 1.627907e-05   p_cons 1.781008e-03   p_joint 3.023256e-05

Joint ci ratio: 4.410276e-01	ci left: 2.380538e-05	ci right 3.758578e-05	k: 78	n:2590000
Cons ci ratio: 5.765806e-02	ci left: 1.730094e-03	ci right 1.833187e-03	k: 4613	n:2590000
KS ci ratio: 5.977893e-01	ci left: 1.168725e-05	ci right 2.191955e-05	k: 42	n:2590000
TP53   2590000 perm   3606 sec   (718 perm/sec)   p_kst 1.621622e-05   p_cons 1.781081e-03   p_joint 3.011583e-05

Joint ci ratio: 4.410277e-01	ci left: 2.371383e-05	ci right 3.744122e-05	k: 78	n:2600000
Cons ci ratio: 5.757082e-02	ci left: 1.728747e-03	ci right 1.831598e-03	k: 4627	n:2600000
KS ci ratio: 5.977893e-01	ci left: 1.164230e-05	ci right 2.183525e-05	k: 42	n:2600000
TP53   2600000 perm   3630 sec   (716 perm/sec)   p_kst 1.615385e-05   p_cons 1.779615e-03   p_joint 3.000000e-05

Joint ci ratio: 4.410277e-01	ci left: 2.362297e-05	ci right 3.729777e-05	k: 78	n:2610000
Cons ci ratio: 5.740970e-02	ci left: 1.731942e-03	ci right 1.834686e-03	k: 4653	n:2610000
KS ci ratio: 5.977894e-01	ci left: 1.159769e-05	ci right 2.175159e-05	k: 42	n:2610000
TP53   2610000 perm   3655 sec   (714 perm/sec)   p_kst 1.609195e-05   p_cons 1.782759e-03   p_joint 2.988506e-05

Joint ci ratio: 4.410277e-01	ci left: 2.353280e-05	ci right 3.715541e-05	k: 78	n:2620000
Cons ci ratio: 5.726830e-02	ci left: 1.733984e-03	ci right 1.836587e-03	k: 4676	n:2620000
KS ci ratio: 5.977894e-01	ci left: 1.155342e-05	ci right 2.166856e-05	k: 42	n:2620000
TP53   2620000 perm   3680 sec   (712 perm/sec)   p_kst 1.603053e-05   p_cons 1.784733e-03   p_joint 2.977099e-05

Joint ci ratio: 4.410277e-01	ci left: 2.344332e-05	ci right 3.701413e-05	k: 78	n:2630000
Cons ci ratio: 5.719504e-02	ci left: 1.731889e-03	ci right 1.834232e-03	k: 4688	n:2630000
KS ci ratio: 5.977894e-01	ci left: 1.150949e-05	ci right 2.158617e-05	k: 42	n:2630000
TP53   2630000 perm   3704 sec   (710 perm/sec)   p_kst 1.596958e-05   p_cons 1.782510e-03   p_joint 2.965779e-05

Joint ci ratio: 4.410278e-01	ci left: 2.335452e-05	ci right 3.687393e-05	k: 78	n:2640000
Cons ci ratio: 5.710989e-02	ci left: 1.730556e-03	ci right 1.832663e-03	k: 4702	n:2640000
KS ci ratio: 5.977894e-01	ci left: 1.146590e-05	ci right 2.150441e-05	k: 42	n:2640000
TP53   2640000 perm   3729 sec   (708 perm/sec)   p_kst 1.590909e-05   p_cons 1.781061e-03   p_joint 2.954545e-05

Joint ci ratio: 4.410278e-01	ci left: 2.326639e-05	ci right 3.673478e-05	k: 78	n:2650000
Cons ci ratio: 5.700091e-02	ci left: 1.730721e-03	ci right 1.832637e-03	k: 4720	n:2650000
KS ci ratio: 5.977894e-01	ci left: 1.142263e-05	ci right 2.142326e-05	k: 42	n:2650000
TP53   2650000 perm   3754 sec   (706 perm/sec)   p_kst 1.584906e-05   p_cons 1.781132e-03   p_joint 2.943396e-05

Joint ci ratio: 4.410278e-01	ci left: 2.317893e-05	ci right 3.659668e-05	k: 78	n:2660000
Cons ci ratio: 5.687452e-02	ci left: 1.731997e-03	ci right 1.833754e-03	k: 4741	n:2660000
KS ci ratio: 5.977895e-01	ci left: 1.137969e-05	ci right 2.134272e-05	k: 42	n:2660000
TP53   2660000 perm   3779 sec   (704 perm/sec)   p_kst 1.578947e-05   p_cons 1.782331e-03   p_joint 2.932331e-05

Joint ci ratio: 4.355489e-01	ci left: 2.375851e-05	ci right 3.729085e-05	k: 80	n:2670000
Cons ci ratio: 5.679079e-02	ci left: 1.730679e-03	ci right 1.832204e-03	k: 4755	n:2670000
KS ci ratio: 5.977895e-01	ci left: 1.133707e-05	ci right 2.126279e-05	k: 42	n:2670000
TP53   2670000 perm   3804 sec   (702 perm/sec)   p_kst 1.573034e-05   p_cons 1.780899e-03   p_joint 2.996255e-05

Joint ci ratio: 4.328849e-01	ci left: 2.400219e-05	ci right 3.756539e-05	k: 81	n:2680000
Cons ci ratio: 5.671934e-02	ci left: 1.728635e-03	ci right 1.829909e-03	k: 4767	n:2680000
KS ci ratio: 5.977895e-01	ci left: 1.129476e-05	ci right 2.118345e-05	k: 42	n:2680000
TP53   2680000 perm   3830 sec   (700 perm/sec)   p_kst 1.567164e-05   p_cons 1.778731e-03   p_joint 3.022388e-05

Joint ci ratio: 4.328849e-01	ci left: 2.391297e-05	ci right 3.742574e-05	k: 81	n:2690000
Cons ci ratio: 5.661258e-02	ci left: 1.728806e-03	ci right 1.829893e-03	k: 4785	n:2690000
KS ci ratio: 5.977895e-01	ci left: 1.125278e-05	ci right 2.110470e-05	k: 42	n:2690000
TP53   2690000 perm   3855 sec   (698 perm/sec)   p_kst 1.561338e-05   p_cons 1.778810e-03   p_joint 3.011152e-05

Joint ci ratio: 4.328849e-01	ci left: 2.382440e-05	ci right 3.728712e-05	k: 81	n:2700000
Cons ci ratio: 5.655361e-02	ci left: 1.726054e-03	ci right 1.826871e-03	k: 4795	n:2700000
KS ci ratio: 5.977895e-01	ci left: 1.121110e-05	ci right 2.102653e-05	k: 42	n:2700000
TP53   2700000 perm   3880 sec   (696 perm/sec)   p_kst 1.555556e-05   p_cons 1.775926e-03   p_joint 3.000000e-05

Joint ci ratio: 4.328850e-01	ci left: 2.373649e-05	ci right 3.714953e-05	k: 81	n:2710000
Cons ci ratio: 5.647717e-02	ci left: 1.724414e-03	ci right 1.824995e-03	k: 4808	n:2710000
KS ci ratio: 5.977895e-01	ci left: 1.116973e-05	ci right 2.094895e-05	k: 42	n:2710000
TP53   2710000 perm   3906 sec   (694 perm/sec)   p_kst 1.549815e-05   p_cons 1.774170e-03   p_joint 2.988930e-05

Joint ci ratio: 4.328850e-01	ci left: 2.364922e-05	ci right 3.701296e-05	k: 81	n:2720000
Cons ci ratio: 5.640690e-02	ci left: 1.722424e-03	ci right 1.822759e-03	k: 4820	n:2720000
KS ci ratio: 5.977896e-01	ci left: 1.112866e-05	ci right 2.087193e-05	k: 42	n:2720000
TP53   2720000 perm   3931 sec   (692 perm/sec)   p_kst 1.544118e-05   p_cons 1.772059e-03   p_joint 2.977941e-05

Joint ci ratio: 4.328850e-01	ci left: 2.356259e-05	ci right 3.687738e-05	k: 81	n:2730000
Cons ci ratio: 5.634272e-02	ci left: 1.720087e-03	ci right 1.820169e-03	k: 4831	n:2730000
KS ci ratio: 5.977896e-01	ci left: 1.108790e-05	ci right 2.079547e-05	k: 42	n:2730000
TP53   2730000 perm   3957 sec   (690 perm/sec)   p_kst 1.538462e-05   p_cons 1.769597e-03   p_joint 2.967033e-05

Joint ci ratio: 4.328850e-01	ci left: 2.347660e-05	ci right 3.674279e-05	k: 81	n:2740000
Cons ci ratio: 5.625550e-02	ci left: 1.719207e-03	ci right 1.819077e-03	k: 4846	n:2740000
KS ci ratio: 5.977896e-01	ci left: 1.104743e-05	ci right 2.071958e-05	k: 42	n:2740000
TP53   2740000 perm   3983 sec   (688 perm/sec)   p_kst 1.532847e-05   p_cons 1.768613e-03   p_joint 2.956204e-05

Joint ci ratio: 4.328850e-01	ci left: 2.339123e-05	ci right 3.660918e-05	k: 81	n:2750000
Cons ci ratio: 5.614555e-02	ci left: 1.719767e-03	ci right 1.819469e-03	k: 4865	n:2750000
KS ci ratio: 5.977896e-01	ci left: 1.100726e-05	ci right 2.064424e-05	k: 42	n:2750000
TP53   2750000 perm   4008 sec   (686 perm/sec)   p_kst 1.527273e-05   p_cons 1.769091e-03   p_joint 2.945455e-05

Joint ci ratio: 4.328851e-01	ci left: 2.330648e-05	ci right 3.647654e-05	k: 81	n:2760000
Cons ci ratio: 5.609379e-02	ci left: 1.716751e-03	ci right 1.816183e-03	k: 4874	n:2760000
KS ci ratio: 5.977896e-01	ci left: 1.096738e-05	ci right 2.056944e-05	k: 42	n:2760000
TP53   2760000 perm   4035 sec   (684 perm/sec)   p_kst 1.521739e-05   p_cons 1.765942e-03   p_joint 2.934783e-05

Joint ci ratio: 4.328851e-01	ci left: 2.322234e-05	ci right 3.634485e-05	k: 81	n:2770000
Cons ci ratio: 5.597333e-02	ci left: 1.718028e-03	ci right 1.817314e-03	k: 4895	n:2770000
KS ci ratio: 5.977896e-01	ci left: 1.092778e-05	ci right 2.049518e-05	k: 42	n:2770000
TP53   2770000 perm   4061 sec   (682 perm/sec)   p_kst 1.516245e-05   p_cons 1.767148e-03   p_joint 2.924188e-05

Joint ci ratio: 4.328851e-01	ci left: 2.313880e-05	ci right 3.621412e-05	k: 81	n:2780000
Cons ci ratio: 5.588781e-02	ci left: 1.717169e-03	ci right 1.816248e-03	k: 4910	n:2780000
KS ci ratio: 5.977897e-01	ci left: 1.088848e-05	ci right 2.042146e-05	k: 42	n:2780000
TP53   2780000 perm   4087 sec   (680 perm/sec)   p_kst 1.510791e-05   p_cons 1.766187e-03   p_joint 2.913669e-05

Joint ci ratio: 4.328851e-01	ci left: 2.305587e-05	ci right 3.608432e-05	k: 81	n:2790000
Cons ci ratio: 5.578566e-02	ci left: 1.717375e-03	ci right 1.816280e-03	k: 4928	n:2790000
KS ci ratio: 5.977897e-01	ci left: 1.084945e-05	ci right 2.034826e-05	k: 42	n:2790000
TP53   2790000 perm   4113 sec   (678 perm/sec)   p_kst 1.505376e-05   p_cons 1.766308e-03   p_joint 2.903226e-05

Joint ci ratio: 4.328852e-01	ci left: 2.297353e-05	ci right 3.595545e-05	k: 81	n:2800000
Cons ci ratio: 5.574620e-02	ci left: 1.713707e-03	ci right 1.812328e-03	k: 4935	n:2800000
KS ci ratio: 5.977897e-01	ci left: 1.081070e-05	ci right 2.027559e-05	k: 42	n:2800000
TP53   2800000 perm   4140 sec   (676 perm/sec)   p_kst 1.500000e-05   p_cons 1.762500e-03   p_joint 2.892857e-05

Joint ci ratio: 4.328852e-01	ci left: 2.289177e-05	ci right 3.582749e-05	k: 81	n:2810000
Cons ci ratio: 5.563358e-02	ci left: 1.714627e-03	ci right 1.813095e-03	k: 4955	n:2810000
KS ci ratio: 5.977897e-01	ci left: 1.077223e-05	ci right 2.020343e-05	k: 42	n:2810000
TP53   2810000 perm   4166 sec   (675 perm/sec)   p_kst 1.494662e-05   p_cons 1.763345e-03   p_joint 2.882562e-05

Joint ci ratio: 4.302695e-01	ci left: 2.312667e-05	ci right 3.609336e-05	k: 82	n:2820000
Cons ci ratio: 5.556641e-02	ci left: 1.712743e-03	ci right 1.810980e-03	k: 4967	n:2820000
KS ci ratio: 5.977897e-01	ci left: 1.073403e-05	ci right 2.013179e-05	k: 42	n:2820000
TP53   2820000 perm   4192 sec   (673 perm/sec)   p_kst 1.489362e-05   p_cons 1.761348e-03   p_joint 2.907801e-05

Joint ci ratio: 4.277006e-01	ci left: 2.336015e-05	ci right 3.635711e-05	k: 83	n:2830000
Cons ci ratio: 5.547158e-02	ci left: 1.712614e-03	ci right 1.810671e-03	k: 4984	n:2830000
KS ci ratio: 5.977897e-01	ci left: 1.069610e-05	ci right 2.006065e-05	k: 42	n:2830000
TP53   2830000 perm   4219 sec   (671 perm/sec)   p_kst 1.484099e-05   p_cons 1.761131e-03   p_joint 2.932862e-05

Joint ci ratio: 4.277007e-01	ci left: 2.327789e-05	ci right 3.622909e-05	k: 83	n:2840000
Cons ci ratio: 5.539944e-02	ci left: 1.711098e-03	ci right 1.808937e-03	k: 4997	n:2840000
KS ci ratio: 5.977898e-01	ci left: 1.065844e-05	ci right 1.999002e-05	k: 42	n:2840000
TP53   2840000 perm   4245 sec   (669 perm/sec)   p_kst 1.478873e-05   p_cons 1.759507e-03   p_joint 2.922535e-05

Joint ci ratio: 4.277007e-01	ci left: 2.319622e-05	ci right 3.610197e-05	k: 83	n:2850000
Cons ci ratio: 5.530547e-02	ci left: 1.710976e-03	ci right 1.808637e-03	k: 5014	n:2850000
KS ci ratio: 5.909576e-01	ci left: 1.091908e-05	ci right 2.032301e-05	k: 43	n:2850000
TP53   2850000 perm   4272 sec   (667 perm/sec)   p_kst 1.508772e-05   p_cons 1.759298e-03   p_joint 2.912281e-05

Joint ci ratio: 4.277007e-01	ci left: 2.311511e-05	ci right 3.597574e-05	k: 83	n:2860000
Cons ci ratio: 5.513519e-02	ci left: 1.715683e-03	ci right 1.813302e-03	k: 5045	n:2860000
KS ci ratio: 5.909576e-01	ci left: 1.088090e-05	ci right 2.025195e-05	k: 43	n:2860000
TP53   2860000 perm   4299 sec   (665 perm/sec)   p_kst 1.503497e-05   p_cons 1.763986e-03   p_joint 2.902098e-05

Joint ci ratio: 4.251773e-01	ci left: 2.334560e-05	ci right 3.623601e-05	k: 84	n:2870000
Cons ci ratio: 5.503711e-02	ci left: 1.715891e-03	ci right 1.813342e-03	k: 5063	n:2870000
KS ci ratio: 5.909576e-01	ci left: 1.084299e-05	ci right 2.018138e-05	k: 43	n:2870000
TP53   2870000 perm   4326 sec   (663 perm/sec)   p_kst 1.498258e-05   p_cons 1.764111e-03   p_joint 2.926829e-05

Joint ci ratio: 4.251773e-01	ci left: 2.326454e-05	ci right 3.611019e-05	k: 84	n:2880000
Cons ci ratio: 5.492332e-02	ci left: 1.717124e-03	ci right 1.814437e-03	k: 5084	n:2880000
KS ci ratio: 5.909576e-01	ci left: 1.080534e-05	ci right 2.011131e-05	k: 43	n:2880000
TP53   2880000 perm   4353 sec   (662 perm/sec)   p_kst 1.493056e-05   p_cons 1.765278e-03   p_joint 2.916667e-05

Joint ci ratio: 4.251774e-01	ci left: 2.318404e-05	ci right 3.598524e-05	k: 84	n:2890000
Cons ci ratio: 5.480485e-02	ci left: 1.718691e-03	ci right 1.815876e-03	k: 5106	n:2890000
KS ci ratio: 5.909576e-01	ci left: 1.076795e-05	ci right 2.004172e-05	k: 43	n:2890000
TP53   2890000 perm   4380 sec   (660 perm/sec)   p_kst 1.487889e-05   p_cons 1.766782e-03   p_joint 2.906574e-05

Joint ci ratio: 4.251774e-01	ci left: 2.310409e-05	ci right 3.586116e-05	k: 84	n:2900000
Cons ci ratio: 5.475135e-02	ci left: 1.716165e-03	ci right 1.813110e-03	k: 5116	n:2900000
KS ci ratio: 5.909577e-01	ci left: 1.073082e-05	ci right 1.997261e-05	k: 43	n:2900000
TP53   2900000 perm   4407 sec   (658 perm/sec)   p_kst 1.482759e-05   p_cons 1.764138e-03   p_joint 2.896552e-05

Joint ci ratio: 4.251774e-01	ci left: 2.302470e-05	ci right 3.573792e-05	k: 84	n:2910000
Cons ci ratio: 5.467130e-02	ci left: 1.715352e-03	ci right 1.812104e-03	k: 5131	n:2910000
KS ci ratio: 5.909577e-01	ci left: 1.069394e-05	ci right 1.990398e-05	k: 43	n:2910000
TP53   2910000 perm   4434 sec   (656 perm/sec)   p_kst 1.477663e-05   p_cons 1.763230e-03   p_joint 2.886598e-05

Joint ci ratio: 4.251774e-01	ci left: 2.294585e-05	ci right 3.561553e-05	k: 84	n:2920000
Cons ci ratio: 5.461818e-02	ci left: 1.712855e-03	ci right 1.809370e-03	k: 5141	n:2920000
KS ci ratio: 5.909577e-01	ci left: 1.065732e-05	ci right 1.983581e-05	k: 43	n:2920000
TP53   2920000 perm   4462 sec   (654 perm/sec)   p_kst 1.472603e-05   p_cons 1.760616e-03   p_joint 2.876712e-05

Joint ci ratio: 4.251775e-01	ci left: 2.286753e-05	ci right 3.549398e-05	k: 84	n:2930000
Cons ci ratio: 5.457053e-02	ci left: 1.710039e-03	ci right 1.806308e-03	k: 5150	n:2930000
KS ci ratio: 5.909577e-01	ci left: 1.062095e-05	ci right 1.976811e-05	k: 43	n:2930000
TP53   2930000 perm   4489 sec   (653 perm/sec)   p_kst 1.467577e-05   p_cons 1.757679e-03   p_joint 2.866894e-05

Joint ci ratio: 4.226982e-01	ci left: 2.309359e-05	ci right 3.574948e-05	k: 85	n:2940000
Cons ci ratio: 5.445432e-02	ci left: 1.711604e-03	ci right 1.807749e-03	k: 5172	n:2940000
KS ci ratio: 5.909577e-01	ci left: 1.058482e-05	ci right 1.970087e-05	k: 43	n:2940000
TP53   2940000 perm   4517 sec   (651 perm/sec)   p_kst 1.462585e-05   p_cons 1.759184e-03   p_joint 2.891156e-05

Joint ci ratio: 4.226982e-01	ci left: 2.301531e-05	ci right 3.562829e-05	k: 85	n:2950000
Cons ci ratio: 5.439132e-02	ci left: 1.709814e-03	ci right 1.805745e-03	k: 5184	n:2950000
KS ci ratio: 5.909577e-01	ci left: 1.054894e-05	ci right 1.963409e-05	k: 43	n:2950000
TP53   2950000 perm   4545 sec   (649 perm/sec)   p_kst 1.457627e-05   p_cons 1.757288e-03   p_joint 2.881356e-05

Joint ci ratio: 4.202619e-01	ci left: 2.323956e-05	ci right 3.588140e-05	k: 86	n:2960000
Cons ci ratio: 5.427104e-02	ci left: 1.711702e-03	ci right 1.807520e-03	k: 5207	n:2960000
KS ci ratio: 5.843546e-01	ci left: 1.080085e-05	ci right 1.995534e-05	k: 44	n:2960000
TP53   2960000 perm   4573 sec   (647 perm/sec)   p_kst 1.486486e-05   p_cons 1.759122e-03   p_joint 2.905405e-05

Joint ci ratio: 4.178671e-01	ci left: 2.346250e-05	ci right 3.613260e-05	k: 87	n:2970000
Cons ci ratio: 5.415154e-02	ci left: 1.713578e-03	ci right 1.809283e-03	k: 5230	n:2970000
KS ci ratio: 5.843546e-01	ci left: 1.076449e-05	ci right 1.988815e-05	k: 44	n:2970000
TP53   2970000 perm   4601 sec   (646 perm/sec)   p_kst 1.481481e-05   p_cons 1.760943e-03   p_joint 2.929293e-05

Joint ci ratio: 4.178672e-01	ci left: 2.338377e-05	ci right 3.601135e-05	k: 87	n:2980000
Cons ci ratio: 5.408442e-02	ci left: 1.712131e-03	ci right 1.807633e-03	k: 5243	n:2980000
KS ci ratio: 5.843546e-01	ci left: 1.072836e-05	ci right 1.982141e-05	k: 44	n:2980000
TP53   2980000 perm   4628 sec   (644 perm/sec)   p_kst 1.476510e-05   p_cons 1.759396e-03   p_joint 2.919463e-05

Joint ci ratio: 4.178672e-01	ci left: 2.330556e-05	ci right 3.589091e-05	k: 87	n:2990000
Cons ci ratio: 5.397129e-02	ci left: 1.713664e-03	ci right 1.809045e-03	k: 5265	n:2990000
KS ci ratio: 5.843546e-01	ci left: 1.069248e-05	ci right 1.975512e-05	k: 44	n:2990000
TP53   2990000 perm   4657 sec   (642 perm/sec)   p_kst 1.471572e-05   p_cons 1.760870e-03   p_joint 2.909699e-05

Joint ci ratio: 4.178672e-01	ci left: 2.322787e-05	ci right 3.577127e-05	k: 87	n:3000000
Cons ci ratio: 5.389461e-02	ci left: 1.712884e-03	ci right 1.808082e-03	k: 5280	n:3000000
KS ci ratio: 5.843546e-01	ci left: 1.065684e-05	ci right 1.968927e-05	k: 44	n:3000000
TP53   3000000 perm   4685 sec   (640 perm/sec)   p_kst 1.466667e-05   p_cons 1.760000e-03   p_joint 2.900000e-05

Joint ci ratio: 4.178672e-01	ci left: 2.315071e-05	ci right 3.565243e-05	k: 87	n:3010000
Cons ci ratio: 5.381317e-02	ci left: 1.712437e-03	ci right 1.807462e-03	k: 5296	n:3010000
KS ci ratio: 5.843546e-01	ci left: 1.062144e-05	ci right 1.962385e-05	k: 44	n:3010000
TP53   3010000 perm   4713 sec   (639 perm/sec)   p_kst 1.461794e-05   p_cons 1.759468e-03   p_joint 2.890365e-05

Joint ci ratio: 4.178672e-01	ci left: 2.307405e-05	ci right 3.553438e-05	k: 87	n:3020000
Cons ci ratio: 5.370678e-02	ci left: 1.713627e-03	ci right 1.808524e-03	k: 5317	n:3020000
KS ci ratio: 5.843546e-01	ci left: 1.058627e-05	ci right 1.955887e-05	k: 44	n:3020000
TP53   3020000 perm   4741 sec   (637 perm/sec)   p_kst 1.456954e-05   p_cons 1.760596e-03   p_joint 2.880795e-05

Joint ci ratio: 4.178673e-01	ci left: 2.299789e-05	ci right 3.541710e-05	k: 87	n:3030000
Cons ci ratio: 5.364634e-02	ci left: 1.711879e-03	ci right 1.806569e-03	k: 5329	n:3030000
KS ci ratio: 5.843547e-01	ci left: 1.055133e-05	ci right 1.949432e-05	k: 44	n:3030000
TP53   3030000 perm   4770 sec   (635 perm/sec)   p_kst 1.452145e-05   p_cons 1.758746e-03   p_joint 2.871287e-05

Joint ci ratio: 4.178673e-01	ci left: 2.292224e-05	ci right 3.530060e-05	k: 87	n:3040000
Cons ci ratio: 5.355598e-02	ci left: 1.712089e-03	ci right 1.806627e-03	k: 5347	n:3040000
KS ci ratio: 5.843547e-01	ci left: 1.051662e-05	ci right 1.943020e-05	k: 44	n:3040000
TP53   3040000 perm   4797 sec   (634 perm/sec)   p_kst 1.447368e-05   p_cons 1.758882e-03   p_joint 2.861842e-05

Joint ci ratio: 4.178673e-01	ci left: 2.284709e-05	ci right 3.518486e-05	k: 87	n:3050000
Cons ci ratio: 5.342619e-02	ci left: 1.714887e-03	ci right 1.809342e-03	k: 5373	n:3050000
KS ci ratio: 5.843547e-01	ci left: 1.048214e-05	ci right 1.936649e-05	k: 44	n:3050000
TP53   3050000 perm   4826 sec   (632 perm/sec)   p_kst 1.442623e-05   p_cons 1.761639e-03   p_joint 2.852459e-05

Joint ci ratio: 4.178673e-01	ci left: 2.277242e-05	ci right 3.506988e-05	k: 87	n:3060000
Cons ci ratio: 5.331218e-02	ci left: 1.716699e-03	ci right 1.811046e-03	k: 5396	n:3060000
KS ci ratio: 5.843547e-01	ci left: 1.044788e-05	ci right 1.930320e-05	k: 44	n:3060000
TP53   3060000 perm   4854 sec   (630 perm/sec)   p_kst 1.437908e-05   p_cons 1.763399e-03   p_joint 2.843137e-05

Joint ci ratio: 4.178673e-01	ci left: 2.269825e-05	ci right 3.495564e-05	k: 87	n:3070000
Cons ci ratio: 5.322842e-02	ci left: 1.716570e-03	ci right 1.810758e-03	k: 5413	n:3070000
KS ci ratio: 5.843547e-01	ci left: 1.041385e-05	ci right 1.924033e-05	k: 44	n:3070000
TP53   3070000 perm   4883 sec   (629 perm/sec)   p_kst 1.433225e-05   p_cons 1.763192e-03   p_joint 2.833876e-05

Joint ci ratio: 4.178674e-01	ci left: 2.262455e-05	ci right 3.484215e-05	k: 87	n:3080000
Cons ci ratio: 5.312546e-02	ci left: 1.717725e-03	ci right 1.811787e-03	k: 5434	n:3080000
KS ci ratio: 5.779681e-01	ci left: 1.065694e-05	ci right 1.954980e-05	k: 45	n:3080000
TP53   3080000 perm   4912 sec   (627 perm/sec)   p_kst 1.461039e-05   p_cons 1.764286e-03   p_joint 2.824675e-05

Joint ci ratio: 4.178674e-01	ci left: 2.255133e-05	ci right 3.472939e-05	k: 87	n:3090000
Cons ci ratio: 5.303283e-02	ci left: 1.718233e-03	ci right 1.812155e-03	k: 5453	n:3090000
KS ci ratio: 5.779681e-01	ci left: 1.062245e-05	ci right 1.948653e-05	k: 45	n:3090000
TP53   3090000 perm   4940 sec   (625 perm/sec)   p_kst 1.456311e-05   p_cons 1.764725e-03   p_joint 2.815534e-05

Joint ci ratio: 4.131982e-01	ci left: 2.305629e-05	ci right 3.532961e-05	k: 89	n:3100000
Cons ci ratio: 5.299892e-02	ci left: 1.714918e-03	ci right 1.808597e-03	k: 5460	n:3100000
KS ci ratio: 5.779681e-01	ci left: 1.058818e-05	ci right 1.942368e-05	k: 45	n:3100000
TP53   3100000 perm   4969 sec   (624 perm/sec)   p_kst 1.451613e-05   p_cons 1.761290e-03   p_joint 2.870968e-05

Joint ci ratio: 4.131982e-01	ci left: 2.298215e-05	ci right 3.521601e-05	k: 89	n:3110000
Cons ci ratio: 5.288762e-02	ci left: 1.716702e-03	ci right 1.810275e-03	k: 5483	n:3110000
KS ci ratio: 5.779681e-01	ci left: 1.055414e-05	ci right 1.936122e-05	k: 45	n:3110000
TP53   3110000 perm   4998 sec   (622 perm/sec)   p_kst 1.446945e-05   p_cons 1.763023e-03   p_joint 2.861736e-05

Joint ci ratio: 4.131983e-01	ci left: 2.290849e-05	ci right 3.510314e-05	k: 89	n:3120000
Cons ci ratio: 5.282509e-02	ci left: 1.715311e-03	ci right 1.808694e-03	k: 5496	n:3120000
KS ci ratio: 5.779681e-01	ci left: 1.052031e-05	ci right 1.929916e-05	k: 45	n:3120000
TP53   3120000 perm   5027 sec   (621 perm/sec)   p_kst 1.442308e-05   p_cons 1.761538e-03   p_joint 2.852564e-05

Joint ci ratio: 4.131983e-01	ci left: 2.283530e-05	ci right 3.499099e-05	k: 89	n:3130000
Cons ci ratio: 5.273881e-02	ci left: 1.715506e-03	ci right 1.808743e-03	k: 5514	n:3130000
KS ci ratio: 5.779681e-01	ci left: 1.048670e-05	ci right 1.923751e-05	k: 45	n:3130000
TP53   3130000 perm   5056 sec   (619 perm/sec)   p_kst 1.437700e-05   p_cons 1.761661e-03   p_joint 2.843450e-05

Joint ci ratio: 4.131983e-01	ci left: 2.276258e-05	ci right 3.487955e-05	k: 89	n:3140000
Cons ci ratio: 5.262437e-02	ci left: 1.717585e-03	ci right 1.810726e-03	k: 5538	n:3140000
KS ci ratio: 5.717864e-01	ci left: 1.072543e-05	ci right 1.954057e-05	k: 46	n:3140000
TP53   3140000 perm   5085 sec   (617 perm/sec)   p_kst 1.464968e-05   p_cons 1.763694e-03   p_joint 2.834395e-05

Joint ci ratio: 4.131983e-01	ci left: 2.269032e-05	ci right 3.476883e-05	k: 89	n:3150000
Cons ci ratio: 5.250595e-02	ci left: 1.719965e-03	ci right 1.813019e-03	k: 5563	n:3150000
KS ci ratio: 5.717864e-01	ci left: 1.069138e-05	ci right 1.947854e-05	k: 46	n:3150000
TP53   3150000 perm   5115 sec   (616 perm/sec)   p_kst 1.460317e-05   p_cons 1.766032e-03   p_joint 2.825397e-05

Joint ci ratio: 4.131983e-01	ci left: 2.261851e-05	ci right 3.465880e-05	k: 89	n:3160000
Cons ci ratio: 5.244947e-02	ci left: 1.718269e-03	ci right 1.811129e-03	k: 5575	n:3160000
KS ci ratio: 5.717864e-01	ci left: 1.065754e-05	ci right 1.941690e-05	k: 46	n:3160000
TP53   3160000 perm   5144 sec   (614 perm/sec)   p_kst 1.455696e-05   p_cons 1.764241e-03   p_joint 2.816456e-05

Joint ci ratio: 4.086823e-01	ci left: 2.311284e-05	ci right 3.524526e-05	k: 91	n:3170000
Cons ci ratio: 5.235564e-02	ci left: 1.719075e-03	ci right 1.811807e-03	k: 5595	n:3170000
KS ci ratio: 5.717864e-01	ci left: 1.062392e-05	ci right 1.935565e-05	k: 46	n:3170000
TP53   3170000 perm   5173 sec   (613 perm/sec)   p_kst 1.451104e-05   p_cons 1.764984e-03   p_joint 2.870662e-05

Joint ci ratio: 4.064791e-01	ci left: 2.332238e-05	ci right 3.548096e-05	k: 92	n:3180000
Cons ci ratio: 5.226697e-02	ci left: 1.719566e-03	ci right 1.812162e-03	k: 5614	n:3180000
KS ci ratio: 5.717865e-01	ci left: 1.059052e-05	ci right 1.929478e-05	k: 46	n:3180000
TP53   3180000 perm   5203 sec   (611 perm/sec)   p_kst 1.446541e-05   p_cons 1.765409e-03   p_joint 2.893082e-05

Joint ci ratio: 4.064791e-01	ci left: 2.324927e-05	ci right 3.536974e-05	k: 92	n:3190000
Cons ci ratio: 5.222521e-02	ci left: 1.716960e-03	ci right 1.809340e-03	k: 5623	n:3190000
KS ci ratio: 5.717865e-01	ci left: 1.055732e-05	ci right 1.923430e-05	k: 46	n:3190000
TP53   3190000 perm   5233 sec   (610 perm/sec)   p_kst 1.442006e-05   p_cons 1.762696e-03   p_joint 2.884013e-05

Joint ci ratio: 4.043111e-01	ci left: 2.345725e-05	ci right 3.560341e-05	k: 93	n:3200000
Cons ci ratio: 5.217426e-02	ci left: 1.714987e-03	ci right 1.807168e-03	k: 5634	n:3200000
KS ci ratio: 5.657989e-01	ci left: 1.079184e-05	ci right 1.953121e-05	k: 47	n:3200000
TP53   3200000 perm   5263 sec   (608 perm/sec)   p_kst 1.468750e-05   p_cons 1.760625e-03   p_joint 2.906250e-05

Joint ci ratio: 4.043111e-01	ci left: 2.338417e-05	ci right 3.549250e-05	k: 93	n:3210000
Cons ci ratio: 5.209574e-02	ci left: 1.714871e-03	ci right 1.806903e-03	k: 5651	n:3210000
KS ci ratio: 5.657989e-01	ci left: 1.075822e-05	ci right 1.947037e-05	k: 47	n:3210000
TP53   3210000 perm   5293 sec   (606 perm/sec)   p_kst 1.464174e-05   p_cons 1.760436e-03   p_joint 2.897196e-05

Joint ci ratio: 4.043112e-01	ci left: 2.331155e-05	ci right 3.538227e-05	k: 93	n:3220000
Cons ci ratio: 5.199920e-02	ci left: 1.715983e-03	ci right 1.807898e-03	k: 5672	n:3220000
KS ci ratio: 5.657990e-01	ci left: 1.072481e-05	ci right 1.940990e-05	k: 47	n:3220000
TP53   3220000 perm   5322 sec   (605 perm/sec)   p_kst 1.459627e-05   p_cons 1.761491e-03   p_joint 2.888199e-05

Joint ci ratio: 4.000773e-01	ci left: 2.379594e-05	ci right 3.595424e-05	k: 95	n:3230000
Cons ci ratio: 5.193062e-02	ci left: 1.715254e-03	ci right 1.807005e-03	k: 5687	n:3230000
KS ci ratio: 5.599957e-01	ci left: 1.095711e-05	ci right 1.970306e-05	k: 48	n:3230000
TP53   3230000 perm   5352 sec   (603 perm/sec)   p_kst 1.486068e-05   p_cons 1.760681e-03   p_joint 2.941176e-05

Joint ci ratio: 4.000773e-01	ci left: 2.372249e-05	ci right 3.584327e-05	k: 95	n:3240000
Cons ci ratio: 5.187141e-02	ci left: 1.713920e-03	ci right 1.805493e-03	k: 5700	n:3240000
KS ci ratio: 5.599957e-01	ci left: 1.092329e-05	ci right 1.964225e-05	k: 48	n:3240000
TP53   3240000 perm   5382 sec   (602 perm/sec)   p_kst 1.481481e-05   p_cons 1.759259e-03   p_joint 2.932099e-05

Joint ci ratio: 4.000774e-01	ci left: 2.364950e-05	ci right 3.573298e-05	k: 95	n:3250000
Cons ci ratio: 5.178518e-02	ci left: 1.714417e-03	ci right 1.805859e-03	k: 5719	n:3250000
KS ci ratio: 5.599957e-01	ci left: 1.088968e-05	ci right 1.958181e-05	k: 48	n:3250000
TP53   3250000 perm   5413 sec   (600 perm/sec)   p_kst 1.476923e-05   p_cons 1.759692e-03   p_joint 2.923077e-05

Joint ci ratio: 4.131985e-01	ci left: 2.192469e-05	ci right 3.359565e-05	k: 89	n:3260000
Cons ci ratio: 5.171743e-02	ci left: 1.713699e-03	ci right 1.804981e-03	k: 5734	n:3260000
KS ci ratio: 5.599957e-01	ci left: 1.085628e-05	ci right 1.952174e-05	k: 48	n:3260000
TP53   3260000 perm   5443 sec   (599 perm/sec)   p_kst 1.472393e-05   p_cons 1.758896e-03   p_joint 2.730061e-05

Joint ci ratio: 4.109219e-01	ci left: 2.213175e-05	ci right 3.383025e-05	k: 90	n:3270000
Cons ci ratio: 5.161848e-02	ci left: 1.715100e-03	ci right 1.806275e-03	k: 5756	n:3270000
KS ci ratio: 5.599957e-01	ci left: 1.082308e-05	ci right 1.946204e-05	k: 48	n:3270000
TP53   3270000 perm   5473 sec   (598 perm/sec)   p_kst 1.467890e-05   p_cons 1.760245e-03   p_joint 2.752294e-05

Joint ci ratio: 4.109219e-01	ci left: 2.206427e-05	ci right 3.372711e-05	k: 90	n:3280000
Cons ci ratio: 5.155139e-02	ci left: 1.714385e-03	ci right 1.805401e-03	k: 5771	n:3280000
KS ci ratio: 5.543674e-01	ci left: 1.105199e-05	ci right 1.975013e-05	k: 49	n:3280000
TP53   3280000 perm   5504 sec   (596 perm/sec)   p_kst 1.493902e-05   p_cons 1.759451e-03   p_joint 2.743902e-05

Joint ci ratio: 4.109219e-01	ci left: 2.199721e-05	ci right 3.362460e-05	k: 90	n:3290000
Cons ci ratio: 5.145784e-02	ci left: 1.715475e-03	ci right 1.806378e-03	k: 5792	n:3290000
KS ci ratio: 5.543674e-01	ci left: 1.101840e-05	ci right 1.969010e-05	k: 49	n:3290000
TP53   3290000 perm   5534 sec   (594 perm/sec)   p_kst 1.489362e-05   p_cons 1.760486e-03   p_joint 2.735562e-05

Joint ci ratio: 4.109219e-01	ci left: 2.193055e-05	ci right 3.352271e-05	k: 90	n:3300000
Cons ci ratio: 5.136480e-02	ci left: 1.716558e-03	ci right 1.807350e-03	k: 5813	n:3300000
KS ci ratio: 5.543674e-01	ci left: 1.098501e-05	ci right 1.963044e-05	k: 49	n:3300000
TP53   3300000 perm   5565 sec   (593 perm/sec)   p_kst 1.484848e-05   p_cons 1.761515e-03   p_joint 2.727273e-05

Joint ci ratio: 4.109219e-01	ci left: 2.186429e-05	ci right 3.342143e-05	k: 90	n:3310000
Cons ci ratio: 5.126786e-02	ci left: 1.717934e-03	ci right 1.808621e-03	k: 5835	n:3310000
KS ci ratio: 5.543674e-01	ci left: 1.095182e-05	ci right 1.957113e-05	k: 49	n:3310000
TP53   3310000 perm   5595 sec   (592 perm/sec)   p_kst 1.480363e-05   p_cons 1.762840e-03   p_joint 2.719033e-05

Joint ci ratio: 4.109220e-01	ci left: 2.179844e-05	ci right 3.332076e-05	k: 90	n:3320000
Cons ci ratio: 5.119774e-02	ci left: 1.717517e-03	ci right 1.808055e-03	k: 5851	n:3320000
KS ci ratio: 5.543675e-01	ci left: 1.091884e-05	ci right 1.951218e-05	k: 49	n:3320000
TP53   3320000 perm   5626 sec   (590 perm/sec)   p_kst 1.475904e-05   p_cons 1.762349e-03   p_joint 2.710843e-05

Joint ci ratio: 4.109220e-01	ci left: 2.173298e-05	ci right 3.322070e-05	k: 90	n:3330000
Cons ci ratio: 5.112790e-02	ci left: 1.717102e-03	ci right 1.807491e-03	k: 5867	n:3330000
KS ci ratio: 5.543675e-01	ci left: 1.088605e-05	ci right 1.945359e-05	k: 49	n:3330000
TP53   3330000 perm   5657 sec   (589 perm/sec)   p_kst 1.471471e-05   p_cons 1.761862e-03   p_joint 2.702703e-05

Joint ci ratio: 4.109220e-01	ci left: 2.166791e-05	ci right 3.312124e-05	k: 90	n:3340000
Cons ci ratio: 5.104532e-02	ci left: 1.717577e-03	ci right 1.807841e-03	k: 5886	n:3340000
KS ci ratio: 5.543675e-01	ci left: 1.085345e-05	ci right 1.939534e-05	k: 49	n:3340000
TP53   3340000 perm   5688 sec   (587 perm/sec)   p_kst 1.467066e-05   p_cons 1.762275e-03   p_joint 2.694611e-05

Joint ci ratio: 4.064794e-01	ci left: 2.213886e-05	ci right 3.368044e-05	k: 92	n:3350000
Cons ci ratio: 5.096746e-02	ci left: 1.717755e-03	ci right 1.807886e-03	k: 5904	n:3350000
KS ci ratio: 5.436019e-01	ci left: 1.133520e-05	ci right 2.001654e-05	k: 51	n:3350000
TP53   3350000 perm   5719 sec   (586 perm/sec)   p_kst 1.522388e-05   p_cons 1.762388e-03   p_joint 2.746269e-05

Joint ci ratio: 4.064794e-01	ci left: 2.207297e-05	ci right 3.358020e-05	k: 92	n:3360000
Cons ci ratio: 5.089425e-02	ci left: 1.717637e-03	ci right 1.807629e-03	k: 5921	n:3360000
KS ci ratio: 5.436019e-01	ci left: 1.130146e-05	ci right 1.995697e-05	k: 51	n:3360000
TP53   3360000 perm   5750 sec   (584 perm/sec)   p_kst 1.517857e-05   p_cons 1.762202e-03   p_joint 2.738095e-05

Joint ci ratio: 4.131987e-01	ci left: 2.120905e-05	ci right 3.249906e-05	k: 89	n:3370000
Cons ci ratio: 5.080851e-02	ci left: 1.718400e-03	ci right 1.808276e-03	k: 5941	n:3370000
KS ci ratio: 5.436019e-01	ci left: 1.126793e-05	ci right 1.989775e-05	k: 51	n:3370000
TP53   3370000 perm   5781 sec   (583 perm/sec)   p_kst 1.513353e-05   p_cons 1.762908e-03   p_joint 2.640950e-05

Joint ci ratio: 4.131987e-01	ci left: 2.114630e-05	ci right 3.240291e-05	k: 89	n:3380000
Cons ci ratio: 5.073173e-02	ci left: 1.718574e-03	ci right 1.808319e-03	k: 5959	n:3380000
KS ci ratio: 5.436019e-01	ci left: 1.123459e-05	ci right 1.983888e-05	k: 51	n:3380000
TP53   3380000 perm   5813 sec   (581 perm/sec)   p_kst 1.508876e-05   p_cons 1.763018e-03   p_joint 2.633136e-05

Joint ci ratio: 4.131987e-01	ci left: 2.108392e-05	ci right 3.230732e-05	k: 89	n:3390000
Cons ci ratio: 5.065953e-02	ci left: 1.718455e-03	ci right 1.808063e-03	k: 5976	n:3390000
KS ci ratio: 5.436019e-01	ci left: 1.120145e-05	ci right 1.978036e-05	k: 51	n:3390000
TP53   3390000 perm   5844 sec   (580 perm/sec)   p_kst 1.504425e-05   p_cons 1.762832e-03   p_joint 2.625369e-05

Joint ci ratio: 4.131988e-01	ci left: 2.102191e-05	ci right 3.221230e-05	k: 89	n:3400000
Cons ci ratio: 5.060033e-02	ci left: 1.717467e-03	ci right 1.806915e-03	k: 5990	n:3400000
KS ci ratio: 5.436020e-01	ci left: 1.116850e-05	ci right 1.972218e-05	k: 51	n:3400000
TP53   3400000 perm   5877 sec   (579 perm/sec)   p_kst 1.500000e-05   p_cons 1.761765e-03   p_joint 2.617647e-05

Joint ci ratio: 4.086827e-01	ci left: 2.148613e-05	ci right 3.276466e-05	k: 91	n:3410000
Cons ci ratio: 5.052028e-02	ci left: 1.717931e-03	ci right 1.807258e-03	k: 6009	n:3410000
KS ci ratio: 5.334401e-01	ci left: 1.164244e-05	ci right 2.032995e-05	k: 53	n:3410000
TP53   3410000 perm   5908 sec   (577 perm/sec)   p_kst 1.554252e-05   p_cons 1.762170e-03   p_joint 2.668622e-05

Joint ci ratio: 4.086827e-01	ci left: 2.142330e-05	ci right 3.266886e-05	k: 91	n:3420000
Cons ci ratio: 5.045317e-02	ci left: 1.717528e-03	ci right 1.806711e-03	k: 6025	n:3420000
KS ci ratio: 5.334401e-01	ci left: 1.160839e-05	ci right 2.027051e-05	k: 53	n:3420000
TP53   3420000 perm   5940 sec   (576 perm/sec)   p_kst 1.549708e-05   p_cons 1.761696e-03   p_joint 2.660819e-05

Joint ci ratio: 4.086827e-01	ci left: 2.136085e-05	ci right 3.257361e-05	k: 91	n:3430000
Cons ci ratio: 5.040724e-02	ci left: 1.715687e-03	ci right 1.804691e-03	k: 6036	n:3430000
KS ci ratio: 5.334402e-01	ci left: 1.157455e-05	ci right 2.021141e-05	k: 53	n:3430000
TP53   3430000 perm   5972 sec   (574 perm/sec)   p_kst 1.545190e-05   p_cons 1.759767e-03   p_joint 2.653061e-05

Joint ci ratio: 4.086827e-01	ci left: 2.129875e-05	ci right 3.247892e-05	k: 91	n:3440000
Cons ci ratio: 5.033225e-02	ci left: 1.715866e-03	ci right 1.804744e-03	k: 6054	n:3440000
KS ci ratio: 5.334402e-01	ci left: 1.154090e-05	ci right 2.015266e-05	k: 53	n:3440000
TP53   3440000 perm   6004 sec   (573 perm/sec)   p_kst 1.540698e-05   p_cons 1.759884e-03   p_joint 2.645349e-05

Joint ci ratio: 4.086827e-01	ci left: 2.123701e-05	ci right 3.238478e-05	k: 91	n:3450000
Cons ci ratio: 5.027834e-02	ci left: 1.714613e-03	ci right 1.803328e-03	k: 6067	n:3450000
KS ci ratio: 5.334402e-01	ci left: 1.150745e-05	ci right 2.009424e-05	k: 53	n:3450000
TP53   3450000 perm   6036 sec   (572 perm/sec)   p_kst 1.536232e-05   p_cons 1.758551e-03   p_joint 2.637681e-05

Joint ci ratio: 4.086828e-01	ci left: 2.117564e-05	ci right 3.229119e-05	k: 91	n:3460000
Cons ci ratio: 5.020393e-02	ci left: 1.714795e-03	ci right 1.803384e-03	k: 6085	n:3460000
KS ci ratio: 5.334402e-01	ci left: 1.147419e-05	ci right 2.003617e-05	k: 53	n:3460000
TP53   3460000 perm   6067 sec   (570 perm/sec)   p_kst 1.531792e-05   p_cons 1.758671e-03   p_joint 2.630058e-05

Joint ci ratio: 4.086828e-01	ci left: 2.111461e-05	ci right 3.219813e-05	k: 91	n:3470000
Cons ci ratio: 5.013397e-02	ci left: 1.714690e-03	ci right 1.803147e-03	k: 6102	n:3470000
KS ci ratio: 5.334402e-01	ci left: 1.144113e-05	ci right 1.997843e-05	k: 53	n:3470000
TP53   3470000 perm   6100 sec   (569 perm/sec)   p_kst 1.527378e-05   p_cons 1.758501e-03   p_joint 2.622478e-05

Joint ci ratio: 4.064796e-01	ci left: 2.131183e-05	ci right 3.242227e-05	k: 92	n:3480000
Cons ci ratio: 5.003154e-02	ci left: 1.716857e-03	ci right 1.805240e-03	k: 6127	n:3480000
KS ci ratio: 5.334402e-01	ci left: 1.140825e-05	ci right 1.992102e-05	k: 53	n:3480000
TP53   3480000 perm   6132 sec   (568 perm/sec)   p_kst 1.522989e-05   p_cons 1.760632e-03   p_joint 2.643678e-05

Joint ci ratio: 4.043116e-01	ci left: 2.150808e-05	ci right 3.264497e-05	k: 93	n:3490000
Cons ci ratio: 4.995415e-02	ci left: 1.717314e-03	ci right 1.805579e-03	k: 6146	n:3490000
KS ci ratio: 5.334402e-01	ci left: 1.137556e-05	ci right 1.986394e-05	k: 53	n:3490000
TP53   3490000 perm   6164 sec   (566 perm/sec)   p_kst 1.518625e-05   p_cons 1.761032e-03   p_joint 2.664756e-05

Joint ci ratio: 4.043116e-01	ci left: 2.144662e-05	ci right 3.255170e-05	k: 93	n:3500000
Cons ci ratio: 4.987307e-02	ci left: 1.718050e-03	ci right 1.806206e-03	k: 6166	n:3500000
KS ci ratio: 5.334402e-01	ci left: 1.134306e-05	ci right 1.980718e-05	k: 53	n:3500000
TP53   3500000 perm   6196 sec   (565 perm/sec)   p_kst 1.514286e-05   p_cons 1.761714e-03   p_joint 2.657143e-05

Joint ci ratio: 4.021780e-01	ci left: 2.164153e-05	ci right 3.277261e-05	k: 94	n:3510000
Cons ci ratio: 4.982466e-02	ci left: 1.716532e-03	ci right 1.804521e-03	k: 6178	n:3510000
KS ci ratio: 5.334403e-01	ci left: 1.131074e-05	ci right 1.975075e-05	k: 53	n:3510000
TP53   3510000 perm   6229 sec   (564 perm/sec)   p_kst 1.509972e-05   p_cons 1.760114e-03   p_joint 2.678063e-05

Joint ci ratio: 4.000778e-01	ci left: 2.183547e-05	ci right 3.299211e-05	k: 95	n:3520000
Cons ci ratio: 4.974018e-02	ci left: 1.717547e-03	ci right 1.805435e-03	k: 6199	n:3520000
KS ci ratio: 5.334403e-01	ci left: 1.127861e-05	ci right 1.969464e-05	k: 53	n:3520000
TP53   3520000 perm   6261 sec   (562 perm/sec)   p_kst 1.505682e-05   p_cons 1.761080e-03   p_joint 2.698864e-05

Joint ci ratio: 4.000778e-01	ci left: 2.177361e-05	ci right 3.289865e-05	k: 95	n:3530000
Cons ci ratio: 4.968414e-02	ci left: 1.716598e-03	ci right 1.804336e-03	k: 6213	n:3530000
KS ci ratio: 5.334403e-01	ci left: 1.124666e-05	ci right 1.963885e-05	k: 53	n:3530000
TP53   3530000 perm   6294 sec   (561 perm/sec)   p_kst 1.501416e-05   p_cons 1.760057e-03   p_joint 2.691218e-05

Joint ci ratio: 4.000778e-01	ci left: 2.171211e-05	ci right 3.280571e-05	k: 95	n:3540000
Cons ci ratio: 4.962031e-02	ci left: 1.716212e-03	ci right 1.803815e-03	k: 6229	n:3540000
KS ci ratio: 5.334403e-01	ci left: 1.121489e-05	ci right 1.958337e-05	k: 53	n:3540000
TP53   3540000 perm   6326 sec   (560 perm/sec)   p_kst 1.497175e-05   p_cons 1.759605e-03   p_joint 2.683616e-05

Joint ci ratio: 4.000779e-01	ci left: 2.165095e-05	ci right 3.271330e-05	k: 95	n:3550000
Cons ci ratio: 4.955673e-02	ci left: 1.715829e-03	ci right 1.803297e-03	k: 6245	n:3550000
KS ci ratio: 5.334403e-01	ci left: 1.118330e-05	ci right 1.952821e-05	k: 53	n:3550000
TP53   3550000 perm   6359 sec   (558 perm/sec)   p_kst 1.492958e-05   p_cons 1.759155e-03   p_joint 2.676056e-05

Joint ci ratio: 4.000779e-01	ci left: 2.159013e-05	ci right 3.262141e-05	k: 95	n:3560000
Cons ci ratio: 4.949735e-02	ci left: 1.715171e-03	ci right 1.802497e-03	k: 6260	n:3560000
KS ci ratio: 5.334403e-01	ci left: 1.115188e-05	ci right 1.947336e-05	k: 53	n:3560000
TP53   3560000 perm   6392 sec   (557 perm/sec)   p_kst 1.488764e-05   p_cons 1.758427e-03   p_joint 2.668539e-05

Joint ci ratio: 3.980102e-01	ci left: 2.178165e-05	ci right 3.283812e-05	k: 96	n:3570000
Cons ci ratio: 4.943423e-02	ci left: 1.714793e-03	ci right 1.801985e-03	k: 6276	n:3570000
KS ci ratio: 5.334403e-01	ci left: 1.112065e-05	ci right 1.941881e-05	k: 53	n:3570000
TP53   3570000 perm   6425 sec   (556 perm/sec)   p_kst 1.484594e-05   p_cons 1.757983e-03   p_joint 2.689076e-05

Joint ci ratio: 3.980102e-01	ci left: 2.172081e-05	ci right 3.274639e-05	k: 96	n:3580000
Cons ci ratio: 4.935958e-02	ci left: 1.715245e-03	ci right 1.802324e-03	k: 6295	n:3580000
KS ci ratio: 5.334403e-01	ci left: 1.108958e-05	ci right 1.936457e-05	k: 53	n:3580000
TP53   3580000 perm   6458 sec   (554 perm/sec)   p_kst 1.480447e-05   p_cons 1.758380e-03   p_joint 2.681564e-05

Joint ci ratio: 3.980103e-01	ci left: 2.166030e-05	ci right 3.265518e-05	k: 96	n:3590000
Cons ci ratio: 4.930481e-02	ci left: 1.714318e-03	ci right 1.801252e-03	k: 6309	n:3590000
KS ci ratio: 5.285686e-01	ci left: 1.129987e-05	ci right 1.962622e-05	k: 54	n:3590000
TP53   3590000 perm   6491 sec   (553 perm/sec)   p_kst 1.504178e-05   p_cons 1.757382e-03   p_joint 2.674095e-05

Joint ci ratio: 3.980103e-01	ci left: 2.160014e-05	ci right 3.256447e-05	k: 96	n:3600000
Cons ci ratio: 4.925804e-02	ci left: 1.712849e-03	ci right 1.799623e-03	k: 6321	n:3600000
KS ci ratio: 5.285686e-01	ci left: 1.126848e-05	ci right 1.957170e-05	k: 54	n:3600000
TP53   3600000 perm   6524 sec   (552 perm/sec)   p_kst 1.500000e-05   p_cons 1.755833e-03   p_joint 2.666667e-05

Joint ci ratio: 3.980103e-01	ci left: 2.154030e-05	ci right 3.247426e-05	k: 96	n:3610000
Cons ci ratio: 4.920750e-02	ci left: 1.711661e-03	ci right 1.798283e-03	k: 6334	n:3610000
KS ci ratio: 5.285686e-01	ci left: 1.123727e-05	ci right 1.951749e-05	k: 54	n:3610000
TP53   3610000 perm   6557 sec   (551 perm/sec)   p_kst 1.495845e-05   p_cons 1.754571e-03   p_joint 2.659280e-05

Joint ci ratio: 3.980103e-01	ci left: 2.148080e-05	ci right 3.238455e-05	k: 96	n:3620000
Cons ci ratio: 4.913386e-02	ci left: 1.712116e-03	ci right 1.798629e-03	k: 6353	n:3620000
KS ci ratio: 5.285686e-01	ci left: 1.120622e-05	ci right 1.946357e-05	k: 54	n:3620000
TP53   3620000 perm   6591 sec   (549 perm/sec)   p_kst 1.491713e-05   p_cons 1.754972e-03   p_joint 2.651934e-05

Joint ci ratio: 3.959744e-01	ci left: 2.166960e-05	ci right 3.259819e-05	k: 97	n:3630000
Cons ci ratio: 4.906441e-02	ci left: 1.712298e-03	ci right 1.798693e-03	k: 6371	n:3630000
KS ci ratio: 5.285686e-01	ci left: 1.117535e-05	ci right 1.940995e-05	k: 54	n:3630000
TP53   3630000 perm   6624 sec   (548 perm/sec)   p_kst 1.487603e-05   p_cons 1.755096e-03   p_joint 2.672176e-05

Joint ci ratio: 3.959744e-01	ci left: 2.161007e-05	ci right 3.250863e-05	k: 97	n:3640000
Cons ci ratio: 4.899910e-02	ci left: 1.712207e-03	ci right 1.798479e-03	k: 6388	n:3640000
KS ci ratio: 5.285686e-01	ci left: 1.114465e-05	ci right 1.935663e-05	k: 54	n:3640000
TP53   3640000 perm   6658 sec   (547 perm/sec)   p_kst 1.483516e-05   p_cons 1.754945e-03   p_joint 2.664835e-05

Joint ci ratio: 3.939694e-01	ci left: 2.179762e-05	ci right 3.272062e-05	k: 98	n:3650000
Cons ci ratio: 4.895318e-02	ci left: 1.710763e-03	ci right 1.796880e-03	k: 6400	n:3650000
KS ci ratio: 5.238279e-01	ci left: 1.135167e-05	ci right 1.961367e-05	k: 55	n:3650000
TP53   3650000 perm   6691 sec   (545 perm/sec)   p_kst 1.506849e-05   p_cons 1.753425e-03   p_joint 2.684932e-05

Joint ci ratio: 3.939694e-01	ci left: 2.173807e-05	ci right 3.263122e-05	k: 98	n:3660000
Cons ci ratio: 4.888068e-02	ci left: 1.711216e-03	ci right 1.797225e-03	k: 6419	n:3660000
KS ci ratio: 5.238280e-01	ci left: 1.132066e-05	ci right 1.956008e-05	k: 55	n:3660000
TP53   3660000 perm   6725 sec   (544 perm/sec)   p_kst 1.502732e-05   p_cons 1.753825e-03   p_joint 2.677596e-05

Joint ci ratio: 3.919946e-01	ci left: 2.192439e-05	ci right 3.284158e-05	k: 99	n:3670000
Cons ci ratio: 4.881990e-02	ci left: 1.710860e-03	ci right 1.796741e-03	k: 6435	n:3670000
KS ci ratio: 5.238280e-01	ci left: 1.128981e-05	ci right 1.950678e-05	k: 55	n:3670000
TP53   3670000 perm   6759 sec   (543 perm/sec)   p_kst 1.498638e-05   p_cons 1.753406e-03   p_joint 2.697548e-05

Joint ci ratio: 3.919946e-01	ci left: 2.186481e-05	ci right 3.275234e-05	k: 99	n:3680000
Cons ci ratio: 4.877448e-02	ci left: 1.709432e-03	ci right 1.795159e-03	k: 6447	n:3680000
KS ci ratio: 5.238280e-01	ci left: 1.125913e-05	ci right 1.945378e-05	k: 55	n:3680000
TP53   3680000 perm   6793 sec   (542 perm/sec)   p_kst 1.494565e-05   p_cons 1.751902e-03   p_joint 2.690217e-05

Joint ci ratio: 3.919946e-01	ci left: 2.180556e-05	ci right 3.266358e-05	k: 99	n:3690000
Cons ci ratio: 4.873298e-02	ci left: 1.707744e-03	ci right 1.793312e-03	k: 6458	n:3690000
KS ci ratio: 5.238280e-01	ci left: 1.122862e-05	ci right 1.940106e-05	k: 55	n:3690000
TP53   3690000 perm   6827 sec   (540 perm/sec)   p_kst 1.490515e-05   p_cons 1.750136e-03   p_joint 2.682927e-05

Joint ci ratio: 3.900492e-01	ci left: 2.199032e-05	ci right 3.287201e-05	k: 100	n:3700000
Cons ci ratio: 4.866521e-02	ci left: 1.707934e-03	ci right 1.793389e-03	k: 6476	n:3700000
KS ci ratio: 5.238280e-01	ci left: 1.119827e-05	ci right 1.934862e-05	k: 55	n:3700000
TP53   3700000 perm   6861 sec   (539 perm/sec)   p_kst 1.486486e-05   p_cons 1.750270e-03   p_joint 2.702703e-05

Joint ci ratio: 3.881324e-01	ci left: 2.217422e-05	ci right 3.307919e-05	k: 101	n:3710000
Cons ci ratio: 4.857900e-02	ci left: 1.709455e-03	ci right 1.794830e-03	k: 6499	n:3710000
KS ci ratio: 5.238280e-01	ci left: 1.116809e-05	ci right 1.929647e-05	k: 55	n:3710000
TP53   3710000 perm   6895 sec   (538 perm/sec)   p_kst 1.482480e-05   p_cons 1.751752e-03   p_joint 2.722372e-05

Joint ci ratio: 3.862437e-01	ci left: 2.235726e-05	ci right 3.328513e-05	k: 102	n:3720000
Cons ci ratio: 4.851933e-02	ci left: 1.709108e-03	ci right 1.794358e-03	k: 6515	n:3720000
KS ci ratio: 5.192126e-01	ci left: 1.137147e-05	ci right 1.954852e-05	k: 56	n:3720000
TP53   3720000 perm   6929 sec   (537 perm/sec)   p_kst 1.505376e-05   p_cons 1.751344e-03   p_joint 2.741935e-05

Joint ci ratio: 3.862437e-01	ci left: 2.229732e-05	ci right 3.319589e-05	k: 102	n:3730000
Cons ci ratio: 4.847103e-02	ci left: 1.707969e-03	ci right 1.793075e-03	k: 6528	n:3730000
KS ci ratio: 5.192126e-01	ci left: 1.134098e-05	ci right 1.949611e-05	k: 56	n:3730000
TP53   3730000 perm   6964 sec   (536 perm/sec)   p_kst 1.501340e-05   p_cons 1.750134e-03   p_joint 2.734584e-05

Joint ci ratio: 3.862437e-01	ci left: 2.223770e-05	ci right 3.310713e-05	k: 102	n:3740000
Cons ci ratio: 4.836736e-02	ci left: 1.710799e-03	ci right 1.795858e-03	k: 6556	n:3740000
KS ci ratio: 5.192127e-01	ci left: 1.131066e-05	ci right 1.944398e-05	k: 56	n:3740000
TP53   3740000 perm   6998 sec   (534 perm/sec)   p_kst 1.497326e-05   p_cons 1.752941e-03   p_joint 2.727273e-05

Joint ci ratio: 3.862437e-01	ci left: 2.217840e-05	ci right 3.301885e-05	k: 102	n:3750000
Cons ci ratio: 4.829743e-02	ci left: 1.711242e-03	ci right 1.796197e-03	k: 6575	n:3750000
KS ci ratio: 5.192127e-01	ci left: 1.128050e-05	ci right 1.939213e-05	k: 56	n:3750000
TP53   3750000 perm   7033 sec   (533 perm/sec)   p_kst 1.493333e-05   p_cons 1.753333e-03   p_joint 2.720000e-05

Joint ci ratio: 3.862437e-01	ci left: 2.211942e-05	ci right 3.293103e-05	k: 102	n:3760000
Cons ci ratio: 4.824245e-02	ci left: 1.710632e-03	ci right 1.795457e-03	k: 6590	n:3760000
KS ci ratio: 5.192127e-01	ci left: 1.125050e-05	ci right 1.934056e-05	k: 56	n:3760000
TP53   3760000 perm   7068 sec   (532 perm/sec)   p_kst 1.489362e-05   p_cons 1.752660e-03   p_joint 2.712766e-05

Joint ci ratio: 3.862437e-01	ci left: 2.206074e-05	ci right 3.284368e-05	k: 102	n:3770000
Cons ci ratio: 4.818767e-02	ci left: 1.710025e-03	ci right 1.794722e-03	k: 6605	n:3770000
KS ci ratio: 5.192127e-01	ci left: 1.122066e-05	ci right 1.928926e-05	k: 56	n:3770000
TP53   3770000 perm   7102 sec   (531 perm/sec)   p_kst 1.485411e-05   p_cons 1.751989e-03   p_joint 2.705570e-05

Joint ci ratio: 3.862438e-01	ci left: 2.200238e-05	ci right 3.275679e-05	k: 102	n:3780000
Cons ci ratio: 4.812579e-02	ci left: 1.709945e-03	ci right 1.794525e-03	k: 6622	n:3780000
KS ci ratio: 5.192127e-01	ci left: 1.119097e-05	ci right 1.923823e-05	k: 56	n:3780000
TP53   3780000 perm   7137 sec   (530 perm/sec)   p_kst 1.481481e-05   p_cons 1.751852e-03   p_joint 2.698413e-05

Joint ci ratio: 3.862438e-01	ci left: 2.194433e-05	ci right 3.267037e-05	k: 102	n:3790000
Cons ci ratio: 4.806414e-02	ci left: 1.709864e-03	ci right 1.794330e-03	k: 6639	n:3790000
KS ci ratio: 5.192127e-01	ci left: 1.116144e-05	ci right 1.918747e-05	k: 56	n:3790000
TP53   3790000 perm   7172 sec   (528 perm/sec)   p_kst 1.477573e-05   p_cons 1.751715e-03   p_joint 2.691293e-05

Joint ci ratio: 3.862438e-01	ci left: 2.188658e-05	ci right 3.258439e-05	k: 102	n:3800000
Cons ci ratio: 4.798469e-02	ci left: 1.711085e-03	ci right 1.795467e-03	k: 6661	n:3800000
KS ci ratio: 5.192127e-01	ci left: 1.113207e-05	ci right 1.913697e-05	k: 56	n:3800000
TP53   3800000 perm   7207 sec   (527 perm/sec)   p_kst 1.473684e-05   p_cons 1.752895e-03   p_joint 2.684211e-05

Joint ci ratio: 3.862438e-01	ci left: 2.182914e-05	ci right 3.249887e-05	k: 102	n:3810000
Cons ci ratio: 4.793437e-02	ci left: 1.710224e-03	ci right 1.794473e-03	k: 6675	n:3810000
KS ci ratio: 5.192127e-01	ci left: 1.110285e-05	ci right 1.908675e-05	k: 56	n:3810000
TP53   3810000 perm   7242 sec   (526 perm/sec)   p_kst 1.469816e-05   p_cons 1.751969e-03   p_joint 2.677165e-05

Joint ci ratio: 3.862438e-01	ci left: 2.177199e-05	ci right 3.241379e-05	k: 102	n:3820000
Cons ci ratio: 4.787704e-02	ci left: 1.709885e-03	ci right 1.794014e-03	k: 6691	n:3820000
KS ci ratio: 5.192127e-01	ci left: 1.107379e-05	ci right 1.903678e-05	k: 56	n:3820000
TP53   3820000 perm   7277 sec   (525 perm/sec)   p_kst 1.465969e-05   p_cons 1.751571e-03   p_joint 2.670157e-05

Joint ci ratio: 3.862438e-01	ci left: 2.171514e-05	ci right 3.232916e-05	k: 102	n:3830000
Cons ci ratio: 4.781278e-02	ci left: 1.710065e-03	ci right 1.794086e-03	k: 6709	n:3830000
KS ci ratio: 5.192128e-01	ci left: 1.104487e-05	ci right 1.898708e-05	k: 56	n:3830000
TP53   3830000 perm   7312 sec   (524 perm/sec)   p_kst 1.462141e-05   p_cons 1.751697e-03   p_joint 2.663185e-05

Joint ci ratio: 3.862438e-01	ci left: 2.165859e-05	ci right 3.224497e-05	k: 102	n:3840000
Cons ci ratio: 4.774522e-02	ci left: 1.710500e-03	ci right 1.794421e-03	k: 6728	n:3840000
KS ci ratio: 5.192128e-01	ci left: 1.101611e-05	ci right 1.893763e-05	k: 56	n:3840000
TP53   3840000 perm   7348 sec   (523 perm/sec)   p_kst 1.458333e-05   p_cons 1.752083e-03   p_joint 2.656250e-05

Joint ci ratio: 3.825476e-01	ci left: 2.207162e-05	ci right 3.273066e-05	k: 104	n:3850000
Cons ci ratio: 4.768503e-02	ci left: 1.710420e-03	ci right 1.794228e-03	k: 6745	n:3850000
KS ci ratio: 5.103366e-01	ci left: 1.143946e-05	ci right 1.947488e-05	k: 58	n:3850000
TP53   3850000 perm   7385 sec   (521 perm/sec)   p_kst 1.506494e-05   p_cons 1.751948e-03   p_joint 2.701299e-05

Joint ci ratio: 3.825476e-01	ci left: 2.201444e-05	ci right 3.264587e-05	k: 104	n:3860000
Cons ci ratio: 4.762506e-02	ci left: 1.710341e-03	ci right 1.794037e-03	k: 6762	n:3860000
KS ci ratio: 5.103366e-01	ci left: 1.140982e-05	ci right 1.942443e-05	k: 58	n:3860000
TP53   3860000 perm   7421 sec   (520 perm/sec)   p_kst 1.502591e-05   p_cons 1.751813e-03   p_joint 2.694301e-05

Joint ci ratio: 3.807388e-01	ci left: 2.219116e-05	ci right 3.284458e-05	k: 105	n:3870000
Cons ci ratio: 4.756180e-02	ci left: 1.710517e-03	ci right 1.794107e-03	k: 6780	n:3870000
KS ci ratio: 5.060658e-01	ci left: 1.160558e-05	ci right 1.966551e-05	k: 59	n:3870000
TP53   3870000 perm   7457 sec   (519 perm/sec)   p_kst 1.524548e-05   p_cons 1.751938e-03   p_joint 2.713178e-05

Joint ci ratio: 3.807388e-01	ci left: 2.213397e-05	ci right 3.275993e-05	k: 105	n:3880000
Cons ci ratio: 4.749880e-02	ci left: 1.710692e-03	ci right 1.794178e-03	k: 6798	n:3880000
KS ci ratio: 5.060658e-01	ci left: 1.157567e-05	ci right 1.961483e-05	k: 59	n:3880000
TP53   3880000 perm   7492 sec   (518 perm/sec)   p_kst 1.520619e-05   p_cons 1.752062e-03   p_joint 2.706186e-05

Joint ci ratio: 3.807388e-01	ci left: 2.207707e-05	ci right 3.267572e-05	k: 105	n:3890000
Cons ci ratio: 4.743953e-02	ci left: 1.710613e-03	ci right 1.793987e-03	k: 6815	n:3890000
KS ci ratio: 5.060659e-01	ci left: 1.154591e-05	ci right 1.956440e-05	k: 59	n:3890000
TP53   3890000 perm   7529 sec   (517 perm/sec)   p_kst 1.516710e-05   p_cons 1.751928e-03   p_joint 2.699229e-05

Joint ci ratio: 3.789555e-01	ci left: 2.225239e-05	ci right 3.287271e-05	k: 106	n:3900000
Cons ci ratio: 4.738049e-02	ci left: 1.710534e-03	ci right 1.793798e-03	k: 6832	n:3900000
KS ci ratio: 5.060659e-01	ci left: 1.151631e-05	ci right 1.951424e-05	k: 59	n:3900000
TP53   3900000 perm   7565 sec   (516 perm/sec)   p_kst 1.512821e-05   p_cons 1.751795e-03   p_joint 2.717949e-05

Joint ci ratio: 3.789555e-01	ci left: 2.219548e-05	ci right 3.278864e-05	k: 106	n:3910000
Cons ci ratio: 4.731128e-02	ci left: 1.711214e-03	ci right 1.794386e-03	k: 6852	n:3910000
KS ci ratio: 5.060659e-01	ci left: 1.148686e-05	ci right 1.946433e-05	k: 59	n:3910000
TP53   3910000 perm   7601 sec   (514 perm/sec)   p_kst 1.508951e-05   p_cons 1.752430e-03   p_joint 2.710997e-05

Joint ci ratio: 3.789555e-01	ci left: 2.213886e-05	ci right 3.270500e-05	k: 106	n:3920000
Cons ci ratio: 4.725960e-02	ci left: 1.710630e-03	ci right 1.793680e-03	k: 6867	n:3920000
KS ci ratio: 5.060659e-01	ci left: 1.145755e-05	ci right 1.941468e-05	k: 59	n:3920000
TP53   3920000 perm   7638 sec   (513 perm/sec)   p_kst 1.505102e-05   p_cons 1.751786e-03   p_joint 2.704082e-05

Joint ci ratio: 3.789555e-01	ci left: 2.208252e-05	ci right 3.262178e-05	k: 106	n:3930000
Cons ci ratio: 4.721497e-02	ci left: 1.709546e-03	ci right 1.792463e-03	k: 6880	n:3930000
KS ci ratio: 5.060659e-01	ci left: 1.142840e-05	ci right 1.936528e-05	k: 59	n:3930000
TP53   3930000 perm   7674 sec   (512 perm/sec)   p_kst 1.501272e-05   p_cons 1.750636e-03   p_joint 2.697201e-05

Joint ci ratio: 3.789555e-01	ci left: 2.202648e-05	ci right 3.253898e-05	k: 106	n:3940000
Cons ci ratio: 4.716018e-02	ci left: 1.709220e-03	ci right 1.792023e-03	k: 6896	n:3940000
KS ci ratio: 5.060659e-01	ci left: 1.139939e-05	ci right 1.931613e-05	k: 59	n:3940000
TP53   3940000 perm   7710 sec   (511 perm/sec)   p_kst 1.497462e-05   p_cons 1.750254e-03   p_joint 2.690355e-05

Joint ci ratio: 3.789555e-01	ci left: 2.197071e-05	ci right 3.245660e-05	k: 106	n:3950000
Cons ci ratio: 4.709876e-02	ci left: 1.709396e-03	ci right 1.792096e-03	k: 6914	n:3950000
KS ci ratio: 5.060659e-01	ci left: 1.137053e-05	ci right 1.926722e-05	k: 59	n:3950000
TP53   3950000 perm   7747 sec   (510 perm/sec)   p_kst 1.493671e-05   p_cons 1.750380e-03   p_joint 2.683544e-05

Joint ci ratio: 3.789555e-01	ci left: 2.191523e-05	ci right 3.237464e-05	k: 106	n:3960000
Cons ci ratio: 4.703418e-02	ci left: 1.709821e-03	ci right 1.792425e-03	k: 6933	n:3960000
KS ci ratio: 5.060659e-01	ci left: 1.134182e-05	ci right 1.921857e-05	k: 59	n:3960000
TP53   3960000 perm   7783 sec   (509 perm/sec)   p_kst 1.489899e-05   p_cons 1.750758e-03   p_joint 2.676768e-05

Joint ci ratio: 3.789555e-01	ci left: 2.186003e-05	ci right 3.229310e-05	k: 106	n:3970000
Cons ci ratio: 4.699356e-02	ci left: 1.708501e-03	ci right 1.790969e-03	k: 6945	n:3970000
KS ci ratio: 5.060659e-01	ci left: 1.131325e-05	ci right 1.917016e-05	k: 59	n:3970000
TP53   3970000 perm   7820 sec   (508 perm/sec)   p_kst 1.486146e-05   p_cons 1.749370e-03   p_joint 2.670025e-05

Joint ci ratio: 3.789556e-01	ci left: 2.180510e-05	ci right 3.221196e-05	k: 106	n:3980000
Cons ci ratio: 4.692941e-02	ci left: 1.708926e-03	ci right 1.791299e-03	k: 6964	n:3980000
KS ci ratio: 5.060659e-01	ci left: 1.128483e-05	ci right 1.912199e-05	k: 59	n:3980000
TP53   3980000 perm   7857 sec   (507 perm/sec)   p_kst 1.482412e-05   p_cons 1.749749e-03   p_joint 2.663317e-05

Joint ci ratio: 3.789556e-01	ci left: 2.175045e-05	ci right 3.213123e-05	k: 106	n:3990000
Cons ci ratio: 4.684537e-02	ci left: 1.710836e-03	ci right 1.793148e-03	k: 6989	n:3990000
KS ci ratio: 5.060660e-01	ci left: 1.125654e-05	ci right 1.907407e-05	k: 59	n:3990000
TP53   3990000 perm   7894 sec   (505 perm/sec)   p_kst 1.478697e-05   p_cons 1.751629e-03   p_joint 2.656642e-05

Joint ci ratio: 3.771970e-01	ci left: 2.192232e-05	ci right 3.232455e-05	k: 107	n:4000000
Cons ci ratio: 4.677180e-02	ci left: 1.711994e-03	ci right 1.794230e-03	k: 7011	n:4000000
KS ci ratio: 5.019007e-01	ci left: 1.144660e-05	ci right 1.930793e-05	k: 60	n:4000000
TP53   4000000 perm   7930 sec   (504 perm/sec)   p_kst 1.500000e-05   p_cons 1.752750e-03   p_joint 2.675000e-05

Joint ci ratio: 3.737522e-01	ci left: 2.231934e-05	ci right 3.278954e-05	k: 109	n:4010000
Cons ci ratio: 4.671521e-02	ci left: 1.711915e-03	ci right 1.794044e-03	k: 7028	n:4010000
KS ci ratio: 4.978366e-01	ci left: 1.163597e-05	ci right 1.954037e-05	k: 61	n:4010000
TP53   4010000 perm   7967 sec   (503 perm/sec)   p_kst 1.521197e-05   p_cons 1.752618e-03   p_joint 2.718204e-05

Joint ci ratio: 3.737522e-01	ci left: 2.226382e-05	ci right 3.270798e-05	k: 109	n:4020000
Cons ci ratio: 4.666877e-02	ci left: 1.711098e-03	ci right 1.793105e-03	k: 7042	n:4020000
KS ci ratio: 4.978366e-01	ci left: 1.160703e-05	ci right 1.949176e-05	k: 61	n:4020000
TP53   4020000 perm   8004 sec   (502 perm/sec)   p_kst 1.517413e-05   p_cons 1.751741e-03   p_joint 2.711443e-05

Joint ci ratio: 3.737522e-01	ci left: 2.220857e-05	ci right 3.262682e-05	k: 109	n:4030000
Cons ci ratio: 4.661917e-02	ci left: 1.710531e-03	ci right 1.792421e-03	k: 7057	n:4030000
KS ci ratio: 4.978366e-01	ci left: 1.157822e-05	ci right 1.944340e-05	k: 61	n:4030000
TP53   4030000 perm   8041 sec   (501 perm/sec)   p_kst 1.513648e-05   p_cons 1.751117e-03   p_joint 2.704715e-05

Joint ci ratio: 3.737522e-01	ci left: 2.215360e-05	ci right 3.254606e-05	k: 109	n:4040000
Cons ci ratio: 4.655325e-02	ci left: 1.711190e-03	ci right 1.792992e-03	k: 7077	n:4040000
KS ci ratio: 4.978366e-01	ci left: 1.154957e-05	ci right 1.939527e-05	k: 61	n:4040000
TP53   4040000 perm   8078 sec   (500 perm/sec)   p_kst 1.509901e-05   p_cons 1.751733e-03   p_joint 2.698020e-05

Joint ci ratio: 3.737522e-01	ci left: 2.209890e-05	ci right 3.246570e-05	k: 109	n:4050000
Cons ci ratio: 4.651715e-02	ci left: 1.709649e-03	ci right 1.791313e-03	k: 7088	n:4050000
KS ci ratio: 4.978366e-01	ci left: 1.152105e-05	ci right 1.934738e-05	k: 61	n:4050000
TP53   4050000 perm   8115 sec   (499 perm/sec)   p_kst 1.506173e-05   p_cons 1.750123e-03   p_joint 2.691358e-05

Joint ci ratio: 3.720648e-01	ci left: 2.226769e-05	ci right 3.265502e-05	k: 110	n:4060000
Cons ci ratio: 4.644184e-02	ci left: 1.711037e-03	ci right 1.792632e-03	k: 7111	n:4060000
KS ci ratio: 4.978366e-01	ci left: 1.149267e-05	ci right 1.929973e-05	k: 61	n:4060000
TP53   4060000 perm   8152 sec   (498 perm/sec)   p_kst 1.502463e-05   p_cons 1.751478e-03   p_joint 2.709360e-05

Joint ci ratio: 3.720648e-01	ci left: 2.221298e-05	ci right 3.257479e-05	k: 110	n:4070000
Cons ci ratio: 4.639948e-02	ci left: 1.709990e-03	ci right 1.791458e-03	k: 7124	n:4070000
KS ci ratio: 4.978366e-01	ci left: 1.146443e-05	ci right 1.925231e-05	k: 61	n:4070000
TP53   4070000 perm   8189 sec   (497 perm/sec)   p_kst 1.498771e-05   p_cons 1.750369e-03   p_joint 2.702703e-05

Joint ci ratio: 3.720648e-01	ci left: 2.215854e-05	ci right 3.249495e-05	k: 110	n:4080000
Cons ci ratio: 4.633773e-02	ci left: 1.710402e-03	ci right 1.791778e-03	k: 7143	n:4080000
KS ci ratio: 4.978367e-01	ci left: 1.143633e-05	ci right 1.920512e-05	k: 61	n:4080000
TP53   4080000 perm   8227 sec   (496 perm/sec)   p_kst 1.495098e-05   p_cons 1.750735e-03   p_joint 2.696078e-05

Joint ci ratio: 3.720648e-01	ci left: 2.210436e-05	ci right 3.241550e-05	k: 110	n:4090000
Cons ci ratio: 4.627946e-02	ci left: 1.710570e-03	ci right 1.791849e-03	k: 7161	n:4090000
KS ci ratio: 4.978367e-01	ci left: 1.140837e-05	ci right 1.915816e-05	k: 61	n:4090000
TP53   4090000 perm   8264 sec   (495 perm/sec)   p_kst 1.491443e-05   p_cons 1.750856e-03   p_joint 2.689487e-05

Joint ci ratio: 3.720649e-01	ci left: 2.205045e-05	ci right 3.233643e-05	k: 110	n:4100000
Cons ci ratio: 4.625046e-02	ci left: 1.708568e-03	ci right 1.789700e-03	k: 7170	n:4100000
KS ci ratio: 4.978367e-01	ci left: 1.138055e-05	ci right 1.911144e-05	k: 61	n:4100000
TP53   4100000 perm   8302 sec   (494 perm/sec)   p_kst 1.487805e-05   p_cons 1.748780e-03   p_joint 2.682927e-05

Joint ci ratio: 3.720649e-01	ci left: 2.199679e-05	ci right 3.225776e-05	k: 110	n:4110000
Cons ci ratio: 4.618608e-02	ci left: 1.709221e-03	ci right 1.790267e-03	k: 7190	n:4110000
KS ci ratio: 4.978367e-01	ci left: 1.135286e-05	ci right 1.906494e-05	k: 61	n:4110000
TP53   4110000 perm   8340 sec   (493 perm/sec)   p_kst 1.484185e-05   p_cons 1.749392e-03   p_joint 2.676399e-05

Joint ci ratio: 3.720649e-01	ci left: 2.194340e-05	ci right 3.217946e-05	k: 110	n:4120000
Cons ci ratio: 4.614441e-02	ci left: 1.708191e-03	ci right 1.789114e-03	k: 7203	n:4120000
KS ci ratio: 4.978367e-01	ci left: 1.132530e-05	ci right 1.901866e-05	k: 61	n:4120000
TP53   4120000 perm   8377 sec   (492 perm/sec)   p_kst 1.480583e-05   p_cons 1.748301e-03   p_joint 2.669903e-05

Joint ci ratio: 3.720649e-01	ci left: 2.189027e-05	ci right 3.210155e-05	k: 110	n:4130000
Cons ci ratio: 4.610606e-02	ci left: 1.706927e-03	ci right 1.787721e-03	k: 7215	n:4130000
KS ci ratio: 4.978367e-01	ci left: 1.129788e-05	ci right 1.897261e-05	k: 61	n:4130000
TP53   4130000 perm   8415 sec   (491 perm/sec)   p_kst 1.476998e-05   p_cons 1.746973e-03   p_joint 2.663438e-05

Joint ci ratio: 3.704001e-01	ci left: 2.205641e-05	ci right 3.228799e-05	k: 111	n:4140000
Cons ci ratio: 4.606142e-02	ci left: 1.706147e-03	ci right 1.786823e-03	k: 7229	n:4140000
KS ci ratio: 4.978367e-01	ci left: 1.127059e-05	ci right 1.892678e-05	k: 61	n:4140000
TP53   4140000 perm   8453 sec   (490 perm/sec)   p_kst 1.473430e-05   p_cons 1.746135e-03   p_joint 2.681159e-05

Joint ci ratio: 3.704001e-01	ci left: 2.200326e-05	ci right 3.221018e-05	k: 111	n:4150000
Cons ci ratio: 4.602009e-02	ci left: 1.705132e-03	ci right 1.785686e-03	k: 7242	n:4150000
KS ci ratio: 4.978367e-01	ci left: 1.124343e-05	ci right 1.888118e-05	k: 61	n:4150000
TP53   4150000 perm   8492 sec   (489 perm/sec)   p_kst 1.469880e-05   p_cons 1.745060e-03   p_joint 2.674699e-05

Joint ci ratio: 3.704002e-01	ci left: 2.195037e-05	ci right 3.213276e-05	k: 111	n:4160000
Cons ci ratio: 4.596618e-02	ci left: 1.705072e-03	ci right 1.785527e-03	k: 7259	n:4160000
KS ci ratio: 4.978367e-01	ci left: 1.121640e-05	ci right 1.883579e-05	k: 61	n:4160000
TP53   4160000 perm   8530 sec   (488 perm/sec)   p_kst 1.466346e-05   p_cons 1.744952e-03   p_joint 2.668269e-05

Joint ci ratio: 3.687575e-01	ci left: 2.211527e-05	ci right 3.231768e-05	k: 112	n:4170000
Cons ci ratio: 4.590298e-02	ci left: 1.705725e-03	ci right 1.786097e-03	k: 7279	n:4170000
KS ci ratio: 4.938698e-01	ci left: 1.139931e-05	ci right 1.906020e-05	k: 62	n:4170000
TP53   4170000 perm   8568 sec   (487 perm/sec)   p_kst 1.486811e-05   p_cons 1.745564e-03   p_joint 2.685851e-05

Joint ci ratio: 3.687576e-01	ci left: 2.206236e-05	ci right 3.224037e-05	k: 112	n:4180000
Cons ci ratio: 4.587153e-02	ci left: 1.704009e-03	ci right 1.784244e-03	k: 7289	n:4180000
KS ci ratio: 4.938698e-01	ci left: 1.137204e-05	ci right 1.901460e-05	k: 62	n:4180000
TP53   4180000 perm   8607 sec   (486 perm/sec)   p_kst 1.483254e-05   p_cons 1.743780e-03   p_joint 2.679426e-05

Joint ci ratio: 3.687576e-01	ci left: 2.200970e-05	ci right 3.216342e-05	k: 112	n:4190000
Cons ci ratio: 4.581814e-02	ci left: 1.703953e-03	ci right 1.784089e-03	k: 7306	n:4190000
KS ci ratio: 4.938698e-01	ci left: 1.134490e-05	ci right 1.896922e-05	k: 62	n:4190000
TP53   4190000 perm   8645 sec   (485 perm/sec)   p_kst 1.479714e-05   p_cons 1.743675e-03   p_joint 2.673031e-05

Joint ci ratio: 3.671366e-01	ci left: 2.217338e-05	ci right 3.234686e-05	k: 113	n:4200000
Cons ci ratio: 4.576181e-02	ci left: 1.704132e-03	ci right 1.784176e-03	k: 7324	n:4200000
KS ci ratio: 4.938698e-01	ci left: 1.131789e-05	ci right 1.892406e-05	k: 62	n:4200000
TP53   4200000 perm   8684 sec   (484 perm/sec)   p_kst 1.476190e-05   p_cons 1.743810e-03   p_joint 2.690476e-05

Joint ci ratio: 3.671366e-01	ci left: 2.212071e-05	ci right 3.227002e-05	k: 113	n:4210000
Cons ci ratio: 4.571504e-02	ci left: 1.703607e-03	ci right 1.783542e-03	k: 7339	n:4210000
KS ci ratio: 4.938698e-01	ci left: 1.129100e-05	ci right 1.887911e-05	k: 62	n:4210000
TP53   4210000 perm   8722 sec   (483 perm/sec)   p_kst 1.472684e-05   p_cons 1.743230e-03   p_joint 2.684086e-05

Joint ci ratio: 3.655369e-01	ci left: 2.228345e-05	ci right 3.245224e-05	k: 114	n:4220000
Cons ci ratio: 4.564976e-02	ci left: 1.704489e-03	ci right 1.784349e-03	k: 7360	n:4220000
KS ci ratio: 4.938698e-01	ci left: 1.126425e-05	ci right 1.883437e-05	k: 62	n:4220000
TP53   4220000 perm   8761 sec   (482 perm/sec)   p_kst 1.469194e-05   p_cons 1.744076e-03   p_joint 2.701422e-05

Joint ci ratio: 4.000787e-01	ci left: 1.817041e-05	ci right 2.745444e-05	k: 95	n:4230000
Cons ci ratio: 4.560024e-02	ci left: 1.704199e-03	ci right 1.783956e-03	k: 7376	n:4230000
KS ci ratio: 4.938698e-01	ci left: 1.123762e-05	ci right 1.878984e-05	k: 62	n:4230000
TP53   4230000 perm   8800 sec   (481 perm/sec)   p_kst 1.465721e-05   p_cons 1.743735e-03   p_joint 2.245863e-05

Joint ci ratio: 4.000787e-01	ci left: 1.812755e-05	ci right 2.738969e-05	k: 95	n:4240000
Cons ci ratio: 4.554162e-02	ci left: 1.704610e-03	ci right 1.784281e-03	k: 7395	n:4240000
KS ci ratio: 4.938699e-01	ci left: 1.121111e-05	ci right 1.874553e-05	k: 62	n:4240000
TP53   4240000 perm   8839 sec   (480 perm/sec)   p_kst 1.462264e-05   p_cons 1.744104e-03   p_joint 2.240566e-05

Joint ci ratio: 4.000788e-01	ci left: 1.808490e-05	ci right 2.732524e-05	k: 95	n:4250000
Cons ci ratio: 4.549552e-02	ci left: 1.704088e-03	ci right 1.783652e-03	k: 7410	n:4250000
KS ci ratio: 4.938699e-01	ci left: 1.118473e-05	ci right 1.870142e-05	k: 62	n:4250000
TP53   4250000 perm   8878 sec   (479 perm/sec)   p_kst 1.458824e-05   p_cons 1.743529e-03   p_joint 2.235294e-05

Joint ci ratio: 4.000788e-01	ci left: 1.804245e-05	ci right 2.726110e-05	k: 95	n:4260000
Cons ci ratio: 4.544649e-02	ci left: 1.703801e-03	ci right 1.783264e-03	k: 7426	n:4260000
KS ci ratio: 4.938699e-01	ci left: 1.115848e-05	ci right 1.865752e-05	k: 62	n:4260000
TP53   4260000 perm   8918 sec   (478 perm/sec)   p_kst 1.455399e-05   p_cons 1.743192e-03   p_joint 2.230047e-05

Joint ci ratio: 3.959752e-01	ci left: 1.842169e-05	ci right 2.771229e-05	k: 97	n:4270000
Cons ci ratio: 4.539763e-02	ci left: 1.703516e-03	ci right 1.782877e-03	k: 7442	n:4270000
KS ci ratio: 4.938699e-01	ci left: 1.113235e-05	ci right 1.861383e-05	k: 62	n:4270000
TP53   4270000 perm   8957 sec   (477 perm/sec)   p_kst 1.451991e-05   p_cons 1.742857e-03   p_joint 2.271663e-05

Joint ci ratio: 3.959752e-01	ci left: 1.837865e-05	ci right 2.764754e-05	k: 97	n:4280000
Cons ci ratio: 4.534892e-02	ci left: 1.703231e-03	ci right 1.782492e-03	k: 7458	n:4280000
KS ci ratio: 4.938699e-01	ci left: 1.110634e-05	ci right 1.857034e-05	k: 62	n:4280000
TP53   4280000 perm   8996 sec   (476 perm/sec)   p_kst 1.448598e-05   p_cons 1.742523e-03   p_joint 2.266355e-05

Joint ci ratio: 3.959752e-01	ci left: 1.833581e-05	ci right 2.758310e-05	k: 97	n:4290000
Cons ci ratio: 4.528520e-02	ci left: 1.704101e-03	ci right 1.783288e-03	k: 7479	n:4290000
KS ci ratio: 4.938699e-01	ci left: 1.108045e-05	ci right 1.852705e-05	k: 62	n:4290000
TP53   4290000 perm   9035 sec   (475 perm/sec)   p_kst 1.445221e-05   p_cons 1.743357e-03   p_joint 2.261072e-05

Joint ci ratio: 4.382652e-01	ci left: 1.454539e-05	ci right 2.289706e-05	k: 79	n:4300000
Cons ci ratio: 4.397377e-02	ci left: 1.804083e-03	ci right 1.885427e-03	k: 7931	n:4300000
KS ci ratio: 4.938699e-01	ci left: 1.105468e-05	ci right 1.848396e-05	k: 62	n:4300000
TP53   4300000 perm   9075 sec   (474 perm/sec)   p_kst 1.441860e-05   p_cons 1.844419e-03   p_joint 1.837209e-05

Joint ci ratio: 4.382652e-01	ci left: 1.451164e-05	ci right 2.284393e-05	k: 79	n:4310000
Cons ci ratio: 4.391567e-02	ci left: 1.804716e-03	ci right 1.885978e-03	k: 7952	n:4310000
KS ci ratio: 4.938699e-01	ci left: 1.102903e-05	ci right 1.844108e-05	k: 62	n:4310000
TP53   4310000 perm   9114 sec   (473 perm/sec)   p_kst 1.438515e-05   p_cons 1.845012e-03   p_joint 1.832947e-05

Joint ci ratio: 4.382652e-01	ci left: 1.447805e-05	ci right 2.279105e-05	k: 79	n:4320000
Cons ci ratio: 4.386330e-02	ci left: 1.804889e-03	ci right 1.886059e-03	k: 7971	n:4320000
KS ci ratio: 4.938699e-01	ci left: 1.100350e-05	ci right 1.839839e-05	k: 62	n:4320000
TP53   4320000 perm   9154 sec   (472 perm/sec)   p_kst 1.435185e-05   p_cons 1.845139e-03   p_joint 1.828704e-05

Joint ci ratio: 4.382652e-01	ci left: 1.444461e-05	ci right 2.273842e-05	k: 79	n:4330000
Cons ci ratio: 4.383311e-02	ci left: 1.803233e-03	ci right 1.884272e-03	k: 7982	n:4330000
KS ci ratio: 4.938699e-01	ci left: 1.097809e-05	ci right 1.835590e-05	k: 62	n:4330000
TP53   4330000 perm   9194 sec   (471 perm/sec)   p_kst 1.431871e-05   p_cons 1.843418e-03   p_joint 1.824480e-05

Joint ci ratio: 4.382652e-01	ci left: 1.441133e-05	ci right 2.268603e-05	k: 79	n:4340000
Cons ci ratio: 4.378926e-02	ci left: 1.802724e-03	ci right 1.883657e-03	k: 7998	n:4340000
KS ci ratio: 4.938699e-01	ci left: 1.095279e-05	ci right 1.831360e-05	k: 62	n:4340000
TP53   4340000 perm   9234 sec   (470 perm/sec)   p_kst 1.428571e-05   p_cons 1.842857e-03   p_joint 1.820276e-05

Joint ci ratio: 4.382652e-01	ci left: 1.437820e-05	ci right 2.263387e-05	k: 79	n:4350000
Cons ci ratio: 4.372368e-02	ci left: 1.804037e-03	ci right 1.884904e-03	k: 8022	n:4350000
KS ci ratio: 4.938699e-01	ci left: 1.092761e-05	ci right 1.827150e-05	k: 62	n:4350000
TP53   4350000 perm   9275 sec   (469 perm/sec)   p_kst 1.425287e-05   p_cons 1.844138e-03   p_joint 1.816092e-05

Joint ci ratio: 4.382653e-01	ci left: 1.434522e-05	ci right 2.258196e-05	k: 79	n:4360000
Cons ci ratio: 4.366928e-02	ci left: 1.804436e-03	ci right 1.885218e-03	k: 8042	n:4360000
KS ci ratio: 4.938700e-01	ci left: 1.090255e-05	ci right 1.822960e-05	k: 62	n:4360000
TP53   4360000 perm   9315 sec   (468 perm/sec)   p_kst 1.422018e-05   p_cons 1.844495e-03   p_joint 1.811927e-05

Joint ci ratio: 4.382653e-01	ci left: 1.431239e-05	ci right 2.253029e-05	k: 79	n:4370000
Cons ci ratio: 4.362050e-02	ci left: 1.804381e-03	ci right 1.885068e-03	k: 8060	n:4370000
KS ci ratio: 4.938700e-01	ci left: 1.087760e-05	ci right 1.818788e-05	k: 62	n:4370000
TP53   4370000 perm   9355 sec   (467 perm/sec)   p_kst 1.418764e-05   p_cons 1.844394e-03   p_joint 1.807780e-05

Joint ci ratio: 4.382653e-01	ci left: 1.427972e-05	ci right 2.247885e-05	k: 79	n:4380000
Cons ci ratio: 4.357999e-02	ci left: 1.803649e-03	ci right 1.884227e-03	k: 8075	n:4380000
KS ci ratio: 4.938700e-01	ci left: 1.085277e-05	ci right 1.814636e-05	k: 62	n:4380000
TP53   4380000 perm   9395 sec   (466 perm/sec)   p_kst 1.415525e-05   p_cons 1.843607e-03   p_joint 1.803653e-05

Joint ci ratio: 4.382653e-01	ci left: 1.424719e-05	ci right 2.242764e-05	k: 79	n:4390000
Cons ci ratio: 4.353420e-02	ci left: 1.803371e-03	ci right 1.883849e-03	k: 8092	n:4390000
KS ci ratio: 4.938700e-01	ci left: 1.082804e-05	ci right 1.810502e-05	k: 62	n:4390000
TP53   4390000 perm   9436 sec   (465 perm/sec)   p_kst 1.412301e-05   p_cons 1.843280e-03   p_joint 1.799544e-05

Joint ci ratio: 4.382653e-01	ci left: 1.421481e-05	ci right 2.237667e-05	k: 79	n:4400000
Cons ci ratio: 4.349124e-02	ci left: 1.802869e-03	ci right 1.883244e-03	k: 8108	n:4400000
KS ci ratio: 4.938700e-01	ci left: 1.080344e-05	ci right 1.806387e-05	k: 62	n:4400000
TP53   4400000 perm   9476 sec   (464 perm/sec)   p_kst 1.409091e-05   p_cons 1.842727e-03   p_joint 1.795455e-05

Joint ci ratio: 4.355515e-01	ci left: 1.438438e-05	ci right 2.257748e-05	k: 80	n:4410000
Cons ci ratio: 4.343770e-02	ci left: 1.803267e-03	ci right 1.883558e-03	k: 8128	n:4410000
KS ci ratio: 4.899964e-01	ci left: 1.097755e-05	ci right 1.827760e-05	k: 63	n:4410000
TP53   4410000 perm   9516 sec   (463 perm/sec)   p_kst 1.428571e-05   p_cons 1.843084e-03   p_joint 1.814059e-05

Joint ci ratio: 4.355515e-01	ci left: 1.435184e-05	ci right 2.252640e-05	k: 80	n:4420000
Cons ci ratio: 4.336836e-02	ci left: 1.805005e-03	ci right 1.885242e-03	k: 8154	n:4420000
KS ci ratio: 4.899964e-01	ci left: 1.095272e-05	ci right 1.823625e-05	k: 63	n:4420000
TP53   4420000 perm   9557 sec   (463 perm/sec)   p_kst 1.425339e-05   p_cons 1.844796e-03   p_joint 1.809955e-05

Joint ci ratio: 4.355515e-01	ci left: 1.431944e-05	ci right 2.247555e-05	k: 80	n:4430000
Cons ci ratio: 4.333386e-02	ci left: 1.803833e-03	ci right 1.883953e-03	k: 8167	n:4430000
KS ci ratio: 4.899964e-01	ci left: 1.092799e-05	ci right 1.819508e-05	k: 63	n:4430000
TP53   4430000 perm   9598 sec   (462 perm/sec)   p_kst 1.422122e-05   p_cons 1.843567e-03   p_joint 1.805869e-05

Joint ci ratio: 4.355515e-01	ci left: 1.428719e-05	ci right 2.242493e-05	k: 80	n:4440000
Cons ci ratio: 4.328885e-02	ci left: 1.803558e-03	ci right 1.883580e-03	k: 8184	n:4440000
KS ci ratio: 4.899964e-01	ci left: 1.090338e-05	ci right 1.815410e-05	k: 63	n:4440000
TP53   4440000 perm   9638 sec   (461 perm/sec)   p_kst 1.418919e-05   p_cons 1.843243e-03   p_joint 1.801802e-05

Joint ci ratio: 4.355515e-01	ci left: 1.425509e-05	ci right 2.237454e-05	k: 80	n:4450000
Cons ci ratio: 4.323077e-02	ci left: 1.804396e-03	ci right 1.884345e-03	k: 8206	n:4450000
KS ci ratio: 4.899964e-01	ci left: 1.087888e-05	ci right 1.811331e-05	k: 63	n:4450000
TP53   4450000 perm   9679 sec   (460 perm/sec)   p_kst 1.415730e-05   p_cons 1.844045e-03   p_joint 1.797753e-05

Joint ci ratio: 4.355516e-01	ci left: 1.422312e-05	ci right 2.232437e-05	k: 80	n:4460000
Cons ci ratio: 4.316767e-02	ci left: 1.805673e-03	ci right 1.885559e-03	k: 8230	n:4460000
KS ci ratio: 4.899964e-01	ci left: 1.085449e-05	ci right 1.807269e-05	k: 63	n:4460000
TP53   4460000 perm   9721 sec   (459 perm/sec)   p_kst 1.412556e-05   p_cons 1.845291e-03   p_joint 1.793722e-05

Joint ci ratio: 4.355516e-01	ci left: 1.419131e-05	ci right 2.227443e-05	k: 80	n:4470000
Cons ci ratio: 4.312841e-02	ci left: 1.804953e-03	ci right 1.884733e-03	k: 8245	n:4470000
KS ci ratio: 4.899964e-01	ci left: 1.083020e-05	ci right 1.803226e-05	k: 63	n:4470000
TP53   4470000 perm   9762 sec   (458 perm/sec)   p_kst 1.409396e-05   p_cons 1.844519e-03   p_joint 1.789709e-05

Joint ci ratio: 4.355516e-01	ci left: 1.415963e-05	ci right 2.222471e-05	k: 80	n:4480000
Cons ci ratio: 4.307358e-02	ci left: 1.805561e-03	ci right 1.885264e-03	k: 8266	n:4480000
KS ci ratio: 4.899964e-01	ci left: 1.080603e-05	ci right 1.799201e-05	k: 63	n:4480000
TP53   4480000 perm   9804 sec   (457 perm/sec)   p_kst 1.406250e-05   p_cons 1.845089e-03   p_joint 1.785714e-05

Joint ci ratio: 4.355516e-01	ci left: 1.412809e-05	ci right 2.217521e-05	k: 80	n:4490000
Cons ci ratio: 4.301636e-02	ci left: 1.806387e-03	ci right 1.886017e-03	k: 8288	n:4490000
KS ci ratio: 4.899965e-01	ci left: 1.078196e-05	ci right 1.795194e-05	k: 63	n:4490000
TP53   4490000 perm   9845 sec   (456 perm/sec)   p_kst 1.403118e-05   p_cons 1.845880e-03   p_joint 1.781737e-05

Joint ci ratio: 4.328876e-01	ci left: 1.429462e-05	ci right 2.237231e-05	k: 81	n:4500000
Cons ci ratio: 4.296715e-02	ci left: 1.806549e-03	ci right 1.886094e-03	k: 8307	n:4500000
KS ci ratio: 4.825151e-01	ci left: 1.114793e-05	ci right 1.841059e-05	k: 65	n:4500000
TP53   4500000 perm   9888 sec   (455 perm/sec)   p_kst 1.444444e-05   p_cons 1.846000e-03   p_joint 1.800000e-05

Joint ci ratio: 4.328876e-01	ci left: 1.426293e-05	ci right 2.232270e-05	k: 81	n:4510000
Cons ci ratio: 4.290003e-02	ci left: 1.808247e-03	ci right 1.887739e-03	k: 8333	n:4510000
KS ci ratio: 4.789006e-01	ci left: 1.131807e-05	ci right 1.861819e-05	k: 66	n:4510000
TP53   4510000 perm   9930 sec   (454 perm/sec)   p_kst 1.463415e-05   p_cons 1.847672e-03   p_joint 1.796009e-05

Joint ci ratio: 4.328876e-01	ci left: 1.423137e-05	ci right 2.227332e-05	k: 81	n:4520000
Cons ci ratio: 4.284351e-02	ci left: 1.809061e-03	ci right 1.888482e-03	k: 8355	n:4520000
KS ci ratio: 4.789006e-01	ci left: 1.129303e-05	ci right 1.857699e-05	k: 66	n:4520000
TP53   4520000 perm   9971 sec   (453 perm/sec)   p_kst 1.460177e-05   p_cons 1.848451e-03   p_joint 1.792035e-05

Joint ci ratio: 4.328876e-01	ci left: 1.419996e-05	ci right 2.222415e-05	k: 81	n:4530000
Cons ci ratio: 4.280000e-02	ci left: 1.808780e-03	ci right 1.888106e-03	k: 8372	n:4530000
KS ci ratio: 4.789006e-01	ci left: 1.126810e-05	ci right 1.853599e-05	k: 66	n:4530000
TP53   4530000 perm   10013 sec   (452 perm/sec)   p_kst 1.456954e-05   p_cons 1.848124e-03   p_joint 1.788079e-05

Joint ci ratio: 4.328876e-01	ci left: 1.416868e-05	ci right 2.217520e-05	k: 81	n:4540000
Cons ci ratio: 4.276428e-02	ci left: 1.807847e-03	ci right 1.887064e-03	k: 8386	n:4540000
KS ci ratio: 4.789006e-01	ci left: 1.124328e-05	ci right 1.849516e-05	k: 66	n:4540000
TP53   4540000 perm   10055 sec   (452 perm/sec)   p_kst 1.453744e-05   p_cons 1.847137e-03   p_joint 1.784141e-05

Joint ci ratio: 4.328876e-01	ci left: 1.413754e-05	ci right 2.212646e-05	k: 81	n:4550000
Cons ci ratio: 4.273375e-02	ci left: 1.806483e-03	ci right 1.885582e-03	k: 8398	n:4550000
KS ci ratio: 4.789006e-01	ci left: 1.121857e-05	ci right 1.845451e-05	k: 66	n:4550000
TP53   4550000 perm   10097 sec   (451 perm/sec)   p_kst 1.450549e-05   p_cons 1.845714e-03   p_joint 1.780220e-05

Joint ci ratio: 4.328876e-01	ci left: 1.410654e-05	ci right 2.207794e-05	k: 81	n:4560000
Cons ci ratio: 4.268804e-02	ci left: 1.806427e-03	ci right 1.885436e-03	k: 8416	n:4560000
KS ci ratio: 4.789007e-01	ci left: 1.119396e-05	ci right 1.841404e-05	k: 66	n:4560000
TP53   4560000 perm   10139 sec   (450 perm/sec)   p_kst 1.447368e-05   p_cons 1.845614e-03   p_joint 1.776316e-05

Joint ci ratio: 4.328877e-01	ci left: 1.407567e-05	ci right 2.202963e-05	k: 81	n:4570000
Cons ci ratio: 4.265767e-02	ci left: 1.805072e-03	ci right 1.883964e-03	k: 8428	n:4570000
KS ci ratio: 4.789007e-01	ci left: 1.116947e-05	ci right 1.837375e-05	k: 66	n:4570000
TP53   4570000 perm   10182 sec   (449 perm/sec)   p_kst 1.444201e-05   p_cons 1.844201e-03   p_joint 1.772429e-05

Joint ci ratio: 4.328877e-01	ci left: 1.404493e-05	ci right 2.198153e-05	k: 81	n:4580000
Cons ci ratio: 4.260967e-02	ci left: 1.805235e-03	ci right 1.884044e-03	k: 8447	n:4580000
KS ci ratio: 4.789007e-01	ci left: 1.114508e-05	ci right 1.833363e-05	k: 66	n:4580000
TP53   4580000 perm   10224 sec   (448 perm/sec)   p_kst 1.441048e-05   p_cons 1.844323e-03   p_joint 1.768559e-05

Joint ci ratio: 4.328877e-01	ci left: 1.401434e-05	ci right 2.193364e-05	k: 81	n:4590000
Cons ci ratio: 4.257695e-02	ci left: 1.804104e-03	ci right 1.882801e-03	k: 8460	n:4590000
KS ci ratio: 4.789007e-01	ci left: 1.112080e-05	ci right 1.829369e-05	k: 66	n:4590000
TP53   4590000 perm   10266 sec   (447 perm/sec)   p_kst 1.437908e-05   p_cons 1.843137e-03   p_joint 1.764706e-05

Joint ci ratio: 4.328877e-01	ci left: 1.398387e-05	ci right 2.188595e-05	k: 81	n:4600000
Cons ci ratio: 4.252169e-02	ci left: 1.804913e-03	ci right 1.883542e-03	k: 8482	n:4600000
KS ci ratio: 4.789007e-01	ci left: 1.109662e-05	ci right 1.825392e-05	k: 66	n:4600000
TP53   4600000 perm   10309 sec   (446 perm/sec)   p_kst 1.434783e-05   p_cons 1.843913e-03   p_joint 1.760870e-05

Joint ci ratio: 4.328877e-01	ci left: 1.395354e-05	ci right 2.183848e-05	k: 81	n:4610000
Cons ci ratio: 4.247665e-02	ci left: 1.804861e-03	ci right 1.883402e-03	k: 8500	n:4610000
KS ci ratio: 4.789007e-01	ci left: 1.107255e-05	ci right 1.821432e-05	k: 66	n:4610000
TP53   4610000 perm   10354 sec   (445 perm/sec)   p_kst 1.431670e-05   p_cons 1.843818e-03   p_joint 1.757050e-05

Joint ci ratio: 4.328877e-01	ci left: 1.392333e-05	ci right 2.179121e-05	k: 81	n:4620000
Cons ci ratio: 4.242925e-02	ci left: 1.805024e-03	ci right 1.883482e-03	k: 8519	n:4620000
KS ci ratio: 4.789007e-01	ci left: 1.104859e-05	ci right 1.817490e-05	k: 66	n:4620000
TP53   4620000 perm   10396 sec   (444 perm/sec)   p_kst 1.428571e-05   p_cons 1.843939e-03   p_joint 1.753247e-05

Joint ci ratio: 4.328877e-01	ci left: 1.389326e-05	ci right 2.174414e-05	k: 81	n:4630000
Cons ci ratio: 4.239695e-02	ci left: 1.803903e-03	ci right 1.882251e-03	k: 8532	n:4630000
KS ci ratio: 4.789007e-01	ci left: 1.102472e-05	ci right 1.813564e-05	k: 66	n:4630000
TP53   4630000 perm   10438 sec   (444 perm/sec)   p_kst 1.425486e-05   p_cons 1.842765e-03   p_joint 1.749460e-05

Joint ci ratio: 4.328877e-01	ci left: 1.386332e-05	ci right 2.169728e-05	k: 81	n:4640000
Cons ci ratio: 4.234486e-02	ci left: 1.804493e-03	ci right 1.882768e-03	k: 8553	n:4640000
KS ci ratio: 4.789007e-01	ci left: 1.100096e-05	ci right 1.809656e-05	k: 66	n:4640000
TP53   4640000 perm   10480 sec   (443 perm/sec)   p_kst 1.422414e-05   p_cons 1.843319e-03   p_joint 1.745690e-05

Joint ci ratio: 4.328877e-01	ci left: 1.383351e-05	ci right 2.165062e-05	k: 81	n:4650000
Cons ci ratio: 4.229791e-02	ci left: 1.804655e-03	ci right 1.882849e-03	k: 8572	n:4650000
KS ci ratio: 4.753663e-01	ci left: 1.116649e-05	ci right 1.829838e-05	k: 67	n:4650000
TP53   4650000 perm   10523 sec   (442 perm/sec)   p_kst 1.440860e-05   p_cons 1.843441e-03   p_joint 1.741935e-05

Joint ci ratio: 4.328877e-01	ci left: 1.380382e-05	ci right 2.160416e-05	k: 81	n:4660000
Cons ci ratio: 4.226097e-02	ci left: 1.803968e-03	ci right 1.882061e-03	k: 8587	n:4660000
KS ci ratio: 4.753663e-01	ci left: 1.114252e-05	ci right 1.825911e-05	k: 67	n:4660000
TP53   4660000 perm   10566 sec   (441 perm/sec)   p_kst 1.437768e-05   p_cons 1.842704e-03   p_joint 1.738197e-05

Joint ci ratio: 4.328877e-01	ci left: 1.377426e-05	ci right 2.155790e-05	k: 81	n:4670000
Cons ci ratio: 4.220938e-02	ci left: 1.804554e-03	ci right 1.882575e-03	k: 8608	n:4670000
KS ci ratio: 4.753663e-01	ci left: 1.111866e-05	ci right 1.822001e-05	k: 67	n:4670000
TP53   4670000 perm   10608 sec   (440 perm/sec)   p_kst 1.434690e-05   p_cons 1.843255e-03   p_joint 1.734475e-05

Joint ci ratio: 4.328877e-01	ci left: 1.374483e-05	ci right 2.151184e-05	k: 81	n:4680000
Cons ci ratio: 4.218002e-02	ci left: 1.803235e-03	ci right 1.881144e-03	k: 8620	n:4680000
KS ci ratio: 4.753663e-01	ci left: 1.109491e-05	ci right 1.818108e-05	k: 67	n:4680000
TP53   4680000 perm   10651 sec   (439 perm/sec)   p_kst 1.431624e-05   p_cons 1.841880e-03   p_joint 1.730769e-05

Joint ci ratio: 4.328878e-01	ci left: 1.371552e-05	ci right 2.146597e-05	k: 81	n:4690000
Cons ci ratio: 4.214095e-02	ci left: 1.802766e-03	ci right 1.880580e-03	k: 8636	n:4690000
KS ci ratio: 4.719090e-01	ci left: 1.125901e-05	ci right 1.838082e-05	k: 68	n:4690000
TP53   4690000 perm   10695 sec   (439 perm/sec)   p_kst 1.449893e-05   p_cons 1.841365e-03   p_joint 1.727079e-05

Joint ci ratio: 4.328878e-01	ci left: 1.368634e-05	ci right 2.142030e-05	k: 81	n:4700000
Cons ci ratio: 4.210198e-02	ci left: 1.802299e-03	ci right 1.880019e-03	k: 8652	n:4700000
KS ci ratio: 4.719090e-01	ci left: 1.123505e-05	ci right 1.834171e-05	k: 68	n:4700000
TP53   4700000 perm   10739 sec   (438 perm/sec)   p_kst 1.446809e-05   p_cons 1.840851e-03   p_joint 1.723404e-05

Joint ci ratio: 4.328878e-01	ci left: 1.365728e-05	ci right 2.137482e-05	k: 81	n:4710000
Cons ci ratio: 4.206555e-02	ci left: 1.801623e-03	ci right 1.879246e-03	k: 8667	n:4710000
KS ci ratio: 4.719090e-01	ci left: 1.121120e-05	ci right 1.830277e-05	k: 68	n:4710000
TP53   4710000 perm   10781 sec   (437 perm/sec)   p_kst 1.443737e-05   p_cons 1.840127e-03   p_joint 1.719745e-05

Joint ci ratio: 4.328878e-01	ci left: 1.362835e-05	ci right 2.132953e-05	k: 81	n:4720000
Cons ci ratio: 4.202922e-02	ci left: 1.800951e-03	ci right 1.878476e-03	k: 8682	n:4720000
KS ci ratio: 4.719090e-01	ci left: 1.118744e-05	ci right 1.826399e-05	k: 68	n:4720000
TP53   4720000 perm   10824 sec   (436 perm/sec)   p_kst 1.440678e-05   p_cons 1.839407e-03   p_joint 1.716102e-05

Joint ci ratio: 4.328878e-01	ci left: 1.359953e-05	ci right 2.128444e-05	k: 81	n:4730000
Cons ci ratio: 4.198814e-02	ci left: 1.800700e-03	ci right 1.878136e-03	k: 8699	n:4730000
KS ci ratio: 4.719091e-01	ci left: 1.116379e-05	ci right 1.822538e-05	k: 68	n:4730000
TP53   4730000 perm   10868 sec   (435 perm/sec)   p_kst 1.437632e-05   p_cons 1.839112e-03   p_joint 1.712474e-05

Joint ci ratio: 4.328878e-01	ci left: 1.357084e-05	ci right 2.123953e-05	k: 81	n:4740000
Cons ci ratio: 4.193754e-02	ci left: 1.801285e-03	ci right 1.878651e-03	k: 8720	n:4740000
KS ci ratio: 4.719091e-01	ci left: 1.114024e-05	ci right 1.818693e-05	k: 68	n:4740000
TP53   4740000 perm   10911 sec   (434 perm/sec)   p_kst 1.434599e-05   p_cons 1.839662e-03   p_joint 1.708861e-05

Joint ci ratio: 4.328878e-01	ci left: 1.354227e-05	ci right 2.119482e-05	k: 81	n:4750000
Cons ci ratio: 4.186794e-02	ci left: 1.803534e-03	ci right 1.880865e-03	k: 8749	n:4750000
KS ci ratio: 4.719091e-01	ci left: 1.111679e-05	ci right 1.814864e-05	k: 68	n:4750000
TP53   4750000 perm   10955 sec   (434 perm/sec)   p_kst 1.431579e-05   p_cons 1.841895e-03   p_joint 1.705263e-05

Joint ci ratio: 4.328878e-01	ci left: 1.351382e-05	ci right 2.115029e-05	k: 81	n:4760000
Cons ci ratio: 4.182973e-02	ci left: 1.803071e-03	ci right 1.880310e-03	k: 8765	n:4760000
KS ci ratio: 4.719091e-01	ci left: 1.109343e-05	ci right 1.811051e-05	k: 68	n:4760000
TP53   4760000 perm   10998 sec   (433 perm/sec)   p_kst 1.428571e-05   p_cons 1.841387e-03   p_joint 1.701681e-05

Joint ci ratio: 4.328878e-01	ci left: 1.348549e-05	ci right 2.110595e-05	k: 81	n:4770000
Cons ci ratio: 4.177732e-02	ci left: 1.803855e-03	ci right 1.881029e-03	k: 8787	n:4770000
KS ci ratio: 4.685261e-01	ci left: 1.125497e-05	ci right 1.830687e-05	k: 69	n:4770000
TP53   4770000 perm   11041 sec   (432 perm/sec)   p_kst 1.446541e-05   p_cons 1.842138e-03   p_joint 1.698113e-05

Joint ci ratio: 4.328878e-01	ci left: 1.345728e-05	ci right 2.106180e-05	k: 81	n:4780000
Cons ci ratio: 4.172748e-02	ci left: 1.804429e-03	ci right 1.881532e-03	k: 8808	n:4780000
KS ci ratio: 4.685261e-01	ci left: 1.123142e-05	ci right 1.826857e-05	k: 69	n:4780000
TP53   4780000 perm   11085 sec   (431 perm/sec)   p_kst 1.443515e-05   p_cons 1.842678e-03   p_joint 1.694561e-05

Joint ci ratio: 4.328878e-01	ci left: 1.342919e-05	ci right 2.101783e-05	k: 81	n:4790000
Cons ci ratio: 4.168965e-02	ci left: 1.803967e-03	ci right 1.880980e-03	k: 8824	n:4790000
KS ci ratio: 4.685261e-01	ci left: 1.120797e-05	ci right 1.823043e-05	k: 69	n:4790000
TP53   4790000 perm   11129 sec   (430 perm/sec)   p_kst 1.440501e-05   p_cons 1.842171e-03   p_joint 1.691023e-05

Joint ci ratio: 4.328878e-01	ci left: 1.340121e-05	ci right 2.097404e-05	k: 81	n:4800000
Cons ci ratio: 4.163069e-02	ci left: 1.805363e-03	ci right 1.882323e-03	k: 8849	n:4800000
KS ci ratio: 4.685261e-01	ci left: 1.118462e-05	ci right 1.819245e-05	k: 69	n:4800000
TP53   4800000 perm   11173 sec   (430 perm/sec)   p_kst 1.437500e-05   p_cons 1.843542e-03   p_joint 1.687500e-05

Joint ci ratio: 4.328878e-01	ci left: 1.337335e-05	ci right 2.093044e-05	k: 81	n:4810000
Cons ci ratio: 4.159312e-02	ci left: 1.804901e-03	ci right 1.881771e-03	k: 8865	n:4810000
KS ci ratio: 4.685262e-01	ci left: 1.116137e-05	ci right 1.815463e-05	k: 69	n:4810000
TP53   4810000 perm   11217 sec   (429 perm/sec)   p_kst 1.434511e-05   p_cons 1.843035e-03   p_joint 1.683992e-05

Joint ci ratio: 4.328879e-01	ci left: 1.334560e-05	ci right 2.088701e-05	k: 81	n:4820000
Cons ci ratio: 4.153926e-02	ci left: 1.805879e-03	ci right 1.882688e-03	k: 8888	n:4820000
KS ci ratio: 4.685262e-01	ci left: 1.113822e-05	ci right 1.811696e-05	k: 69	n:4820000
TP53   4820000 perm   11261 sec   (428 perm/sec)   p_kst 1.431535e-05   p_cons 1.843983e-03   p_joint 1.680498e-05

Joint ci ratio: 4.328879e-01	ci left: 1.331797e-05	ci right 2.084377e-05	k: 81	n:4830000
Cons ci ratio: 4.149493e-02	ci left: 1.806033e-03	ci right 1.882765e-03	k: 8907	n:4830000
KS ci ratio: 4.685262e-01	ci left: 1.111515e-05	ci right 1.807945e-05	k: 69	n:4830000
TP53   4830000 perm   11306 sec   (427 perm/sec)   p_kst 1.428571e-05   p_cons 1.844099e-03   p_joint 1.677019e-05

Joint ci ratio: 4.328879e-01	ci left: 1.329045e-05	ci right 2.080070e-05	k: 81	n:4840000
Cons ci ratio: 4.143215e-02	ci left: 1.807822e-03	ci right 1.884511e-03	k: 8934	n:4840000
KS ci ratio: 4.685262e-01	ci left: 1.109219e-05	ci right 1.804210e-05	k: 69	n:4840000
TP53   4840000 perm   11350 sec   (426 perm/sec)   p_kst 1.425620e-05   p_cons 1.845868e-03   p_joint 1.673554e-05

Joint ci ratio: 4.328879e-01	ci left: 1.326305e-05	ci right 2.075781e-05	k: 81	n:4850000
Cons ci ratio: 4.139280e-02	ci left: 1.807564e-03	ci right 1.884167e-03	k: 8951	n:4850000
KS ci ratio: 4.685262e-01	ci left: 1.106932e-05	ci right 1.800490e-05	k: 69	n:4850000
TP53   4850000 perm   11394 sec   (426 perm/sec)   p_kst 1.422680e-05   p_cons 1.845567e-03   p_joint 1.670103e-05

Joint ci ratio: 4.328879e-01	ci left: 1.323576e-05	ci right 2.071510e-05	k: 81	n:4860000
Cons ci ratio: 4.135356e-02	ci left: 1.807306e-03	ci right 1.883824e-03	k: 8968	n:4860000
KS ci ratio: 4.685262e-01	ci left: 1.104654e-05	ci right 1.796785e-05	k: 69	n:4860000
TP53   4860000 perm   11438 sec   (425 perm/sec)   p_kst 1.419753e-05   p_cons 1.845267e-03   p_joint 1.666667e-05

Joint ci ratio: 4.302722e-01	ci left: 1.339161e-05	ci right 2.090009e-05	k: 82	n:4870000
Cons ci ratio: 4.132826e-02	ci left: 1.805830e-03	ci right 1.882238e-03	k: 8979	n:4870000
KS ci ratio: 4.652150e-01	ci left: 1.120503e-05	ci right 1.816029e-05	k: 70	n:4870000
TP53   4870000 perm   11483 sec   (424 perm/sec)   p_kst 1.437372e-05   p_cons 1.843737e-03   p_joint 1.683778e-05

Joint ci ratio: 4.277033e-01	ci left: 1.354696e-05	ci right 2.108418e-05	k: 83	n:4880000
Cons ci ratio: 4.128920e-02	ci left: 1.805577e-03	ci right 1.881901e-03	k: 8996	n:4880000
KS ci ratio: 4.619730e-01	ci left: 1.136305e-05	ci right 1.835178e-05	k: 71	n:4880000
TP53   4880000 perm   11528 sec   (423 perm/sec)   p_kst 1.454918e-05   p_cons 1.843443e-03   p_joint 1.700820e-05

Joint ci ratio: 4.277033e-01	ci left: 1.351925e-05	ci right 2.104106e-05	k: 83	n:4890000
Cons ci ratio: 4.124796e-02	ci left: 1.805528e-03	ci right 1.881771e-03	k: 9014	n:4890000
KS ci ratio: 4.619730e-01	ci left: 1.133981e-05	ci right 1.831425e-05	k: 71	n:4890000
TP53   4890000 perm   11572 sec   (423 perm/sec)   p_kst 1.451943e-05   p_cons 1.843354e-03   p_joint 1.697342e-05

Joint ci ratio: 4.277034e-01	ci left: 1.349166e-05	ci right 2.099812e-05	k: 83	n:4900000
Cons ci ratio: 4.120456e-02	ci left: 1.805681e-03	ci right 1.881848e-03	k: 9033	n:4900000
KS ci ratio: 4.619730e-01	ci left: 1.131667e-05	ci right 1.827687e-05	k: 71	n:4900000
TP53   4900000 perm   11617 sec   (422 perm/sec)   p_kst 1.448980e-05   p_cons 1.843469e-03   p_joint 1.693878e-05

Joint ci ratio: 4.277034e-01	ci left: 1.346418e-05	ci right 2.095535e-05	k: 83	n:4910000
Cons ci ratio: 4.115446e-02	ci left: 1.806438e-03	ci right 1.882543e-03	k: 9055	n:4910000
KS ci ratio: 4.619730e-01	ci left: 1.129362e-05	ci right 1.823965e-05	k: 71	n:4910000
TP53   4910000 perm   11662 sec   (421 perm/sec)   p_kst 1.446029e-05   p_cons 1.844196e-03   p_joint 1.690428e-05

Joint ci ratio: 4.277034e-01	ci left: 1.343682e-05	ci right 2.091276e-05	k: 83	n:4920000
Cons ci ratio: 4.112271e-02	ci left: 1.805582e-03	ci right 1.881591e-03	k: 9069	n:4920000
KS ci ratio: 4.619730e-01	ci left: 1.127066e-05	ci right 1.820258e-05	k: 71	n:4920000
TP53   4920000 perm   11706 sec   (420 perm/sec)   p_kst 1.443089e-05   p_cons 1.843293e-03   p_joint 1.686992e-05

Joint ci ratio: 4.277034e-01	ci left: 1.340956e-05	ci right 2.087034e-05	k: 83	n:4930000
Cons ci ratio: 4.107517e-02	ci left: 1.806136e-03	ci right 1.882078e-03	k: 9090	n:4930000
KS ci ratio: 4.619730e-01	ci left: 1.124780e-05	ci right 1.816565e-05	k: 71	n:4930000
TP53   4930000 perm   11752 sec   (420 perm/sec)   p_kst 1.440162e-05   p_cons 1.843813e-03   p_joint 1.683570e-05

Joint ci ratio: 4.251800e-01	ci left: 1.356312e-05	ci right 2.105213e-05	k: 84	n:4940000
Cons ci ratio: 4.104586e-02	ci left: 1.805084e-03	ci right 1.880927e-03	k: 9103	n:4940000
KS ci ratio: 4.587979e-01	ci left: 1.140398e-05	ci right 1.835464e-05	k: 72	n:4940000
TP53   4940000 perm   11798 sec   (419 perm/sec)   p_kst 1.457490e-05   p_cons 1.842713e-03   p_joint 1.700405e-05

Joint ci ratio: 4.227008e-01	ci left: 1.371618e-05	ci right 2.123305e-05	k: 85	n:4950000
Cons ci ratio: 4.100309e-02	ci left: 1.805237e-03	ci right 1.881004e-03	k: 9122	n:4950000
KS ci ratio: 4.587979e-01	ci left: 1.138094e-05	ci right 1.831756e-05	k: 72	n:4950000
TP53   4950000 perm   11846 sec   (418 perm/sec)   p_kst 1.454545e-05   p_cons 1.842828e-03   p_joint 1.717172e-05

Joint ci ratio: 4.227008e-01	ci left: 1.368853e-05	ci right 2.119024e-05	k: 85	n:4960000
Cons ci ratio: 4.097169e-02	ci left: 1.804391e-03	ci right 1.880064e-03	k: 9136	n:4960000
KS ci ratio: 4.587979e-01	ci left: 1.135799e-05	ci right 1.828063e-05	k: 72	n:4960000
TP53   4960000 perm   11892 sec   (417 perm/sec)   p_kst 1.451613e-05   p_cons 1.841935e-03   p_joint 1.713710e-05

Joint ci ratio: 4.227008e-01	ci left: 1.366098e-05	ci right 2.114761e-05	k: 85	n:4970000
Cons ci ratio: 4.093363e-02	ci left: 1.804146e-03	ci right 1.879736e-03	k: 9153	n:4970000
KS ci ratio: 4.587979e-01	ci left: 1.133514e-05	ci right 1.824385e-05	k: 72	n:4970000
TP53   4970000 perm   11937 sec   (416 perm/sec)   p_kst 1.448692e-05   p_cons 1.841650e-03   p_joint 1.710262e-05

Joint ci ratio: 4.227008e-01	ci left: 1.363355e-05	ci right 2.110514e-05	k: 85	n:4980000
Cons ci ratio: 4.087336e-02	ci left: 1.805889e-03	ci right 1.881439e-03	k: 9180	n:4980000
KS ci ratio: 4.587979e-01	ci left: 1.131238e-05	ci right 1.820721e-05	k: 72	n:4980000
TP53   4980000 perm   11982 sec   (416 perm/sec)   p_kst 1.445783e-05   p_cons 1.843373e-03   p_joint 1.706827e-05

Joint ci ratio: 4.227008e-01	ci left: 1.360623e-05	ci right 2.106285e-05	k: 85	n:4990000
Cons ci ratio: 4.084002e-02	ci left: 1.805245e-03	ci right 1.880705e-03	k: 9195	n:4990000
KS ci ratio: 4.587979e-01	ci left: 1.128971e-05	ci right 1.817072e-05	k: 72	n:4990000
TP53   4990000 perm   12028 sec   (415 perm/sec)   p_kst 1.442886e-05   p_cons 1.842685e-03   p_joint 1.703407e-05

Joint ci ratio: 4.202644e-01	ci left: 1.375780e-05	ci right 2.124182e-05	k: 86	n:5000000
Cons ci ratio: 4.078903e-02	ci left: 1.806188e-03	ci right 1.881591e-03	k: 9218	n:5000000
KS ci ratio: 4.587979e-01	ci left: 1.126713e-05	ci right 1.813438e-05	k: 72	n:5000000
TP53   5000000 perm   12073 sec   (414 perm/sec)   p_kst 1.440000e-05   p_cons 1.843600e-03   p_joint 1.720000e-05

Outputting figure to mutsig2_images.part000000000180/TP53.14_1311_5000000_1.44e-05_0.0018436_1.72e-05.png
                gene_name: TP53
               theta_stop: 0.46 
                    nperm: 5000000 
                     p_ks: 1.44e-05 
        ci_ks_bounds_left: 1.13e-05 
       ci_ks_bounds_right: 1.81e-05 
                   p_cons: 0.0018 
      ci_cons_bounds_left: 0.0018 
     ci_cons_bounds_right: 0.0019 
                  p_joint: 1.72e-05 
     ci_joint_bounds_left: 1.38e-05 
    ci_joint_bounds_right: 2.12e-05 

Current progress: 14 percent done.
TPR
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: 2.469315e-02	ci left: 7.069489e-01	ci right 7.247252e-01	k: 7159	n:10000
KS ci ratio: 9.198086e-02	ci left: 1.465847e-01	ci right 1.608177e-01	k: 1536	n:10000
TPR   10000 perm   3 sec   (3417 perm/sec)   p_kst 1.536000e-01   p_cons 7.159000e-01   p_joint 2.796000e-01

Outputting figure to mutsig2_images.part000000000180/TPR.5_7296_10000_0.1536_0.7159_0.2796.png
                gene_name: TPR
               theta_stop: 0.092 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.72 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.28 
     ci_joint_bounds_left: 0.27 
    ci_joint_bounds_right: 0.29 

Current progress: 29 percent done.
TOPORS
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.438752e-02	ci left: 1.401132e-01	ci right 1.540931e-01	k: 1470	n:10000
Cons ci ratio: 6.903667e-02	ci left: 2.353112e-01	ci right 2.522383e-01	k: 2437	n:10000
KS ci ratio: 1.134190e-01	ci left: 1.006167e-01	ci right 1.128135e-01	k: 1066	n:10000
TOPORS   10000 perm   3 sec   (3953 perm/sec)   p_kst 1.066000e-01   p_cons 2.437000e-01   p_joint 1.470000e-01

Joint ci ratio: 6.391496e-02	ci left: 1.532167e-01	ci right 1.633828e-01	k: 3165	n:20000
Cons ci ratio: 4.931161e-02	ci left: 2.341437e-01	ci right 2.460319e-01	k: 4801	n:20000
KS ci ratio: 8.053930e-02	ci left: 1.016188e-01	ci right 1.101961e-01	k: 2117	n:20000
TOPORS   20000 perm   5 sec   (4032 perm/sec)   p_kst 1.058500e-01   p_cons 2.400500e-01   p_joint 1.582500e-01

Outputting figure to mutsig2_images.part000000000180/TOPORS.4_3150_20000_0.10585_0.24005_0.15825.png
                gene_name: TOPORS
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.16 
     ci_joint_bounds_left: 0.15 
    ci_joint_bounds_right: 0.16 

Current progress: 43 percent done.
TP53BP1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.238439e-02	ci left: 7.455367e-01	ci right 7.625150e-01	k: 7541	n:10000
Cons ci ratio: 3.068591e-02	ci left: 6.104028e-01	ci right 6.295273e-01	k: 6200	n:10000
KS ci ratio: 2.039378e-02	ci left: 7.788424e-01	ci right 7.949902e-01	k: 7870	n:10000
TP53BP1   10000 perm   3 sec   (3990 perm/sec)   p_kst 7.870000e-01   p_cons 6.200000e-01   p_joint 7.541000e-01

Outputting figure to mutsig2_images.part000000000180/TP53BP1.2_6046_10000_0.787_0.62_0.7541.png
                gene_name: TP53BP1
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.79 
                   p_cons: 0.62 
      ci_cons_bounds_left: 0.61 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.75 
     ci_joint_bounds_left: 0.75 
    ci_joint_bounds_right: 0.76 

Current progress: 57 percent done.
TP53I3
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: 8.516963e-03	ci left: 9.507523e-01	ci right 9.589800e-01	k: 9550	n:10000
KS ci ratio: 8.751644e-03	ci left: 9.482515e-01	ci right 9.566824e-01	k: 9526	n:10000
TP53I3   10000 perm   1 sec   (6834 perm/sec)   p_kst 9.526000e-01   p_cons 9.550000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000180/TP53I3.2_1019_10000_0.9526_0.955_1.png
                gene_name: TP53I3
               theta_stop: 0.0088 
                    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: 71 percent done.
TPK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.824276e-02	ci left: 8.143595e-01	ci right 8.294525e-01	k: 8220	n:10000
Cons ci ratio: 1.904803e-02	ci left: 8.011560e-01	ci right 8.166636e-01	k: 8090	n:10000
KS ci ratio: 4.450408e-02	ci left: 4.270484e-01	ci right 4.465885e-01	k: 4368	n:10000
TPK1   10000 perm   1 sec   (6916 perm/sec)   p_kst 4.368000e-01   p_cons 8.090000e-01   p_joint 8.220000e-01

Outputting figure to mutsig2_images.part000000000180/TPK1.2_764_10000_0.4368_0.809_0.822.png
                gene_name: TPK1
               theta_stop: 0.045 
                    nperm: 10000 
                     p_ks: 0.44 
        ci_ks_bounds_left: 0.43 
       ci_ks_bounds_right: 0.45 
                   p_cons: 0.81 
      ci_cons_bounds_left: 0.80 
     ci_cons_bounds_right: 0.82 
                  p_joint: 0.82 
     ci_joint_bounds_left: 0.81 
    ci_joint_bounds_right: 0.83 

Current progress: 86 percent done.
TPO
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.600512e-02	ci left: 1.645515e-01	ci right 1.794401e-01	k: 1719	n:10000
Cons ci ratio: 1.323001e-01	ci left: 7.533730e-02	ci right 8.610844e-02	k: 806	n:10000
KS ci ratio: 1.839213e-02	ci left: 8.119208e-01	ci right 8.270926e-01	k: 8196	n:10000
TPO   10000 perm   2 sec   (5525 perm/sec)   p_kst 8.196000e-01   p_cons 8.060000e-02   p_joint 1.719000e-01

Joint ci ratio: 7.677970e-02	ci left: 1.108556e-01	ci right 1.197565e-01	k: 2305	n:20000
Cons ci ratio: 9.620311e-02	ci left: 7.295085e-02	ci right 8.037278e-02	k: 1532	n:20000
KS ci ratio: 1.289252e-02	ci left: 8.167788e-01	ci right 8.274274e-01	k: 16443	n:20000
TPO   20000 perm   4 sec   (4883 perm/sec)   p_kst 8.221500e-01   p_cons 7.660000e-02   p_joint 1.152500e-01

Outputting figure to mutsig2_images.part000000000180/TPO.2_2866_20000_0.82215_0.0766_0.11525.png
                gene_name: TPO
               theta_stop: 0.096 
                    nperm: 20000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.82 
       ci_ks_bounds_right: 0.83 
                   p_cons: 0.077 
      ci_cons_bounds_left: 0.073 
     ci_cons_bounds_right: 0.080 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.12 

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.165.3896/
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/181708/iteration1/scatter.0000000180
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 180 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120320: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000181> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:47:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000181.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000181.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 181  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    136.19 sec.
    Max Memory :      1219 MB
    Max Swap   :      3838 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.165.3896/
-whichjob
181
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 181: processing genes 16286 - 16375
Calculating significance of each gene.
Using projection method.
16286	TRAF3IP2	2.524861e-01
16287	TRAF3IP3	1
16288	TRAF4	1
16289	TRAF5	1
16290	TRAF6	1
16291	TRAF7	1
16292	TRAFD1	1
16293	TRAIP	1
16294	TRAK1	1
16295	TRAK2	1
16296	TRAM1	1
16297	TRAM1L1	1
16298	TRAM2	1
16299	TRANK1	6.638794e-01
16300	TRAP1	1
16301	TRAPPC1	1
16302	TRAPPC10	1.354870e-01
16303	TRAPPC2	1
16304	TRAPPC2L	1
16305	TRAPPC3	1
16306	TRAPPC4	1
16307	TRAPPC5	1
16308	TRAPPC6A	1
16309	TRAPPC6B	1.609536e-02
16310	TRAPPC9	1
16311	TRAT1	1
16312	TRDMT1	1
16313	TRDN	1
16314	TREH	6.461322e-02
16315	TREM1	1
16316	TREM2	1
16317	TREML1	1
16318	TREML2	1
16319	TREML4	1
16320	TRERF1	5.282304e-02
16321	TREX1	1
16322	TREX2	1
16323	TRH	1
16324	TRHDE	2.710045e-02
16325	TRHR	9.661433e-02
16326	TRIAP1	1
16327	TRIB1	1
16328	TRIB2	1
16329	TRIB3	1
16330	TRIL	1
16331	TRIM10	8.751245e-03
16332	TRIM11	1
16333	TRIM13	1
16334	TRIM14	1
16335	TRIM15	2.163739e-01
16336	TRIM16	1
16337	TRIM16L	1
16338	TRIM17	1
16339	TRIM2	1
16340	TRIM21	1
16341	TRIM22	1
16342	TRIM23	3.796152e-02
16343	TRIM24	1
16344	TRIM25	1.778251e-01
16345	TRIM26	1.320844e-01
16346	TRIM27	1
16347	TRIM28	2.884620e-01
16348	TRIM29	1
16349	TRIM3	1
16350	TRIM31	1
16351	TRIM32	1.154067e-01
16352	TRIM33	1
16353	TRIM34	1
16354	TRIM35	1
16355	TRIM36	3.062262e-02
16356	TRIM37	5.372237e-02
16357	TRIM38	1
16358	TRIM39	1
16359	TRIM4	1
16360	TRIM40	1
16361	TRIM41	1.519183e-01
16362	TRIM42	4.861505e-02
16363	TRIM43	1
16364	TRIM44	1.665523e-01
16365	TRIM45	1
16366	TRIM46	1.647070e-01
16367	TRIM47	1
16368	TRIM48	5.661579e-02
16369	TRIM49	1
16370	TRIM5	1
16371	TRIM50	1
16372	TRIM52	1
16373	TRIM54	1
16374	TRIM55	1
16375	TRIM56	2.624748e-01
Done

Running MutSig 2:
Scatter job 181: processing genes 16286 - 16375
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TRAPPC10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.006938e-01	ci left: 1.249344e-01	ci right 1.382810e-01	k: 1315	n:10000
Cons ci ratio: 3.048442e-02	ci left: 6.135171e-01	ci right 6.326112e-01	k: 6231	n:10000
KS ci ratio: 1.202867e-01	ci left: 9.019709e-02	ci right 1.018395e-01	k: 959	n:10000
TRAPPC10   10000 perm   2 sec   (4266 perm/sec)   p_kst 9.590000e-02   p_cons 6.231000e-01   p_joint 1.315000e-01

Joint ci ratio: 5.736144e-02	ci left: 1.838418e-01	ci right 1.947487e-01	k: 3785	n:20000
Cons ci ratio: 2.161189e-02	ci left: 6.151372e-01	ci right 6.286273e-01	k: 12438	n:20000
KS ci ratio: 8.402037e-02	ci left: 9.401126e-02	ci right 1.023060e-01	k: 1962	n:20000
TRAPPC10   20000 perm   9 sec   (2316 perm/sec)   p_kst 9.810000e-02   p_cons 6.219000e-01   p_joint 1.892500e-01

Outputting figure to mutsig2_images.part000000000181/TRAPPC10.3_3872_20000_0.0981_0.6219_0.18925.png
                gene_name: TRAPPC10
               theta_stop: 0.084 
                    nperm: 20000 
                     p_ks: 0.098 
        ci_ks_bounds_left: 0.094 
       ci_ks_bounds_right: 0.10 
                   p_cons: 0.62 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.19 
     ci_joint_bounds_left: 0.18 
    ci_joint_bounds_right: 0.19 

Current progress: 14 percent done.
TRHDE
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: 3.800521e-02	ci left: 5.055515e-01	ci right 5.252395e-01	k: 5154	n:10000
KS ci ratio: 2.981969e-02	ci left: 6.238676e-01	ci right 6.428546e-01	k: 6334	n:10000
TRHDE   10000 perm   2 sec   (4987 perm/sec)   p_kst 6.334000e-01   p_cons 5.154000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000181/TRHDE.3_3151_10000_0.6334_0.5154_1.png
                gene_name: TRHDE
               theta_stop: 0.038 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   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: 29 percent done.
TRERF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.063575e-02	ci left: 9.263722e-01	ci right 9.363747e-01	k: 9315	n:10000
Cons ci ratio: 5.867464e-02	ci left: 2.994543e-01	ci right 3.176574e-01	k: 3085	n:10000
KS ci ratio: 4.891266e-02	ci left: 3.814188e-01	ci right 4.006447e-01	k: 3910	n:10000
TRERF1   10000 perm   2 sec   (4998 perm/sec)   p_kst 3.910000e-01   p_cons 3.085000e-01   p_joint 9.315000e-01

Outputting figure to mutsig2_images.part000000000181/TRERF1.2_3659_10000_0.391_0.3085_0.9315.png
                gene_name: TRERF1
               theta_stop: 0.059 
                    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: 0.93 
     ci_joint_bounds_left: 0.93 
    ci_joint_bounds_right: 0.94 

Current progress: 43 percent done.
TRIM10
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.644672e-02	ci left: 4.062155e-01	ci right 4.256335e-01	k: 4159	n:10000
Cons ci ratio: 6.726746e-02	ci left: 2.448978e-01	ci right 2.620461e-01	k: 2534	n:10000
KS ci ratio: 3.284991e-02	ci left: 5.776768e-01	ci right 5.970723e-01	k: 5874	n:10000
TRIM10   10000 perm   2 sec   (4926 perm/sec)   p_kst 5.874000e-01   p_cons 2.534000e-01   p_joint 4.159000e-01

Outputting figure to mutsig2_images.part000000000181/TRIM10.2_1562_10000_0.5874_0.2534_0.4159.png
                gene_name: TRIM10
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.42 
     ci_joint_bounds_left: 0.41 
    ci_joint_bounds_right: 0.43 

Current progress: 57 percent done.
TRIM36
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: 4.728838e-02	ci left: 3.975486e-01	ci right 4.169054e-01	k: 4072	n:10000
KS ci ratio: 2.425669e-02	ci left: 7.142157e-01	ci right 7.318542e-01	k: 7231	n:10000
TRIM36   10000 perm   2 sec   (5112 perm/sec)   p_kst 7.231000e-01   p_cons 4.072000e-01   p_joint 7.712000e-01

Outputting figure to mutsig2_images.part000000000181/TRIM36.2_2478_10000_0.7231_0.4072_0.7712.png
                gene_name: TRIM36
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.73 
                   p_cons: 0.41 
      ci_cons_bounds_left: 0.40 
     ci_cons_bounds_right: 0.42 
                  p_joint: 0.77 
     ci_joint_bounds_left: 0.76 
    ci_joint_bounds_right: 0.78 

Current progress: 71 percent done.
TRIM37
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: 5.505688e-02	ci left: 3.270391e-01	ci right 3.456564e-01	k: 3363	n:10000
KS ci ratio: 1.548872e-02	ci left: 8.581460e-01	ci right 8.716407e-01	k: 8650	n:10000
TRIM37   10000 perm   2 sec   (5182 perm/sec)   p_kst 8.650000e-01   p_cons 3.363000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000181/TRIM37.2_2999_10000_0.865_0.3363_1.png
                gene_name: TRIM37
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.86 
        ci_ks_bounds_left: 0.86 
       ci_ks_bounds_right: 0.87 
                   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: 86 percent done.
TRIM42
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.685049e-02	ci left: 4.020311e-01	ci right 4.214204e-01	k: 4117	n:10000
Cons ci ratio: 2.205851e-02	ci left: 7.509985e-01	ci right 7.678501e-01	k: 7595	n:10000
KS ci ratio: 7.899090e-02	ci left: 1.897361e-01	ci right 2.054405e-01	k: 1975	n:10000
TRIM42   10000 perm   2 sec   (5768 perm/sec)   p_kst 1.975000e-01   p_cons 7.595000e-01   p_joint 4.117000e-01

Outputting figure to mutsig2_images.part000000000181/TRIM42.2_2192_10000_0.1975_0.7595_0.4117.png
                gene_name: TRIM42
               theta_stop: 0.079 
                    nperm: 10000 
                     p_ks: 0.20 
        ci_ks_bounds_left: 0.19 
       ci_ks_bounds_right: 0.21 
                   p_cons: 0.76 
      ci_cons_bounds_left: 0.75 
     ci_cons_bounds_right: 0.77 
                  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.165.3896/
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/181708/iteration1/scatter.0000000181
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 181 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1537>
Subject: Job 1120323: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1537>, 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/181708/iteration1/scatter.0000000182> was used as the working directory.
Started at Wed Oct 10 10:45:34 2012
Results reported at Wed Oct 10 10:48:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000182.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000182.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 182  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    173.25 sec.
    Max Memory :      1471 MB
    Max Swap   :      3877 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.165.3896/
-whichjob
182
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 182: processing genes 16376 - 16466
Calculating significance of each gene.
Using projection method.
16376	TRIM58	1
16377	TRIM59	1.073298e-02
16378	TRIM6	1
16379	TRIM6-TRIM34	3.050755e-01
16380	TRIM60	1
16381	TRIM61	1
16382	TRIM62	1
16383	TRIM63	1
16384	TRIM65	8.982127e-02
16385	TRIM67	5.767159e-02
16386	TRIM68	7.383932e-02
16387	TRIM69	1
16388	TRIM7	1
16389	TRIM71	1
16390	TRIM72	1
16391	TRIM73	1
16392	TRIM74	1
16393	TRIM8	1
16394	TRIM9	2.153294e-01
16395	TRIML1	1
16396	TRIML2	1
16397	TRIO	9.169091e-02
16398	TRIOBP	4.819149e-01
16399	TRIP10	3.505898e-02
16400	TRIP11	3.198646e-01
16401	TRIP12	1
16402	TRIP13	1
16403	TRIP4	1
16404	TRIP6	1
16405	TRIT1	2.038147e-01
16406	TRMT1	1
16407	TRMT11	1
16408	TRMT112	1
16409	TRMT12	1
16410	TRMT2A	1
16411	TRMT2B	1
16412	TRMT5	1
16413	TRMT6	1
16414	TRMT61A	1
16415	TRMT61B	1
16416	TRMU	1
16417	TRNAU1AP	1
16418	TRNT1	1
16419	TRO	2.692817e-01
16420	TROAP	6.207533e-03
16421	TROVE2	1.227290e-01
16422	TRPA1	1
16423	TRPC1	1.507639e-01
16424	TRPC3	3.474595e-01
16425	TRPC4	6.437928e-02
16426	TRPC4AP	1
16427	TRPC5	1
16428	TRPC6	3.046110e-01
16429	TRPC7	1
16430	TRPM1	1
16431	TRPM2	1
16432	TRPM3	1
16433	TRPM4	1
16434	TRPM5	1.279367e-01
16435	TRPM6	1
16436	TRPM7	1
16437	TRPM8	1
16438	TRPS1	3.068414e-01
16439	TRPT1	1
16440	TRPV1	7.672832e-02
16441	TRPV2	1
16442	TRPV3	1.975334e-01
16443	TRPV4	1
16444	TRPV5	4.761432e-02
16445	TRPV6	1
16446	TRRAP	6.223132e-01
16447	TRUB1	9.708648e-03
16448	TRUB2	1
16449	TRYX3	1
16450	TSC1	7.888144e-03
16451	TSC2	1
16452	TSC22D1	2.306112e-01
16453	TSC22D2	1
16454	TSC22D3	1
16455	TSC22D4	2.003283e-02
16456	TSEN15	1
16457	TSEN2	1
16458	TSEN34	1
16459	TSEN54	1
16460	TSFM	1
16461	TSG101	1
16462	TSGA10	1
16463	TSGA10IP	1
16464	TSGA13	1
16465	TSGA14	1.567998e-01
16466	TSHB	1
Done

Running MutSig 2:
Scatter job 182: processing genes 16376 - 16466
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TRIO
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: 1.360009e-01	ci left: 7.146123e-02	ci right 8.198693e-02	k: 766	n:10000
KS ci ratio: 3.631366e-02	ci left: 5.282688e-01	ci right 5.479090e-01	k: 5381	n:10000
TRIO   10000 perm   3 sec   (2890 perm/sec)   p_kst 5.381000e-01   p_cons 7.660000e-02   p_joint 1

Joint ci ratio: 1.719095e-02	ci left: 7.159353e-01	ci right 7.284000e-01	k: 14444	n:20000
Cons ci ratio: 9.473848e-02	ci left: 7.510243e-02	ci right 8.262055e-02	k: 1576	n:20000
KS ci ratio: 2.574659e-02	ci left: 5.298593e-01	ci right 5.437300e-01	k: 10736	n:20000
TRIO   20000 perm   11 sec   (1881 perm/sec)   p_kst 5.368000e-01   p_cons 7.880000e-02   p_joint 7.222000e-01

Outputting figure to mutsig2_images.part000000000182/TRIO.4_9522_20000_0.5368_0.0788_0.7222.png
                gene_name: TRIO
               theta_stop: 0.095 
                    nperm: 20000 
                     p_ks: 0.54 
        ci_ks_bounds_left: 0.53 
       ci_ks_bounds_right: 0.54 
                   p_cons: 0.079 
      ci_cons_bounds_left: 0.075 
     ci_cons_bounds_right: 0.083 
                  p_joint: 0.72 
     ci_joint_bounds_left: 0.72 
    ci_joint_bounds_right: 0.73 

Current progress: 12 percent done.
TROAP
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.504931e-02	ci left: 2.576556e-01	ci right 2.750807e-01	k: 2663	n:10000
Cons ci ratio: 1.721173e-02	ci left: 8.310374e-01	ci right 8.455650e-01	k: 8384	n:10000
KS ci ratio: 1.367749e-01	ci left: 7.068651e-02	ci right 8.116213e-02	k: 758	n:10000
TROAP   10000 perm   2 sec   (4616 perm/sec)   p_kst 7.580000e-02   p_cons 8.384000e-01   p_joint 2.663000e-01

Joint ci ratio: 5.589978e-02	ci left: 1.918039e-01	ci right 2.028842e-01	k: 3946	n:20000
Cons ci ratio: 1.228647e-02	ci left: 8.305921e-01	ci right 8.409101e-01	k: 16716	n:20000
KS ci ratio: 9.569699e-02	ci left: 7.368425e-02	ci right 8.113917e-02	k: 1547	n:20000
TROAP   20000 perm   5 sec   (4024 perm/sec)   p_kst 7.735000e-02   p_cons 8.358000e-01   p_joint 1.973000e-01

Outputting figure to mutsig2_images.part000000000182/TROAP.3_2495_20000_0.07735_0.8358_0.1973.png
                gene_name: TROAP
               theta_stop: 0.096 
                    nperm: 20000 
                     p_ks: 0.077 
        ci_ks_bounds_left: 0.074 
       ci_ks_bounds_right: 0.081 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.84 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.20 

Current progress: 25 percent done.
TSC1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.907736e-02	ci left: 3.798263e-01	ci right 3.990382e-01	k: 3894	n:10000
Cons ci ratio: 2.981327e-02	ci left: 6.239682e-01	ci right 6.429540e-01	k: 6335	n:10000
KS ci ratio: 1.158652e-01	ci left: 9.671912e-02	ci right 1.087134e-01	k: 1026	n:10000
TSC1   10000 perm   2 sec   (4116 perm/sec)   p_kst 1.026000e-01   p_cons 6.335000e-01   p_joint 3.894000e-01

Joint ci ratio: 3.665541e-02	ci left: 3.570779e-01	ci right 3.704617e-01	k: 7275	n:20000
Cons ci ratio: 2.122764e-02	ci left: 6.235664e-01	ci right 6.369957e-01	k: 12606	n:20000
KS ci ratio: 8.081697e-02	ci left: 1.009805e-01	ci right 1.095346e-01	k: 2104	n:20000
TSC1   20000 perm   5 sec   (3859 perm/sec)   p_kst 1.052000e-01   p_cons 6.303000e-01   p_joint 3.637500e-01

Outputting figure to mutsig2_images.part000000000182/TSC1.3_3579_20000_0.1052_0.6303_0.36375.png
                gene_name: TSC1
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.64 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.36 
    ci_joint_bounds_right: 0.37 

Current progress: 38 percent done.
TRIM59
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.929105e-02	ci left: 1.885544e-01	ci right 2.042229e-01	k: 1963	n:10000
Cons ci ratio: 9.316556e-02	ci left: 1.433484e-01	ci right 1.574560e-01	k: 1503	n:10000
KS ci ratio: 8.735789e-02	ci left: 1.602287e-01	ci right 1.749655e-01	k: 1675	n:10000
TRIM59   10000 perm   2 sec   (5428 perm/sec)   p_kst 1.675000e-01   p_cons 1.503000e-01   p_joint 1.963000e-01

Outputting figure to mutsig2_images.part000000000182/TRIM59.2_1216_10000_0.1675_0.1503_0.1963.png
                gene_name: TRIM59
               theta_stop: 0.093 
                    nperm: 10000 
                     p_ks: 0.17 
        ci_ks_bounds_left: 0.16 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.15 
      ci_cons_bounds_left: 0.14 
     ci_cons_bounds_right: 0.16 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.20 

Current progress: 50 percent done.
TRPC4
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: 2.257745e-02	ci left: 7.423010e-01	ci right 7.593527e-01	k: 7509	n:10000
KS ci ratio: 2.901577e-02	ci left: 6.365358e-01	ci right 6.553791e-01	k: 6460	n:10000
TRPC4   10000 perm   2 sec   (4941 perm/sec)   p_kst 6.460000e-01   p_cons 7.509000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000182/TRPC4.2_2989_10000_0.646_0.7509_1.png
                gene_name: TRPC4
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.65 
        ci_ks_bounds_left: 0.64 
       ci_ks_bounds_right: 0.66 
                   p_cons: 0.75 
      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: 62 percent done.
TRPV5
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.637744e-02	ci left: 3.166160e-01	ci right 3.350856e-01	k: 3258	n:10000
Cons ci ratio: 1.107643e-01	ci left: 1.051021e-01	ci right 1.175253e-01	k: 1112	n:10000
KS ci ratio: 2.531331e-02	ci left: 6.966589e-01	ci right 7.146211e-01	k: 7057	n:10000
TRPV5   10000 perm   2 sec   (5551 perm/sec)   p_kst 7.057000e-01   p_cons 1.112000e-01   p_joint 3.258000e-01

Joint ci ratio: 4.539295e-02	ci left: 2.653946e-01	ci right 2.777718e-01	k: 5431	n:20000
Cons ci ratio: 7.854219e-02	ci left: 1.063834e-01	ci right 1.151301e-01	k: 2214	n:20000
KS ci ratio: 1.808512e-02	ci left: 6.950035e-01	ci right 7.077379e-01	k: 14028	n:20000
TRPV5   20000 perm   4 sec   (4833 perm/sec)   p_kst 7.014000e-01   p_cons 1.107000e-01   p_joint 2.715500e-01

Outputting figure to mutsig2_images.part000000000182/TRPV5.2_2250_20000_0.7014_0.1107_0.27155.png
                gene_name: TRPV5
               theta_stop: 0.079 
                    nperm: 20000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.70 
       ci_ks_bounds_right: 0.71 
                   p_cons: 0.11 
      ci_cons_bounds_left: 0.11 
     ci_cons_bounds_right: 0.12 
                  p_joint: 0.27 
     ci_joint_bounds_left: 0.27 
    ci_joint_bounds_right: 0.28 

Current progress: 75 percent done.
TRRAP
Processing conservation and coverage...
84% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.509415e-02	ci left: 7.002900e-01	ci right 7.181879e-01	k: 7093	n:10000
Cons ci ratio: 6.086234e-02	ci left: 2.841899e-01	ci right 3.021308e-01	k: 2931	n:10000
KS ci ratio: 3.016084e-02	ci left: 6.185410e-01	ci right 6.375843e-01	k: 6281	n:10000
TRRAP   10000 perm   4 sec   (2628 perm/sec)   p_kst 6.281000e-01   p_cons 2.931000e-01   p_joint 7.093000e-01

Outputting figure to mutsig2_images.part000000000182/TRRAP.2_11773_10000_0.6281_0.2931_0.7093.png
                gene_name: TRRAP
               theta_stop: 0.061 
                    nperm: 10000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.64 
                   p_cons: 0.29 
      ci_cons_bounds_left: 0.28 
     ci_cons_bounds_right: 0.30 
                  p_joint: 0.71 
     ci_joint_bounds_left: 0.70 
    ci_joint_bounds_right: 0.72 

Current progress: 88 percent done.
TRUB1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.078848e-02	ci left: 7.722565e-01	ci right 7.885799e-01	k: 7805	n:10000
Cons ci ratio: 3.073802e-02	ci left: 6.095991e-01	ci right 6.287314e-01	k: 6192	n:10000
KS ci ratio: 4.743559e-02	ci left: 3.960547e-01	ci right 4.154003e-01	k: 4057	n:10000
TRUB1   10000 perm   2 sec   (6312 perm/sec)   p_kst 4.057000e-01   p_cons 6.192000e-01   p_joint 7.805000e-01

Outputting figure to mutsig2_images.part000000000182/TRUB1.2_1082_10000_0.4057_0.6192_0.7805.png
                gene_name: TRUB1
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.62 
      ci_cons_bounds_left: 0.61 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.79 

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.165.3896/
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/181708/iteration1/scatter.0000000182
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 182 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120328: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000183> was used as the working directory.
Started at Wed Oct 10 10:45:39 2012
Results reported at Wed Oct 10 10:47:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000183.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000183.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 183  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    117.04 sec.
    Max Memory :      1367 MB
    Max Swap   :      3842 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.165.3896/
-whichjob
183
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 183: processing genes 16467 - 16556
Calculating significance of each gene.
Using projection method.
16467	TSHR	1
16468	TSHZ1	1
16469	TSHZ2	6.421937e-02
16470	TSHZ3	1
16471	TSKS	1
16472	TSKU	7.060003e-03
16473	TSLP	1
16474	TSN	1
16475	TSNARE1	9.720775e-02
16476	TSNAX	4.280444e-02
16477	TSNAXIP1	3.011833e-01
16478	TSPAN1	1
16479	TSPAN10	1
16480	TSPAN11	1
16481	TSPAN12	1
16482	TSPAN13	1
16483	TSPAN14	1
16484	TSPAN15	1
16485	TSPAN16	1
16486	TSPAN17	1
16487	TSPAN18	1
16488	TSPAN19	1
16489	TSPAN2	1
16490	TSPAN3	7.575977e-03
16491	TSPAN31	1
16492	TSPAN32	1
16493	TSPAN33	1
16494	TSPAN4	1
16495	TSPAN5	1
16496	TSPAN6	1
16497	TSPAN7	5.076746e-02
16498	TSPAN8	8.017777e-02
16499	TSPAN9	1
16500	TSPO	1
16501	TSPO2	1
16502	TSPY1	1
16503	TSPY2	1
16504	TSPYL1	1.261737e-01
16505	TSPYL2	1
16506	TSPYL4	1
16507	TSPYL5	1
16508	TSPYL6	1
16509	TSR1	1
16510	TSR2	1
16511	TSSC1	1
16512	TSSC4	1
16513	TSSK1B	1.379559e-01
16514	TSSK2	1
16515	TSSK3	1
16516	TSSK4	1
16517	TSSK6	1
16518	TST	1
16519	TSTA3	1
16520	TSTD2	1.494577e-01
16521	TTBK1	1.458999e-01
16522	TTBK2	1
16523	TTC1	1
16524	TTC12	1
16525	TTC13	1
16526	TTC14	1
16527	TTC15	1
16528	TTC16	1
16529	TTC17	1
16530	TTC18	2.615812e-01
16531	TTC19	1
16532	TTC21A	1
16533	TTC21B	4.468575e-01
16534	TTC22	1
16535	TTC23	1.812158e-02
16536	TTC23L	1
16537	TTC24	1
16538	TTC25	1.418901e-01
16539	TTC26	1.369086e-01
16540	TTC27	1
16541	TTC29	1
16542	TTC3	2.216285e-01
16543	TTC30A	2.237919e-01
16544	TTC30B	1
16545	TTC31	1
16546	TTC32	1
16547	TTC33	1.248900e-01
16548	TTC35	1
16549	TTC36	1
16550	TTC37	1
16551	TTC38	1
16552	TTC39A	2.275645e-01
16553	TTC39B	1
16554	TTC39C	1
16555	TTC4	1
16556	TTC5	1
Done

Running MutSig 2:
Scatter job 183: processing genes 16467 - 16556
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
TSHZ2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.691880e-02	ci left: 8.357199e-01	ci right 8.500797e-01	k: 8430	n:10000
Cons ci ratio: 1.881661e-03	ci left: 9.966711e-01	ci right 9.986208e-01	k: 9978	n:10000
KS ci ratio: 2.696950e-02	ci left: 6.694464e-01	ci right 6.878494e-01	k: 6787	n:10000
TSHZ2   10000 perm   2 sec   (5716 perm/sec)   p_kst 6.787000e-01   p_cons 9.978000e-01   p_joint 8.430000e-01

Outputting figure to mutsig2_images.part000000000183/TSHZ2.2_3113_10000_0.6787_0.9978_0.843.png
                gene_name: TSHZ2
               theta_stop: 0.027 
                    nperm: 10000 
                     p_ks: 0.68 
        ci_ks_bounds_left: 0.67 
       ci_ks_bounds_right: 0.69 
                   p_cons: 1.00 
      ci_cons_bounds_left: 1.00 
     ci_cons_bounds_right: 1.00 
                  p_joint: 0.84 
     ci_joint_bounds_left: 0.84 
    ci_joint_bounds_right: 0.85 

Current progress: 25 percent done.
TSKU
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.499718e-02	ci left: 5.465975e-01	ci right 5.661697e-01	k: 5564	n:10000
Cons ci ratio: 6.531663e-02	ci left: 2.560727e-01	ci right 2.734646e-01	k: 2647	n:10000
KS ci ratio: 3.530301e-02	ci left: 5.422895e-01	ci right 5.618801e-01	k: 5521	n:10000
TSKU   10000 perm   1 sec   (6923 perm/sec)   p_kst 5.521000e-01   p_cons 2.647000e-01   p_joint 5.564000e-01

Outputting figure to mutsig2_images.part000000000183/TSKU.2_1066_10000_0.5521_0.2647_0.5564.png
                gene_name: TSKU
               theta_stop: 0.065 
                    nperm: 10000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.54 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.26 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.56 
     ci_joint_bounds_left: 0.55 
    ci_joint_bounds_right: 0.57 

Current progress: 50 percent done.
TTC23
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.004989e-02	ci left: 4.793568e-01	ci right 4.990495e-01	k: 4892	n:10000
Cons ci ratio: 1.712220e-01	ci left: 4.552219e-02	ci right 5.414247e-02	k: 497	n:10000
KS ci ratio: 3.814236e-02	ci left: 5.037510e-01	ci right 5.234410e-01	k: 5136	n:10000
TTC23   10000 perm   1 sec   (6701 perm/sec)   p_kst 5.136000e-01   p_cons 4.970000e-02   p_joint 4.892000e-01

Joint ci ratio: 6.338064e-02	ci left: 1.554374e-01	ci right 1.656615e-01	k: 3210	n:20000
Cons ci ratio: 1.200010e-01	ci left: 4.760289e-02	ci right 5.372858e-02	k: 1012	n:20000
KS ci ratio: 2.669869e-02	ci left: 5.117480e-01	ci right 5.256465e-01	k: 10374	n:20000
TTC23   20000 perm   3 sec   (5936 perm/sec)   p_kst 5.187000e-01   p_cons 5.060000e-02   p_joint 1.605000e-01

Joint ci ratio: 4.578916e-02	ci left: 1.918183e-01	ci right 2.008406e-01	k: 5889	n:30000
Cons ci ratio: 9.924309e-02	ci left: 4.697490e-02	ci right 5.191282e-02	k: 1482	n:30000
KS ci ratio: 2.171275e-02	ci left: 5.150285e-01	ci right 5.263675e-01	k: 15621	n:30000
TTC23   30000 perm   5 sec   (5623 perm/sec)   p_kst 5.207000e-01   p_cons 4.940000e-02   p_joint 1.963000e-01

Outputting figure to mutsig2_images.part000000000183/TTC23.2_1384_30000_0.5207_0.0494_0.1963.png
                gene_name: TTC23
               theta_stop: 0.099 
                    nperm: 30000 
                     p_ks: 0.52 
        ci_ks_bounds_left: 0.52 
       ci_ks_bounds_right: 0.53 
                   p_cons: 0.049 
      ci_cons_bounds_left: 0.047 
     ci_cons_bounds_right: 0.052 
                  p_joint: 0.20 
     ci_joint_bounds_left: 0.19 
    ci_joint_bounds_right: 0.20 

Current progress: 75 percent done.
TTC3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.271375e-02	ci left: 4.473000e-01	ci right 4.669250e-01	k: 4571	n:10000
Cons ci ratio: 7.439508e-02	ci left: 2.091515e-01	ci right 2.254135e-01	k: 2172	n:10000
KS ci ratio: 4.091696e-02	ci left: 4.686667e-01	ci right 4.883458e-01	k: 4785	n:10000
TTC3   10000 perm   2 sec   (4810 perm/sec)   p_kst 4.785000e-01   p_cons 2.172000e-01   p_joint 4.571000e-01

Outputting figure to mutsig2_images.part000000000183/TTC3.2_6258_10000_0.4785_0.2172_0.4571.png
                gene_name: TTC3
               theta_stop: 0.074 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  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.165.3896/
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/181708/iteration1/scatter.0000000183
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 183 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120331: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000184> was used as the working directory.
Started at Wed Oct 10 10:45:39 2012
Results reported at Wed Oct 10 10:50:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000184.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000184.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 184  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    289.02 sec.
    Max Memory :      1253 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.165.3896/
-whichjob
184
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 184: processing genes 16557 - 16646
Calculating significance of each gene.
Using projection method.
16557	TTC7A	3.472411e-01
16558	TTC7B	1
16559	TTC8	1
16560	TTC9	1
16561	TTC9B	1
16562	TTC9C	1
16563	TTF1	1
16564	TTF2	3.759209e-02
16565	TTK	1.042266e-01
16566	TTL	1
16567	TTLL1	1
16568	TTLL10	1
16569	TTLL11	1
16570	TTLL12	1
16571	TTLL13	1
16572	TTLL2	1
16573	TTLL3	1
16574	TTLL4	1
16575	TTLL5	5.116686e-01
16576	TTLL6	1
16577	TTLL7	1.066229e-01
16578	TTLL8	1
16579	TTLL9	1
16580	TTN	1.369303e-01
16581	TTPA	1
16582	TTPAL	1
16583	TTR	1
16584	TTYH1	1.355501e-01
16585	TTYH2	1
16586	TTYH3	1
16587	TUB	1
16588	TUBA1A	1
16589	TUBA1B	1
16590	TUBA1C	1
16591	TUBA3C	5.567262e-02
16592	TUBA3D	1
16593	TUBA3E	1
16594	TUBA4A	1
16595	TUBA8	1
16596	TUBAL3	1
16597	TUBB	7.224299e-02
16598	TUBB1	1
16599	TUBB2A	1
16600	TUBB2B	1
16601	TUBB2C	9.212402e-02
16602	TUBB3	2.160210e-01
16603	TUBB4	1
16604	TUBB4Q	1
16605	TUBB6	1
16606	TUBB8	1
16607	TUBD1	1
16608	TUBE1	1
16609	TUBG1	1
16610	TUBG2	1
16611	TUBGCP2	1
16612	TUBGCP3	1
16613	TUBGCP4	1
16614	TUBGCP5	1.798759e-01
16615	TUBGCP6	1
16616	TUFM	1
16617	TUFT1	1
16618	TULP1	1
16619	TULP2	1
16620	TULP3	1
16621	TULP4	5.613036e-01
16622	TUSC2	1
16623	TUSC3	1
16624	TUSC5	1
16625	TUT1	1
16626	TWF1	1
16627	TWF2	1
16628	TWIST1	1
16629	TWISTNB	1
16630	TWSG1	1
16631	TXK	1
16632	TXLNA	1
16633	TXLNB	1
16634	TXLNG	1
16635	TXN	1
16636	TXN2	1
16637	TXNDC11	3.436314e-01
16638	TXNDC12	1
16639	TXNDC15	1
16640	TXNDC16	1
16641	TXNDC17	1
16642	TXNDC2	4.722277e-02
16643	TXNDC3	1
16644	TXNDC5	1.246102e-01
16645	TXNDC6	1.474889e-01
16646	TXNDC8	1
Done

Running MutSig 2:
Scatter job 184: processing genes 16557 - 16646
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: 4.134564e-02	ci left: 4.634731e-01	ci right 4.831424e-01	k: 4733	n:10000
Cons ci ratio: 7.079331e-03	ci left: 9.648873e-01	ci right 9.718363e-01	k: 9685	n:10000
KS ci ratio: 5.415671e-02	ci left: 3.343879e-01	ci right 3.531032e-01	k: 3437	n:10000
TTN   10000 perm   16 sec   (636 perm/sec)   p_kst 3.437000e-01   p_cons 9.685000e-01   p_joint 4.733000e-01

Outputting figure to mutsig2_images.part000000000184/TTN.33_111433_10000_0.3437_0.9685_0.4733.png
                gene_name: TTN
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.34 
        ci_ks_bounds_left: 0.33 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.97 
      ci_cons_bounds_left: 0.96 
     ci_cons_bounds_right: 0.97 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    ci_joint_bounds_right: 0.48 

Current progress: 50 percent done.
TTF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.121859e-02	ci left: 7.650660e-01	ci right 7.815745e-01	k: 7734	n:10000
Cons ci ratio: 5.376300e-02	ci left: 3.376659e-01	ci right 3.564232e-01	k: 3470	n:10000
KS ci ratio: 5.213117e-02	ci left: 3.516775e-01	ci right 3.706035e-01	k: 3611	n:10000
TTF2   10000 perm   2 sec   (5328 perm/sec)   p_kst 3.611000e-01   p_cons 3.470000e-01   p_joint 7.734000e-01

Outputting figure to mutsig2_images.part000000000184/TTF2.2_3581_10000_0.3611_0.347_0.7734.png
                gene_name: TTF2
               theta_stop: 0.054 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.35 
      ci_cons_bounds_left: 0.34 
     ci_cons_bounds_right: 0.36 
                  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.165.3896/
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/181708/iteration1/scatter.0000000184
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 184 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120335: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000185> was used as the working directory.
Started at Wed Oct 10 10:45:39 2012
Results reported at Wed Oct 10 10:47:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000185.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000185.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 185  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    117.57 sec.
    Max Memory :      1274 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.165.3896/
-whichjob
185
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 185: processing genes 16647 - 16737
Calculating significance of each gene.
Using projection method.
16647	TXNDC9	1
16648	TXNIP	7.515168e-02
16649	TXNL1	1.118604e-01
16650	TXNL4A	1
16651	TXNL4B	1
16652	TXNRD1	2.327509e-01
16653	TXNRD2	1.218625e-01
16654	TXNRD3IT1	1
16655	TYK2	4.082533e-01
16656	TYMP	1
16657	TYMS	1.019034e-01
16658	TYR	1
16659	TYRO3	1
16660	TYROBP	1
16661	TYRP1	1
16662	TYSND1	1
16663	TYW1	1.264747e-01
16664	TYW1B	1
16665	TYW3	1
16666	U2AF1	1
16667	U2AF1L4	1
16668	U2AF2	2.151881e-02
16669	UACA	1
16670	UAP1	1
16671	UAP1L1	1
16672	UBA1	1
16673	UBA2	1
16674	UBA3	1
16675	UBA5	1
16676	UBA52	1
16677	UBA6	1
16678	UBA7	1
16679	UBAC1	1
16680	UBAC2	1
16681	UBAP1	1
16682	UBAP2	1
16683	UBAP2L	7.256466e-02
16684	UBASH3A	1
16685	UBASH3B	1
16686	UBB	1
16687	UBC	1
16688	UBD	1
16689	UBE2A	1
16690	UBE2B	1
16691	UBE2C	1
16692	UBE2CBP	1
16693	UBE2D1	1
16694	UBE2D2	1
16695	UBE2D3	1
16696	UBE2D4	1
16697	UBE2E1	1
16698	UBE2E2	1
16699	UBE2E3	1
16700	UBE2F	1
16701	UBE2G1	1
16702	UBE2G2	1
16703	UBE2H	1
16704	UBE2I	1
16705	UBE2J1	1
16706	UBE2J2	8.255723e-02
16707	UBE2K	1
16708	UBE2L3	1
16709	UBE2L6	1
16710	UBE2M	1
16711	UBE2N	1
16712	UBE2NL	1
16713	UBE2O	1
16714	UBE2Q1	1
16715	UBE2Q2	1
16716	UBE2R2	1
16717	UBE2S	1
16718	UBE2T	1
16719	UBE2U	1
16720	UBE2V1	1
16721	UBE2V2	1
16722	UBE2W	1
16723	UBE2Z	1.190274e-01
16724	UBE3A	1
16725	UBE3B	3.800841e-01
16726	UBE3C	1
16727	UBE4A	4.006849e-01
16728	UBE4B	2.750587e-01
16729	UBFD1	1
16730	UBIAD1	1
16731	UBL3	1
16732	UBL4A	2.473115e-02
16733	UBL4B	1
16734	UBL5	1
16735	UBL7	1
16736	UBLCP1	1
16737	UBN1	1
Done

Running MutSig 2:
Scatter job 185: processing genes 16647 - 16737
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
U2AF2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.539235e-02	ci left: 4.173773e-01	ci right 4.368652e-01	k: 4271	n:10000
Cons ci ratio: 4.288625e-02	ci left: 4.453040e-01	ci right 4.649221e-01	k: 4551	n:10000
KS ci ratio: 7.150104e-02	ci left: 2.227686e-01	ci right 2.393884e-01	k: 2310	n:10000
U2AF2   10000 perm   2 sec   (5545 perm/sec)   p_kst 2.310000e-01   p_cons 4.551000e-01   p_joint 4.271000e-01

Outputting figure to mutsig2_images.part000000000185/U2AF2.2_1476_10000_0.231_0.4551_0.4271.png
                gene_name: U2AF2
               theta_stop: 0.072 
                    nperm: 10000 
                     p_ks: 0.23 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.24 
                   p_cons: 0.46 
      ci_cons_bounds_left: 0.45 
     ci_cons_bounds_right: 0.46 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 33 percent done.
UBAP2L
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.224924e-02	ci left: 9.053515e-01	ci right 9.166077e-01	k: 9111	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: 2.944842e-02	ci left: 6.296981e-01	ci right 6.486207e-01	k: 6392	n:10000
UBAP2L   10000 perm   2 sec   (5479 perm/sec)   p_kst 6.392000e-01   p_cons 7.777000e-01   p_joint 9.111000e-01

Outputting figure to mutsig2_images.part000000000185/UBAP2L.2_3422_10000_0.6392_0.7777_0.9111.png
                gene_name: UBAP2L
               theta_stop: 0.029 
                    nperm: 10000 
                     p_ks: 0.64 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.65 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.91 
     ci_joint_bounds_left: 0.91 
    ci_joint_bounds_right: 0.92 

Current progress: 67 percent done.
UBE4A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.284292e-02	ci left: 7.378529e-01	ci right 7.550034e-01	k: 7465	n:10000
Cons ci ratio: 1.113507e-02	ci left: 9.200754e-01	ci right 9.304753e-01	k: 9254	n:10000
KS ci ratio: 2.125218e-01	ci left: 2.939568e-02	ci right 3.647982e-02	k: 328	n:10000
UBE4A   10000 perm   2 sec   (5430 perm/sec)   p_kst 3.280000e-02   p_cons 9.254000e-01   p_joint 7.465000e-01

Joint ci ratio: 1.564056e-01	ci left: 2.806407e-02	ci right 3.287372e-02	k: 608	n:20000
Cons ci ratio: 8.080745e-03	ci left: 9.178902e-01	ci right 9.253866e-01	k: 18434	n:20000
KS ci ratio: 1.564056e-01	ci left: 2.806407e-02	ci right 3.287372e-02	k: 608	n:20000
UBE4A   20000 perm   4 sec   (4945 perm/sec)   p_kst 3.040000e-02   p_cons 9.217000e-01   p_joint 3.040000e-02

Joint ci ratio: 1.277417e-01	ci left: 2.848615e-02	ci right 3.240548e-02	k: 912	n:30000
Cons ci ratio: 6.609600e-03	ci left: 9.183310e-01	ci right 9.244537e-01	k: 27643	n:30000
KS ci ratio: 1.277417e-01	ci left: 2.848615e-02	ci right 3.240548e-02	k: 912	n:30000
UBE4A   30000 perm   6 sec   (4754 perm/sec)   p_kst 3.040000e-02   p_cons 9.214333e-01   p_joint 3.040000e-02

Joint ci ratio: 1.103633e-01	ci left: 2.888515e-02	ci right 3.228345e-02	k: 1222	n:40000
Cons ci ratio: 5.755761e-03	ci left: 9.179327e-01	ci right 9.232560e-01	k: 36825	n:40000
KS ci ratio: 1.103633e-01	ci left: 2.888515e-02	ci right 3.228345e-02	k: 1222	n:40000
UBE4A   40000 perm   9 sec   (4610 perm/sec)   p_kst 3.055000e-02   p_cons 9.206250e-01   p_joint 3.055000e-02

Joint ci ratio: 9.897129e-02	ci left: 2.891245e-02	ci right 3.194239e-02	k: 1520	n:50000
Cons ci ratio: 4.980063e-03	ci left: 9.230013e-01	ci right 9.276291e-01	k: 46267	n:50000
KS ci ratio: 9.897129e-02	ci left: 2.891245e-02	ci right 3.194239e-02	k: 1520	n:50000
UBE4A   50000 perm   11 sec   (4482 perm/sec)   p_kst 3.040000e-02   p_cons 9.253400e-01   p_joint 3.040000e-02

Outputting figure to mutsig2_images.part000000000185/UBE4A.2_3298_50000_0.0304_0.92534_0.0304.png
                gene_name: UBE4A
               theta_stop: 0.099 
                    nperm: 50000 
                     p_ks: 0.030 
        ci_ks_bounds_left: 0.029 
       ci_ks_bounds_right: 0.032 
                   p_cons: 0.93 
      ci_cons_bounds_left: 0.92 
     ci_cons_bounds_right: 0.93 
                  p_joint: 0.030 
     ci_joint_bounds_left: 0.029 
    ci_joint_bounds_right: 0.032 

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.165.3896/
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/181708/iteration1/scatter.0000000185
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 185 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120337: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000186> was used as the working directory.
Started at Wed Oct 10 10:45:53 2012
Results reported at Wed Oct 10 10:47:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000186.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000186.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 186  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     95.21 sec.
    Max Memory :      1138 MB
    Max Swap   :      3965 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.165.3896/
-whichjob
186
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 186: processing genes 16738 - 16827
Calculating significance of each gene.
Using projection method.
16738	UBN2	2.149725e-01
16739	UBOX5	1
16740	UBP1	2.578475e-01
16741	UBQLN1	1
16742	UBQLN2	1
16743	UBQLN3	1
16744	UBQLN4	1
16745	UBQLNL	1
16746	UBR1	3.503942e-01
16747	UBR2	1
16748	UBR3	1
16749	UBR4	8.365621e-01
16750	UBR5	6.615272e-01
16751	UBR7	8.284221e-02
16752	UBTD1	1
16753	UBTD2	1
16754	UBTF	9.387073e-02
16755	UBTFL1	5.257165e-02
16756	UBXN1	1
16757	UBXN10	1
16758	UBXN11	1
16759	UBXN2A	1
16760	UBXN2B	1
16761	UBXN4	1
16762	UBXN6	1
16763	UBXN7	1
16764	UBXN8	1
16765	UCHL1	1
16766	UCHL3	1
16767	UCHL5	1
16768	UCK1	1
16769	UCK2	1
16770	UCKL1	2.274761e-01
16771	UCMA	1
16772	UCN	1
16773	UCN2	1
16774	UCN3	1
16775	UCP1	1
16776	UCP2	1
16777	UCP3	1
16778	UEVLD	1
16779	UFC1	1
16780	UFD1L	1
16781	UFM1	1
16782	UFSP1	1
16783	UFSP2	2.561567e-02
16784	UGCG	1.363051e-01
16785	UGDH	2.098362e-02
16786	UGGT1	5.255497e-01
16787	UGGT2	4.229082e-01
16788	UGP2	1
16789	UGT1A1	3.401755e-02
16790	UGT1A10	1
16791	UGT1A3	3.594690e-02
16792	UGT1A4	1
16793	UGT1A5	2.201005e-01
16794	UGT1A6	1
16795	UGT1A7	1
16796	UGT1A8	1
16797	UGT1A9	1
16798	UGT2A1	1
16799	UGT2A2	1
16800	UGT2A3	1
16801	UGT2B10	1
16802	UGT2B11	1
16803	UGT2B15	1
16804	UGT2B17	1
16805	UGT2B28	1
16806	UGT2B4	1
16807	UGT2B7	1.048883e-01
16808	UGT3A1	1
16809	UGT3A2	1
16810	UGT8	9.171774e-02
16811	UHMK1	1
16812	UHRF1	1
16813	UHRF1BP1	1
16814	UHRF1BP1L	1
16815	UHRF2	1
16816	UIMC1	1
16817	ULBP1	1
16818	ULBP2	1
16819	ULBP3	4.282431e-02
16820	ULK1	2.331921e-01
16821	ULK2	4.338626e-01
16822	ULK3	1
16823	ULK4	1
16824	UMOD	1
16825	UMODL1	1
16826	UMPS	1
16827	UNC119	1
Done

Running MutSig 2:
Scatter job 186: processing genes 16738 - 16827
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: 1.055019e-01	ci left: 1.148645e-01	ci right 1.277571e-01	k: 1212	n:10000
Cons ci ratio: 2.873093e-02	ci left: 6.410619e-01	ci right 6.598504e-01	k: 6505	n:10000
KS ci ratio: 1.137175e-01	ci left: 1.001293e-01	ci right 1.123011e-01	k: 1061	n:10000
UBR4   10000 perm   3 sec   (2997 perm/sec)   p_kst 1.061000e-01   p_cons 6.505000e-01   p_joint 1.212000e-01

Joint ci ratio: 5.989268e-02	ci left: 1.710904e-01	ci right 1.817039e-01	k: 3527	n:20000
Cons ci ratio: 1.935139e-02	ci left: 6.657452e-01	ci right 6.788047e-01	k: 13446	n:20000
KS ci ratio: 8.120554e-02	ci left: 1.000967e-01	ci right 1.086187e-01	k: 2086	n:20000
UBR4   20000 perm   9 sec   (2226 perm/sec)   p_kst 1.043000e-01   p_cons 6.723000e-01   p_joint 1.763500e-01

Outputting figure to mutsig2_images.part000000000186/UBR4.3_15976_20000_0.1043_0.6723_0.17635.png
                gene_name: UBR4
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.10 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.68 
                  p_joint: 0.18 
     ci_joint_bounds_left: 0.17 
    ci_joint_bounds_right: 0.18 

Current progress: 33 percent done.
UGDH
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: 2.563659e-02	ci left: 6.913143e-01	ci right 7.093688e-01	k: 7004	n:10000
KS ci ratio: 1.063575e-02	ci left: 9.263722e-01	ci right 9.363747e-01	k: 9315	n:10000
UGDH   10000 perm   2 sec   (6520 perm/sec)   p_kst 9.315000e-01   p_cons 7.004000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000186/UGDH.2_1529_10000_0.9315_0.7004_1.png
                gene_name: UGDH
               theta_stop: 0.026 
                    nperm: 10000 
                     p_ks: 0.93 
        ci_ks_bounds_left: 0.93 
       ci_ks_bounds_right: 0.94 
                   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: 67 percent done.
UGT1A1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.128566e-01	ci left: 2.930086e-02	ci right 3.637471e-02	k: 327	n:10000
Cons ci ratio: 1.893706e-02	ci left: 8.029834e-01	ci right 8.184352e-01	k: 8108	n:10000
KS ci ratio: 2.595468e-01	ci left: 1.940213e-02	ci right 2.528070e-02	k: 222	n:10000
UGT1A1   10000 perm   2 sec   (6471 perm/sec)   p_kst 2.220000e-02   p_cons 8.108000e-01   p_joint 3.270000e-02

Joint ci ratio: 1.246736e-01	ci left: 4.415643e-02	ci right 5.007613e-02	k: 941	n:20000
Cons ci ratio: 1.345994e-02	ci left: 8.036846e-01	ci right 8.146254e-01	k: 16184	n:20000
KS ci ratio: 1.885661e-01	ci left: 1.915306e-02	ci right 2.318783e-02	k: 422	n:20000
UGT1A1   20000 perm   3 sec   (5745 perm/sec)   p_kst 2.110000e-02   p_cons 8.092000e-01   p_joint 4.705000e-02

Joint ci ratio: 1.028705e-01	ci left: 4.378695e-02	ci right 4.856811e-02	k: 1384	n:30000
Cons ci ratio: 1.134566e-02	ci left: 7.945877e-01	ci right 8.036876e-01	k: 23975	n:30000
KS ci ratio: 1.570918e-01	ci left: 1.873410e-02	ci right 2.195973e-02	k: 609	n:30000
UGT1A1   30000 perm   5 sec   (5459 perm/sec)   p_kst 2.030000e-02   p_cons 7.991667e-01   p_joint 4.613333e-02

Joint ci ratio: 1.295554e-01	ci left: 2.092365e-02	ci right 2.384626e-02	k: 894	n:40000
Cons ci ratio: 9.834530e-03	ci left: 7.949127e-01	ci right 8.027939e-01	k: 31955	n:40000
KS ci ratio: 1.365898e-01	ci left: 1.879541e-02	ci right 2.157486e-02	k: 806	n:40000
UGT1A1   40000 perm   8 sec   (5273 perm/sec)   p_kst 2.015000e-02   p_cons 7.988750e-01   p_joint 2.235000e-02

Joint ci ratio: 1.198123e-01	ci left: 1.970283e-02	ci right 2.223321e-02	k: 1047	n:50000
Cons ci ratio: 8.810896e-03	ci left: 7.947958e-01	ci right 8.018496e-01	k: 39917	n:50000
KS ci ratio: 1.224023e-01	ci left: 1.886839e-02	ci right 2.134777e-02	k: 1004	n:50000
UGT1A1   50000 perm   10 sec   (5121 perm/sec)   p_kst 2.008000e-02   p_cons 7.983400e-01   p_joint 2.094000e-02

Joint ci ratio: 1.096229e-01	ci left: 1.972161e-02	ci right 2.202506e-02	k: 1251	n:60000
Cons ci ratio: 8.010883e-03	ci left: 7.964077e-01	ci right 8.028299e-01	k: 47978	n:60000
KS ci ratio: 1.120701e-01	ci left: 1.886230e-02	ci right 2.111780e-02	k: 1198	n:60000
UGT1A1   60000 perm   12 sec   (4987 perm/sec)   p_kst 1.996667e-02   p_cons 7.996333e-01   p_joint 2.085000e-02

Joint ci ratio: 1.015504e-01	ci left: 1.978339e-02	ci right 2.191373e-02	k: 1458	n:70000
Cons ci ratio: 7.420047e-03	ci left: 7.965001e-01	ci right 8.024464e-01	k: 55964	n:70000
KS ci ratio: 1.039402e-01	ci left: 1.887822e-02	ci right 2.096184e-02	k: 1393	n:70000
UGT1A1   70000 perm   14 sec   (4868 perm/sec)   p_kst 1.990000e-02   p_cons 7.994857e-01   p_joint 2.082857e-02

Joint ci ratio: 6.835342e-02	ci left: 3.813614e-02	ci right 4.084738e-02	k: 3158	n:80000
Cons ci ratio: 6.709679e-03	ci left: 8.073898e-01	ci right 8.128377e-01	k: 64810	n:80000
KS ci ratio: 9.726288e-02	ci left: 1.893123e-02	ci right 2.087880e-02	k: 1591	n:80000
UGT1A1   80000 perm   17 sec   (4762 perm/sec)   p_kst 1.988750e-02   p_cons 8.101250e-01   p_joint 3.947500e-02

Outputting figure to mutsig2_images.part000000000186/UGT1A1.2_1622_80000_0.019887_0.81012_0.039475.png
                gene_name: UGT1A1
               theta_stop: 0.097 
                    nperm: 80000 
                     p_ks: 0.020 
        ci_ks_bounds_left: 0.019 
       ci_ks_bounds_right: 0.021 
                   p_cons: 0.81 
      ci_cons_bounds_left: 0.81 
     ci_cons_bounds_right: 0.81 
                  p_joint: 0.039 
     ci_joint_bounds_left: 0.038 
    ci_joint_bounds_right: 0.041 

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.165.3896/
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/181708/iteration1/scatter.0000000186
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 186 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120340: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000187> was used as the working directory.
Started at Wed Oct 10 10:45:53 2012
Results reported at Wed Oct 10 10:47:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000187.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000187.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 187  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    106.31 sec.
    Max Memory :      1360 MB
    Max Swap   :      3800 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.165.3896/
-whichjob
187
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 187: processing genes 16828 - 16918
Calculating significance of each gene.
Using projection method.
16828	UNC119B	1
16829	UNC13A	1
16830	UNC13B	5.063009e-01
16831	UNC13C	7.157848e-02
16832	UNC13D	1
16833	UNC45A	2.547599e-01
16834	UNC45B	6.971029e-02
16835	UNC50	1
16836	UNC5A	1
16837	UNC5B	1
16838	UNC5C	1
16839	UNC5CL	1
16840	UNC5D	1
16841	UNC93A	1
16842	UNC93B1	1
16843	UNCX	1
16844	UNG	1
16845	UNK	1
16846	UNKL	1
16847	UPB1	9.358888e-02
16848	UPF1	1
16849	UPF2	5.137389e-01
16850	UPF3A	1
16851	UPF3B	1
16852	UPK1A	1
16853	UPK1B	1
16854	UPK2	1
16855	UPK3A	1
16856	UPK3B	1
16857	UPP1	1
16858	UPP2	1
16859	UPRT	1
16860	UQCC	3.079278e-02
16861	UQCR10	1
16862	UQCR11	1
16863	UQCRB	1
16864	UQCRC1	1
16865	UQCRC2	1
16866	UQCRFS1	1
16867	UQCRH	1
16868	UQCRHL	1
16869	UQCRQ	1
16870	URB2	1.375600e-01
16871	URGCP	1
16872	URM1	1
16873	UROC1	1
16874	UROD	1
16875	UROS	1
16876	USE1	1
16877	USF1	1
16878	USF2	1
16879	USH1C	1.956667e-01
16880	USH1G	1
16881	USH2A	5.207834e-01
16882	USHBP1	1
16883	USMG5	1
16884	USO1	2.008709e-01
16885	USP1	1
16886	USP10	1.929754e-01
16887	USP11	1
16888	USP12	1.023866e-01
16889	USP13	2.093705e-02
16890	USP14	1
16891	USP15	1
16892	USP16	1
16893	USP17L2	1
16894	USP18	1
16895	USP19	2.424550e-01
16896	USP2	1
16897	USP20	1.056178e-01
16898	USP21	1
16899	USP22	1
16900	USP24	1
16901	USP25	3.827927e-01
16902	USP26	1
16903	USP28	2.792371e-01
16904	USP29	2.228770e-01
16905	USP3	1
16906	USP30	1
16907	USP31	3.382402e-01
16908	USP32	2.596325e-01
16909	USP33	1
16910	USP34	5.680858e-01
16911	USP35	1
16912	USP36	1
16913	USP37	1
16914	USP38	1.164403e-02
16915	USP39	2.542497e-01
16916	USP4	1
16917	USP40	1
16918	USP42	3.661176e-01
Done

Running MutSig 2:
Scatter job 187: processing genes 16828 - 16918
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
UNC45B
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.389067e-02	ci left: 5.624330e-01	ci right 5.819249e-01	k: 5722	n:10000
Cons ci ratio: 1.745679e-01	ci left: 4.379660e-02	ci right 5.226918e-02	k: 479	n:10000
KS ci ratio: 1.724980e-02	ci left: 8.304267e-01	ci right 8.449760e-01	k: 8378	n:10000
UNC45B   10000 perm   2 sec   (5382 perm/sec)   p_kst 8.378000e-01   p_cons 4.790000e-02   p_joint 5.722000e-01

Joint ci ratio: 2.745996e-02	ci left: 4.976955e-01	ci right 5.116031e-01	k: 10093	n:20000
Cons ci ratio: 1.253735e-01	ci left: 4.367138e-02	ci right 4.956134e-02	k: 931	n:20000
KS ci ratio: 1.218563e-02	ci left: 8.328702e-01	ci right 8.431313e-01	k: 16761	n:20000
UNC45B   20000 perm   6 sec   (3325 perm/sec)   p_kst 8.380500e-01   p_cons 4.655000e-02   p_joint 5.046500e-01

Joint ci ratio: 2.168087e-02	ci left: 5.157621e-01	ci right 5.271004e-01	k: 15643	n:30000
Cons ci ratio: 1.019858e-01	ci left: 4.453486e-02	ci right 4.935337e-02	k: 1407	n:30000
KS ci ratio: 9.893727e-03	ci left: 8.353642e-01	ci right 8.437033e-01	k: 25187	n:30000
UNC45B   30000 perm   8 sec   (3608 perm/sec)   p_kst 8.395667e-01   p_cons 4.690000e-02   p_joint 5.214333e-01

Joint ci ratio: 1.784679e-02	ci left: 5.418058e-01	ci right 5.515875e-01	k: 21868	n:40000
Cons ci ratio: 8.830621e-02	ci left: 4.487300e-02	ci right 4.904308e-02	k: 1877	n:40000
KS ci ratio: 8.561520e-03	ci left: 8.361431e-01	ci right 8.433575e-01	k: 33591	n:40000
UNC45B   40000 perm   11 sec   (3741 perm/sec)   p_kst 8.397750e-01   p_cons 4.692500e-02   p_joint 5.467000e-01

Outputting figure to mutsig2_images.part000000000187/UNC45B.3_2872_40000_0.83978_0.046925_0.5467.png
                gene_name: UNC45B
               theta_stop: 0.088 
                    nperm: 40000 
                     p_ks: 0.84 
        ci_ks_bounds_left: 0.84 
       ci_ks_bounds_right: 0.84 
                   p_cons: 0.047 
      ci_cons_bounds_left: 0.045 
     ci_cons_bounds_right: 0.049 
                  p_joint: 0.55 
     ci_joint_bounds_left: 0.54 
    ci_joint_bounds_right: 0.55 

Current progress: 14 percent done.
URB2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.935644e-02	ci left: 2.336317e-01	ci right 2.505188e-01	k: 2420	n:10000
Cons ci ratio: 6.651539e-03	ci left: 9.686815e-01	ci right 9.752397e-01	k: 9721	n:10000
KS ci ratio: 1.176608e-01	ci left: 9.399250e-02	ci right 1.058417e-01	k: 998	n:10000
URB2   10000 perm   2 sec   (5140 perm/sec)   p_kst 9.980000e-02   p_cons 9.721000e-01   p_joint 2.420000e-01

Joint ci ratio: 5.410391e-02	ci left: 2.022442e-01	ci right 2.135408e-01	k: 4157	n:20000
Cons ci ratio: 4.410579e-03	ci left: 9.731057e-01	ci right 9.774546e-01	k: 19507	n:20000
KS ci ratio: 8.056057e-02	ci left: 1.015697e-01	ci right 1.101452e-01	k: 2116	n:20000
URB2   20000 perm   4 sec   (4640 perm/sec)   p_kst 1.058000e-01   p_cons 9.753500e-01   p_joint 2.078500e-01

Outputting figure to mutsig2_images.part000000000187/URB2.3_4611_20000_0.1058_0.97535_0.20785.png
                gene_name: URB2
               theta_stop: 0.081 
                    nperm: 20000 
                     p_ks: 0.11 
        ci_ks_bounds_left: 0.10 
       ci_ks_bounds_right: 0.11 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.97 
     ci_cons_bounds_right: 0.98 
                  p_joint: 0.21 
     ci_joint_bounds_left: 0.20 
    ci_joint_bounds_right: 0.21 

Current progress: 29 percent done.
USH2A
Processing conservation and coverage...
62% 
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: 2.819591e-02	ci left: 6.496136e-01	ci right 6.682937e-01	k: 6590	n:10000
KS ci ratio: 2.556333e-02	ci left: 6.925243e-01	ci right 7.105582e-01	k: 7016	n:10000
USH2A   10000 perm   3 sec   (3109 perm/sec)   p_kst 7.016000e-01   p_cons 6.590000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000187/USH2A.3_15907_10000_0.7016_0.659_1.png
                gene_name: USH2A
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.70 
        ci_ks_bounds_left: 0.69 
       ci_ks_bounds_right: 0.71 
                   p_cons: 0.66 
      ci_cons_bounds_left: 0.65 
     ci_cons_bounds_right: 0.67 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 43 percent done.
USP38
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.721990e-02	ci left: 3.982459e-01	ci right 4.176078e-01	k: 4079	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: 5.453085e-02	ci left: 3.313090e-01	ci right 3.499839e-01	k: 3406	n:10000
USP38   10000 perm   2 sec   (5508 perm/sec)   p_kst 3.406000e-01   p_cons 6.565000e-01   p_joint 4.079000e-01

Outputting figure to mutsig2_images.part000000000187/USP38.3_3169_10000_0.3406_0.6565_0.4079.png
                gene_name: USP38
               theta_stop: 0.055 
                    nperm: 10000 
                     p_ks: 0.34 
        ci_ks_bounds_left: 0.33 
       ci_ks_bounds_right: 0.35 
                   p_cons: 0.66 
      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: 57 percent done.
UNC13C
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: 2.412351e-02	ci left: 7.164367e-01	ci right 7.340319e-01	k: 7253	n:10000
KS ci ratio: 7.385874e-03	ci left: 9.620496e-01	ci right 9.692759e-01	k: 9658	n:10000
UNC13C   10000 perm   2 sec   (4709 perm/sec)   p_kst 9.658000e-01   p_cons 7.253000e-01   p_joint 9.816000e-01

Outputting figure to mutsig2_images.part000000000187/UNC13C.2_6769_10000_0.9658_0.7253_0.9816.png
                gene_name: UNC13C
               theta_stop: 0.024 
                    nperm: 10000 
                     p_ks: 0.97 
        ci_ks_bounds_left: 0.96 
       ci_ks_bounds_right: 0.97 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.72 
     ci_cons_bounds_right: 0.73 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.98 
    ci_joint_bounds_right: 0.98 

Current progress: 71 percent done.
USP13
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: 3.198987e-02	ci left: 5.905209e-01	ci right 6.098207e-01	k: 6002	n:10000
KS ci ratio: 2.333176e-02	ci left: 7.296672e-01	ci right 7.469937e-01	k: 7384	n:10000
USP13   10000 perm   2 sec   (6027 perm/sec)   p_kst 7.384000e-01   p_cons 6.002000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000187/USP13.2_2676_10000_0.7384_0.6002_1.png
                gene_name: USP13
               theta_stop: 0.032 
                    nperm: 10000 
                     p_ks: 0.74 
        ci_ks_bounds_left: 0.73 
       ci_ks_bounds_right: 0.75 
                   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: 86 percent done.
USP34
Processing conservation and coverage...
91% 
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: 6.236713e-03	ci left: 9.721719e-01	ci right 9.783470e-01	k: 9754	n:10000
KS ci ratio: 3.958604e-03	ci left: 9.878505e-01	ci right 9.918564e-01	k: 9900	n:10000
USP34   10000 perm   3 sec   (3814 perm/sec)   p_kst 9.900000e-01   p_cons 9.754000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000187/USP34.2_10961_10000_0.99_0.9754_1.png
                gene_name: USP34
               theta_stop: 0.0062 
                    nperm: 10000 
                     p_ks: 0.99 
        ci_ks_bounds_left: 0.99 
       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: 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.165.3896/
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/181708/iteration1/scatter.0000000187
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 187 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120344: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000188> was used as the working directory.
Started at Wed Oct 10 10:45:53 2012
Results reported at Wed Oct 10 10:47:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000188.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000188.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 188  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     85.69 sec.
    Max Memory :      1097 MB
    Max Swap   :      3779 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.165.3896/
-whichjob
188
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 188: processing genes 16919 - 17008
Calculating significance of each gene.
Using projection method.
16919	USP43	1.266292e-02
16920	USP44	1
16921	USP45	1
16922	USP46	1
16923	USP47	1.072386e-01
16924	USP48	1
16925	USP49	1
16926	USP5	1.343674e-01
16927	USP50	1
16928	USP51	1
16929	USP53	1
16930	USP54	1
16931	USP6	1
16932	USP6NL	1
16933	USP7	1
16934	USP8	1.388942e-01
16935	USP9X	4.187594e-01
16936	USP9Y	3.879375e-01
16937	USPL1	1
16938	UST	1
16939	UTP11L	1
16940	UTP14A	1.656967e-01
16941	UTP14C	1.955175e-01
16942	UTP15	1
16943	UTP18	2.522035e-02
16944	UTP20	5.436503e-01
16945	UTP23	2.046177e-02
16946	UTP3	1
16947	UTP6	1
16948	UTRN	7.188554e-01
16949	UTS2	1
16950	UTS2D	1
16951	UTS2R	1
16952	UTY	1
16953	UVRAG	1
16954	UXS1	1
16955	UXT	1
16956	VAC14	3.513224e-01
16957	VAMP1	1
16958	VAMP2	1
16959	VAMP3	1
16960	VAMP4	1
16961	VAMP5	1
16962	VAMP7	1
16963	VAMP8	1
16964	VANGL1	2.227654e-01
16965	VANGL2	3.588251e-02
16966	VAPA	1
16967	VAPB	1
16968	VARS	1
16969	VARS2	3.564737e-01
16970	VASH1	5.801781e-02
16971	VASH2	1
16972	VASN	1
16973	VASP	1
16974	VAT1	1
16975	VAT1L	1
16976	VAV1	1
16977	VAV2	1
16978	VAV3	1.310557e-01
16979	VAX1	1
16980	VAX2	1
16981	VBP1	1
16982	VCAM1	1
16983	VCAN	4.439058e-02
16984	VCL	1
16985	VCP	1
16986	VCPIP1	1
16987	VCX	1
16988	VCX2	1
16989	VCX3A	1
16990	VCX3B	5.146520e-02
16991	VDAC1	1
16992	VDAC2	2.673580e-02
16993	VDAC3	1
16994	VDR	1
16995	VEGFA	1
16996	VEGFB	1
16997	VEGFC	1
16998	VENTX	1
16999	VEPH1	1
17000/18094 17000	VEZF1	1
17001	VEZT	1
17002	VGF	1
17003	VGLL1	1
17004	VGLL2	1
17005	VGLL3	1
17006	VGLL4	7.973929e-02
17007	VHL	1
17008	VHLL	1
Done

Running MutSig 2:
Scatter job 188: processing genes 16919 - 17008
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
VCAN
Processing conservation and coverage...
97% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.013153e-01	ci left: 1.235648e-01	ci right 1.368514e-01	k: 1301	n:10000
Cons ci ratio: 1.247192e-01	ci left: 8.426661e-02	ci right 9.557360e-02	k: 898	n:10000
KS ci ratio: 4.429668e-02	ci left: 4.293421e-01	ci right 4.488934e-01	k: 4391	n:10000
VCAN   10000 perm   3 sec   (3737 perm/sec)   p_kst 4.391000e-01   p_cons 8.980000e-02   p_joint 1.301000e-01

Joint ci ratio: 7.486609e-02	ci left: 1.160187e-01	ci right 1.250920e-01	k: 2410	n:20000
Cons ci ratio: 8.984865e-02	ci left: 8.298234e-02	ci right 9.083824e-02	k: 1737	n:20000
KS ci ratio: 3.064454e-02	ci left: 4.430380e-01	ci right 4.568766e-01	k: 8999	n:20000
VCAN   20000 perm   8 sec   (2627 perm/sec)   p_kst 4.499500e-01   p_cons 8.685000e-02   p_joint 1.205000e-01

Outputting figure to mutsig2_images.part000000000188/VCAN.4_10247_20000_0.44995_0.08685_0.1205.png
                gene_name: VCAN
               theta_stop: 0.090 
                    nperm: 20000 
                     p_ks: 0.45 
        ci_ks_bounds_left: 0.44 
       ci_ks_bounds_right: 0.46 
                   p_cons: 0.087 
      ci_cons_bounds_left: 0.083 
     ci_cons_bounds_right: 0.091 
                  p_joint: 0.12 
     ci_joint_bounds_left: 0.12 
    ci_joint_bounds_right: 0.13 

Current progress: 20 percent done.
USP43
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.039732e-03	ci left: 9.737631e-01	ci right 9.797547e-01	k: 9769	n:10000
Cons ci ratio: 3.016084e-02	ci left: 6.185410e-01	ci right 6.375843e-01	k: 6281	n:10000
KS ci ratio: 1.360105e-02	ci left: 8.863668e-01	ci right 8.986035e-01	k: 8926	n:10000
USP43   10000 perm   2 sec   (5682 perm/sec)   p_kst 8.926000e-01   p_cons 6.281000e-01   p_joint 9.769000e-01

Outputting figure to mutsig2_images.part000000000188/USP43.2_3432_10000_0.8926_0.6281_0.9769.png
                gene_name: USP43
               theta_stop: 0.030 
                    nperm: 10000 
                     p_ks: 0.89 
        ci_ks_bounds_left: 0.89 
       ci_ks_bounds_right: 0.90 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.64 
                  p_joint: 0.98 
     ci_joint_bounds_left: 0.97 
    ci_joint_bounds_right: 0.98 

Current progress: 40 percent done.
USP47
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.847238e-02	ci left: 6.451864e-01	ci right 6.639235e-01	k: 6546	n:10000
Cons ci ratio: 2.976194e-02	ci left: 6.247723e-01	ci right 6.437494e-01	k: 6343	n:10000
KS ci ratio: 6.730302e-02	ci left: 2.447000e-01	ci right 2.618439e-01	k: 2532	n:10000
USP47   10000 perm   2 sec   (5497 perm/sec)   p_kst 2.532000e-01   p_cons 6.343000e-01   p_joint 6.546000e-01

Outputting figure to mutsig2_images.part000000000188/USP47.2_3972_10000_0.2532_0.6343_0.6546.png
                gene_name: USP47
               theta_stop: 0.067 
                    nperm: 10000 
                     p_ks: 0.25 
        ci_ks_bounds_left: 0.24 
       ci_ks_bounds_right: 0.26 
                   p_cons: 0.63 
      ci_cons_bounds_left: 0.62 
     ci_cons_bounds_right: 0.64 
                  p_joint: 0.65 
     ci_joint_bounds_left: 0.65 
    ci_joint_bounds_right: 0.66 

Current progress: 60 percent done.
UTP18
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.083093e-02	ci left: 7.715474e-01	ci right 7.878893e-01	k: 7798	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: 3.458089e-02	ci left: 5.525096e-01	ci right 5.720541e-01	k: 5623	n:10000
UTP18   10000 perm   2 sec   (6352 perm/sec)   p_kst 5.623000e-01   p_cons 4.032000e-01   p_joint 7.798000e-01

Outputting figure to mutsig2_images.part000000000188/UTP18.2_1723_10000_0.5623_0.4032_0.7798.png
                gene_name: UTP18
               theta_stop: 0.048 
                    nperm: 10000 
                     p_ks: 0.56 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.57 
                   p_cons: 0.40 
      ci_cons_bounds_left: 0.39 
     ci_cons_bounds_right: 0.41 
                  p_joint: 0.78 
     ci_joint_bounds_left: 0.77 
    ci_joint_bounds_right: 0.79 

Current progress: 80 percent done.
UTP20
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.789543e-02	ci left: 6.544443e-01	ci right 6.730602e-01	k: 6638	n:10000
Cons ci ratio: 5.029588e-02	ci left: 3.682841e-01	ci right 3.873871e-01	k: 3778	n:10000
KS ci ratio: 2.002843e-02	ci left: 7.849243e-01	ci right 8.009047e-01	k: 7930	n:10000
UTP20   10000 perm   2 sec   (4398 perm/sec)   p_kst 7.930000e-01   p_cons 3.778000e-01   p_joint 6.638000e-01

Outputting figure to mutsig2_images.part000000000188/UTP20.2_8606_10000_0.793_0.3778_0.6638.png
                gene_name: UTP20
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.78 
       ci_ks_bounds_right: 0.80 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  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.165.3896/
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/181708/iteration1/scatter.0000000188
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 188 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120347: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000189> was used as the working directory.
Started at Wed Oct 10 10:45:53 2012
Results reported at Wed Oct 10 10:47:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000189.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000189.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 189  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    123.02 sec.
    Max Memory :      1319 MB
    Max Swap   :      3837 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.165.3896/
-whichjob
189
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 189: processing genes 17009 - 17099
Calculating significance of each gene.
Using projection method.
17009	VIL1	1
17010	VILL	1
17011	VIM	1.420914e-01
17012	VIP	1
17013	VIPAR	1
17014	VIPR1	6.323505e-02
17015	VIPR2	1
17016	VIT	7.718281e-02
17017	VKORC1	3.697719e-02
17018	VKORC1L1	1
17019	VLDLR	2.733887e-01
17020	VMA21	1
17021	VMAC	1
17022	VMO1	1
17023	VN1R1	1
17024	VN1R2	1
17025	VN1R4	1.211356e-01
17026	VN1R5	1
17027	VNN1	1
17028	VNN2	1.936574e-01
17029	VOPP1	1
17030	VPRBP	1
17031	VPREB1	1
17032	VPREB3	1
17033	VPS11	2.344031e-01
17034	VPS13A	1
17035	VPS13B	6.979850e-02
17036	VPS13C	6.111758e-01
17037	VPS13D	4.302865e-01
17038	VPS16	1
17039	VPS18	1
17040	VPS24	1
17041	VPS25	1
17042	VPS26A	1
17043	VPS26B	1
17044	VPS28	1
17045	VPS29	1
17046	VPS33A	8.065943e-02
17047	VPS33B	1
17048	VPS35	1
17049	VPS36	1
17050	VPS37A	1
17051	VPS37B	1.159049e-01
17052	VPS37C	1
17053	VPS37D	1
17054	VPS39	1
17055	VPS41	1
17056	VPS45	1
17057	VPS4A	1
17058	VPS4B	1
17059	VPS52	1
17060	VPS53	1
17061	VPS54	1
17062	VPS72	1
17063	VPS8	1.038143e-01
17064	VRK1	1
17065	VRK2	1
17066	VRK3	6.733415e-02
17067	VSIG1	1
17068	VSIG10	1.761238e-01
17069	VSIG2	1
17070	VSIG4	1
17071	VSIG8	1
17072	VSNL1	1.005441e-01
17073	VSTM1	1
17074	VSTM2A	1
17075	VSTM2L	1
17076	VSX1	1
17077	VSX2	1
17078	VTA1	1.246607e-01
17079	VTCN1	1
17080	VTI1A	1
17081	VTI1B	1
17082	VTN	1
17083	VWA1	1.027495e-01
17084	VWA2	1
17085	VWA3A	1
17086	VWA3B	9.324975e-02
17087	VWA5A	3.147006e-01
17088	VWC2	1
17089	VWC2L	1
17090	VWCE	2.668209e-01
17091	VWF	1
17092	WAC	1.918318e-01
17093	WAPAL	1
17094	WARS	1
17095	WARS2	1
17096	WAS	1
17097	WASF1	1
17098	WASF2	2.176284e-01
17099	WASF3	1
Done

Running MutSig 2:
Scatter job 189: processing genes 17009 - 17099
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
VPS13B
Processing conservation and coverage...
79% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 6.095056e-02	ci left: 2.835954e-01	ci right 3.015256e-01	k: 2925	n:10000
Cons ci ratio: 4.050932e-02	ci left: 4.736615e-01	ci right 4.933481e-01	k: 4835	n:10000
KS ci ratio: 8.146546e-02	ci left: 1.802855e-01	ci right 1.956967e-01	k: 1879	n:10000
VPS13B   10000 perm   3 sec   (3189 perm/sec)   p_kst 1.879000e-01   p_cons 4.835000e-01   p_joint 2.925000e-01

Outputting figure to mutsig2_images.part000000000189/VPS13B.4_12507_10000_0.1879_0.4835_0.2925.png
                gene_name: VPS13B
               theta_stop: 0.081 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.20 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.30 

Current progress: 25 percent done.
VPS13D
Processing conservation and coverage...
74% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.518891e-02	ci left: 4.195704e-01	ci right 4.390708e-01	k: 4293	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: 4.743559e-02	ci left: 3.960547e-01	ci right 4.154003e-01	k: 4057	n:10000
VPS13D   10000 perm   3 sec   (3296 perm/sec)   p_kst 4.057000e-01   p_cons 6.839000e-01   p_joint 4.293000e-01

Outputting figure to mutsig2_images.part000000000189/VPS13D.3_13443_10000_0.4057_0.6839_0.4293.png
                gene_name: VPS13D
               theta_stop: 0.047 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.40 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.68 
      ci_cons_bounds_left: 0.67 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.43 
     ci_joint_bounds_left: 0.42 
    ci_joint_bounds_right: 0.44 

Current progress: 50 percent done.
VPS8
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.141202e-02	ci left: 4.626742e-01	ci right 4.823418e-01	k: 4725	n:10000
Cons ci ratio: 6.513262e-02	ci left: 2.571609e-01	ci right 2.745757e-01	k: 2658	n:10000
KS ci ratio: 1.040429e-01	ci left: 1.177960e-01	ci right 1.308238e-01	k: 1242	n:10000
VPS8   10000 perm   2 sec   (4765 perm/sec)   p_kst 1.242000e-01   p_cons 2.658000e-01   p_joint 4.725000e-01

Joint ci ratio: 3.461893e-02	ci left: 3.838297e-01	ci right 3.974021e-01	k: 7812	n:20000
Cons ci ratio: 4.584463e-02	ci left: 2.615233e-01	ci right 2.738444e-01	k: 5353	n:20000
KS ci ratio: 7.323477e-02	ci left: 1.206923e-01	ci right 1.299169e-01	k: 2505	n:20000
VPS8   20000 perm   4 sec   (4508 perm/sec)   p_kst 1.252500e-01   p_cons 2.676500e-01   p_joint 3.906000e-01

Outputting figure to mutsig2_images.part000000000189/VPS8.2_4471_20000_0.12525_0.26765_0.3906.png
                gene_name: VPS8
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.13 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.27 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.27 
                  p_joint: 0.39 
     ci_joint_bounds_left: 0.38 
    ci_joint_bounds_right: 0.40 

Current progress: 75 percent done.
VWA3B
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: 2.789543e-02	ci left: 6.544443e-01	ci right 6.730602e-01	k: 6638	n:10000
KS ci ratio: 2.754627e-02	ci left: 6.600814e-01	ci right 6.786198e-01	k: 6694	n:10000
VWA3B   10000 perm   2 sec   (5346 perm/sec)   p_kst 6.694000e-01   p_cons 6.638000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000189/VWA3B.2_3993_10000_0.6694_0.6638_1.png
                gene_name: VWA3B
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.68 
                   p_cons: 0.66 
      ci_cons_bounds_left: 0.65 
     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.165.3896/
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/181708/iteration1/scatter.0000000189
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 189 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120350: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000190> was used as the working directory.
Started at Wed Oct 10 10:45:53 2012
Results reported at Wed Oct 10 10:47:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000190.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000190.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 190  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :     91.51 sec.
    Max Memory :      1270 MB
    Max Swap   :      3876 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.165.3896/
-whichjob
190
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 190: processing genes 17100 - 17189
Calculating significance of each gene.
Using projection method.
17100	WASL	2.303218e-01
17101	WBP1	3.880975e-02
17102	WBP11	1
17103	WBP2	1
17104	WBP2NL	1
17105	WBP4	1
17106	WBP5	2.525284e-02
17107	WBSCR16	1
17108	WBSCR17	1
17109	WBSCR22	1
17110	WBSCR27	1
17111	WBSCR28	1
17112	WDFY1	1
17113	WDFY2	1
17114	WDFY3	4.973255e-01
17115	WDHD1	3.860428e-01
17116	WDR1	1
17117	WDR11	1
17118	WDR12	1
17119	WDR13	1
17120	WDR16	1
17121	WDR17	5.004448e-01
17122	WDR18	1
17123	WDR19	1
17124	WDR20	1
17125	WDR24	1
17126	WDR25	1
17127	WDR26	1
17128	WDR27	1
17129	WDR3	1
17130	WDR31	1
17131	WDR33	1
17132	WDR34	1
17133	WDR35	1
17134	WDR36	2.837180e-01
17135	WDR37	1
17136	WDR38	1
17137	WDR4	1
17138	WDR41	1
17139	WDR43	1
17140	WDR44	1
17141	WDR45	1
17142	WDR45L	1
17143	WDR46	1
17144	WDR47	1
17145	WDR48	1
17146	WDR49	4.161137e-02
17147	WDR5	1
17148	WDR52	1.468916e-01
17149	WDR53	1
17150	WDR54	1
17151	WDR55	1
17152	WDR59	1
17153	WDR5B	1
17154	WDR6	2.045558e-01
17155	WDR60	2.208304e-01
17156	WDR61	1
17157	WDR62	1.141341e-01
17158	WDR63	1
17159	WDR64	3.113438e-01
17160	WDR65	1
17161	WDR66	2.836317e-01
17162	WDR67	3.616087e-01
17163	WDR69	9.698097e-02
17164	WDR7	1
17165	WDR70	2.400319e-01
17166	WDR72	1.077890e-01
17167	WDR73	1
17168	WDR74	1
17169	WDR75	1
17170	WDR76	1
17171	WDR77	1.138325e-01
17172	WDR78	1
17173	WDR8	1
17174	WDR81	1
17175	WDR82	1
17176	WDR83	1
17177	WDR85	1
17178	WDR86	1
17179	WDR88	1
17180	WDR89	1
17181	WDR90	3.162451e-01
17182	WDR91	1
17183	WDR92	1
17184	WDR93	1
17185	WDSUB1	1
17186	WDTC1	1
17187	WDYHV1	1
17188	WEE1	4.101954e-02
17189	WEE2	1
Done

Running MutSig 2:
Scatter job 190: processing genes 17100 - 17189
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
WDR62
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.548895e-02	ci left: 5.396851e-01	ci right 5.592861e-01	k: 5495	n:10000
Cons ci ratio: 4.054989e-02	ci left: 4.731620e-01	ci right 4.928479e-01	k: 4830	n:10000
KS ci ratio: 4.889213e-02	ci left: 3.816178e-01	ci right 4.008456e-01	k: 3912	n:10000
WDR62   10000 perm   2 sec   (4917 perm/sec)   p_kst 3.912000e-01   p_cons 4.830000e-01   p_joint 5.495000e-01

Outputting figure to mutsig2_images.part000000000190/WDR62.3_4700_10000_0.3912_0.483_0.5495.png
                gene_name: WDR62
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.39 
        ci_ks_bounds_left: 0.38 
       ci_ks_bounds_right: 0.40 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.55 
     ci_joint_bounds_left: 0.54 
    ci_joint_bounds_right: 0.56 

Current progress: 25 percent done.
WDFY3
Processing conservation and coverage...
91% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.518912e-02	ci left: 8.627401e-01	ci right 8.760439e-01	k: 8695	n:10000
Cons ci ratio: 1.957624e-02	ci left: 7.924290e-01	ci right 8.081956e-01	k: 8004	n:10000
KS ci ratio: 2.001624e-02	ci left: 7.851271e-01	ci right 8.011018e-01	k: 7932	n:10000
WDFY3   10000 perm   3 sec   (3764 perm/sec)   p_kst 7.932000e-01   p_cons 8.004000e-01   p_joint 8.695000e-01

Outputting figure to mutsig2_images.part000000000190/WDFY3.2_10884_10000_0.7932_0.8004_0.8695.png
                gene_name: WDFY3
               theta_stop: 0.020 
                    nperm: 10000 
                     p_ks: 0.79 
        ci_ks_bounds_left: 0.79 
       ci_ks_bounds_right: 0.80 
                   p_cons: 0.80 
      ci_cons_bounds_left: 0.79 
     ci_cons_bounds_right: 0.81 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.88 

Current progress: 50 percent done.
WDHD1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.285505e-02	ci left: 2.162545e-01	ci right 2.327063e-01	k: 2244	n:10000
Cons ci ratio: 2.389735e-01	ci left: 2.306380e-02	ci right 2.941625e-02	k: 261	n:10000
KS ci ratio: 2.990320e-02	ci left: 6.225610e-01	ci right 6.415620e-01	k: 6321	n:10000
WDHD1   10000 perm   2 sec   (5912 perm/sec)   p_kst 6.321000e-01   p_cons 2.610000e-02   p_joint 2.244000e-01

Joint ci ratio: 7.086189e-02	ci left: 1.279777e-01	ci right 1.374294e-01	k: 2653	n:20000
Cons ci ratio: 1.716948e-01	ci left: 2.321577e-02	ci right 2.762368e-02	k: 507	n:20000
KS ci ratio: 2.113665e-02	ci left: 6.255736e-01	ci right 6.389879e-01	k: 12646	n:20000
WDHD1   20000 perm   4 sec   (5247 perm/sec)   p_kst 6.323000e-01   p_cons 2.535000e-02   p_joint 1.326500e-01

Joint ci ratio: 5.611593e-02	ci left: 1.359601e-01	ci right 1.438431e-01	k: 4196	n:30000
Cons ci ratio: 1.420166e-01	ci left: 2.300533e-02	ci right 2.655419e-02	k: 742	n:30000
KS ci ratio: 1.731274e-02	ci left: 6.253434e-01	ci right 6.362979e-01	k: 18925	n:30000
WDHD1   30000 perm   6 sec   (4992 perm/sec)   p_kst 6.308333e-01   p_cons 2.473333e-02   p_joint 1.398667e-01

Joint ci ratio: 5.073180e-02	ci left: 1.265704e-01	ci right 1.331835e-01	k: 5194	n:40000
Cons ci ratio: 1.230329e-01	ci left: 2.322530e-02	ci right 2.629422e-02	k: 989	n:40000
KS ci ratio: 1.505246e-02	ci left: 6.242442e-01	ci right 6.337370e-01	k: 25160	n:40000
WDHD1   40000 perm   8 sec   (4823 perm/sec)   p_kst 6.290000e-01   p_cons 2.472500e-02   p_joint 1.298500e-01

Joint ci ratio: 4.520712e-02	ci left: 1.277570e-01	ci right 1.336860e-01	k: 6535	n:50000
Cons ci ratio: 1.097491e-01	ci left: 2.351291e-02	ci right 2.626263e-02	k: 1243	n:50000
KS ci ratio: 1.350900e-02	ci left: 6.231648e-01	ci right 6.316604e-01	k: 31371	n:50000
WDHD1   50000 perm   11 sec   (4689 perm/sec)   p_kst 6.274200e-01   p_cons 2.486000e-02   p_joint 1.307000e-01

Joint ci ratio: 4.500491e-02	ci left: 1.097181e-01	ci right 1.147861e-01	k: 6734	n:60000
Cons ci ratio: 1.000769e-01	ci left: 2.368415e-02	ci right 2.619543e-02	k: 1495	n:60000
KS ci ratio: 1.229916e-02	ci left: 6.247862e-01	ci right 6.325347e-01	k: 37720	n:60000
WDHD1   60000 perm   13 sec   (4572 perm/sec)   p_kst 6.286667e-01   p_cons 2.491667e-02   p_joint 1.122333e-01

Joint ci ratio: 4.166798e-02	ci left: 1.098992e-01	ci right 1.145901e-01	k: 7856	n:70000
Cons ci ratio: 9.228346e-02	ci left: 2.396772e-02	ci right 2.630044e-02	k: 1758	n:70000
KS ci ratio: 1.137766e-02	ci left: 6.254519e-01	ci right 6.326231e-01	k: 44033	n:70000
WDHD1   70000 perm   16 sec   (4469 perm/sec)   p_kst 6.290429e-01   p_cons 2.511429e-02   p_joint 1.122286e-01

Outputting figure to mutsig2_images.part000000000190/WDHD1.2_3490_70000_0.62904_0.025114_0.11223.png
                gene_name: WDHD1
               theta_stop: 0.092 
                    nperm: 70000 
                     p_ks: 0.63 
        ci_ks_bounds_left: 0.63 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.025 
      ci_cons_bounds_left: 0.024 
     ci_cons_bounds_right: 0.026 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.11 

Current progress: 75 percent done.
WDR49
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.048516e-02	ci left: 9.282324e-01	ci right 9.381134e-01	k: 9333	n:10000
Cons ci ratio: 5.028518e-02	ci left: 3.683836e-01	ci right 3.874876e-01	k: 3779	n:10000
KS ci ratio: 5.043521e-02	ci left: 3.669909e-01	ci right 3.860810e-01	k: 3765	n:10000
WDR49   10000 perm   2 sec   (6365 perm/sec)   p_kst 3.765000e-01   p_cons 3.779000e-01   p_joint 9.333000e-01

Outputting figure to mutsig2_images.part000000000190/WDR49.2_2150_10000_0.3765_0.3779_0.9333.png
                gene_name: WDR49
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.38 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.39 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  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.165.3896/
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/181708/iteration1/scatter.0000000190
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 190 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120354: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000191> was used as the working directory.
Started at Wed Oct 10 10:45:53 2012
Results reported at Wed Oct 10 10:48:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000191.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000191.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 191  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    173.04 sec.
    Max Memory :      1381 MB
    Max Swap   :      3902 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.165.3896/
-whichjob
191
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 191: processing genes 17190 - 17280
Calculating significance of each gene.
Using projection method.
17190	WFDC1	1
17191	WFDC10A	1
17192	WFDC10B	1
17193	WFDC11	1
17194	WFDC12	1
17195	WFDC13	1
17196	WFDC2	1
17197	WFDC3	1
17198	WFDC5	1
17199	WFDC6	1
17200	WFDC8	1
17201	WFDC9	1
17202	WFIKKN1	1
17203	WFIKKN2	1
17204	WFS1	9.571109e-02
17205	WHAMM	1
17206	WHSC1	1.494134e-01
17207	WHSC1L1	1
17208	WHSC2	1
17209	WIBG	1
17210	WIF1	4.352810e-02
17211	WIPF1	1
17212	WIPF2	1
17213	WIPF3	1
17214	WIPI1	1
17215	WIPI2	1
17216	WISP1	1
17217	WISP2	1
17218	WISP3	1
17219	WIZ	1.446540e-01
17220	WLS	1
17221	WNK1	4.097181e-01
17222	WNK2	1
17223	WNK3	2.948250e-01
17224	WNK4	1
17225	WNT1	1
17226	WNT10A	1
17227	WNT10B	1
17228	WNT11	1
17229	WNT16	1
17230	WNT2	1
17231	WNT2B	1
17232	WNT3	1
17233	WNT3A	1
17234	WNT4	1
17235	WNT5A	9.829160e-02
17236	WNT5B	1
17237	WNT6	1
17238	WNT7A	1
17239	WNT7B	1
17240	WNT8A	1
17241	WNT8B	1
17242	WNT9A	1
17243	WNT9B	1
17244	WRAP53	1
17245	WRB	1
17246	WRN	1
17247	WRNIP1	1
17248	WSB1	1
17249	WSB2	1
17250	WSCD1	1
17251	WSCD2	1
17252	WT1	1
17253	WTAP	4.890685e-02
17254	WTIP	1
17255	WWC1	1
17256	WWC2	1.230623e-02
17257	WWC3	1
17258	WWOX	1
17259	WWP1	1.169000e-01
17260	WWP2	1.734187e-01
17261	WWTR1	1
17262	XAB2	3.347958e-01
17263	XAF1	1
17264	XAGE3	1
17265	XAGE5	1
17266	XBP1	1
17267	XCL1	1
17268	XCL2	1
17269	XCR1	1
17270	XDH	1
17271	XG	1
17272	XIAP	1
17273	XIRP1	1
17274	XIRP2	1
17275	XK	1
17276	XKR3	1
17277	XKR4	1
17278	XKR5	1
17279	XKR6	1
17280	XKR7	1
Done

Running MutSig 2:
Scatter job 191: processing genes 17190 - 17280
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
XIRP2
Processing conservation and coverage...
81% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.537586e-02	ci left: 8.598813e-01	ci right 8.733044e-01	k: 8667	n:10000
Cons ci ratio: 3.062084e-02	ci left: 6.114073e-01	ci right 6.305221e-01	k: 6210	n:10000
KS ci ratio: 2.726672e-02	ci left: 6.646124e-01	ci right 6.830863e-01	k: 6739	n:10000
XIRP2   10000 perm   3 sec   (3287 perm/sec)   p_kst 6.739000e-01   p_cons 6.210000e-01   p_joint 8.667000e-01

Outputting figure to mutsig2_images.part000000000191/XIRP2.5_12236_10000_0.6739_0.621_0.8667.png
                gene_name: XIRP2
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.68 
                   p_cons: 0.62 
      ci_cons_bounds_left: 0.61 
     ci_cons_bounds_right: 0.63 
                  p_joint: 0.87 
     ci_joint_bounds_left: 0.86 
    ci_joint_bounds_right: 0.87 

Current progress: 25 percent done.
WWC2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.324445e-02	ci left: 5.718590e-01	ci right 5.912935e-01	k: 5816	n:10000
Cons ci ratio: 7.731236e-02	ci left: 1.965332e-01	ci right 2.124394e-01	k: 2044	n:10000
KS ci ratio: 2.983895e-02	ci left: 6.235661e-01	ci right 6.425563e-01	k: 6331	n:10000
WWC2   10000 perm   2 sec   (5240 perm/sec)   p_kst 6.331000e-01   p_cons 2.044000e-01   p_joint 5.816000e-01

Outputting figure to mutsig2_images.part000000000191/WWC2.3_3671_10000_0.6331_0.2044_0.5816.png
                gene_name: WWC2
               theta_stop: 0.077 
                    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: 0.20 
     ci_cons_bounds_right: 0.21 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 50 percent done.
WHSC1
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: 6.960300e-02	ci left: 2.323474e-01	ci right 2.492038e-01	k: 2407	n:10000
KS ci ratio: 9.644065e-03	ci left: 9.382754e-01	ci right 9.474645e-01	k: 9430	n:10000
WHSC1   10000 perm   2 sec   (5192 perm/sec)   p_kst 9.430000e-01   p_cons 2.407000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000191/WHSC1.2_4258_10000_0.943_0.2407_1.png
                gene_name: WHSC1
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.94 
        ci_ks_bounds_left: 0.94 
       ci_ks_bounds_right: 0.95 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.25 
                  p_joint: 1 
     ci_joint_bounds_left: 1.00 
    ci_joint_bounds_right: 1 

Current progress: 75 percent done.
WNK1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.690855e-02	ci left: 4.014334e-01	ci right 4.208184e-01	k: 4111	n:10000
Cons ci ratio: 4.922212e-02	ci left: 3.784330e-01	ci right 3.976323e-01	k: 3880	n:10000
KS ci ratio: 3.842359e-01	ci left: 8.324320e-03	ci right 1.236857e-02	k: 102	n:10000
WNK1   10000 perm   2 sec   (4075 perm/sec)   p_kst 1.020000e-02   p_cons 3.880000e-01   p_joint 4.111000e-01

Joint ci ratio: 1.959804e-04	ci left: 9.998156e-01	ci right 1	k: 20000	n:20000
Cons ci ratio: 3.548131e-02	ci left: 3.722196e-01	ci right 3.857156e-01	k: 7579	n:20000
KS ci ratio: 2.684301e-01	ci left: 9.133859e-03	ci right 1.201110e-02	k: 210	n:20000
WNK1   20000 perm   5 sec   (3744 perm/sec)   p_kst 1.050000e-02   p_cons 3.789500e-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: 2.902167e-02	ci left: 3.726414e-01	ci right 3.836489e-01	k: 11344	n:30000
KS ci ratio: 2.207657e-01	ci left: 9.251451e-03	ci right 1.157816e-02	k: 311	n:30000
WNK1   30000 perm   8 sec   (3626 perm/sec)   p_kst 1.036667e-02   p_cons 3.781333e-01   p_joint 1

Joint ci ratio: 1.102704e-01	ci left: 2.893381e-02	ci right 3.233478e-02	k: 1224	n:40000
Cons ci ratio: 2.526850e-02	ci left: 3.708758e-01	ci right 3.803923e-01	k: 15025	n:40000
KS ci ratio: 1.900387e-01	ci left: 9.524262e-03	ci right 1.154774e-02	k: 420	n:40000
WNK1   40000 perm   11 sec   (3545 perm/sec)   p_kst 1.050000e-02   p_cons 3.756250e-01   p_joint 3.060000e-02

Joint ci ratio: 9.941030e-02	ci left: 2.865872e-02	ci right 3.167616e-02	k: 1507	n:50000
Cons ci ratio: 2.187049e-02	ci left: 3.868789e-01	ci right 3.954537e-01	k: 19558	n:50000
KS ci ratio: 1.726913e-01	ci left: 9.318665e-03	ci right 1.109889e-02	k: 509	n:50000
WNK1   50000 perm   14 sec   (3475 perm/sec)   p_kst 1.018000e-02   p_cons 3.911600e-01   p_joint 3.014000e-02

Joint ci ratio: 1.108499e-01	ci left: 1.928378e-02	ci right 2.156294e-02	k: 1224	n:60000
Cons ci ratio: 1.999975e-02	ci left: 3.864270e-01	ci right 3.942502e-01	k: 23420	n:60000
KS ci ratio: 1.569985e-01	ci left: 9.475512e-03	ci right 1.110571e-02	k: 616	n:60000
WNK1   60000 perm   18 sec   (3420 perm/sec)   p_kst 1.026667e-02   p_cons 3.903333e-01   p_joint 2.040000e-02

Joint ci ratio: 1.020155e-01	ci left: 1.960231e-02	ci right 2.172340e-02	k: 1445	n:70000
Cons ci ratio: 1.850811e-02	ci left: 3.869262e-01	ci right 3.941686e-01	k: 27338	n:70000
KS ci ratio: 1.428504e-01	ci left: 9.882112e-03	ci right 1.141600e-02	k: 744	n:70000
WNK1   70000 perm   21 sec   (3337 perm/sec)   p_kst 1.062857e-02   p_cons 3.905429e-01   p_joint 2.064286e-02

Joint ci ratio: 9.485907e-02	ci left: 1.990768e-02	ci right 2.190228e-02	k: 1671	n:80000
Cons ci ratio: 1.730392e-02	ci left: 3.874042e-01	ci right 3.941788e-01	k: 31263	n:80000
KS ci ratio: 1.327159e-01	ci left: 1.007112e-02	ci right 1.151469e-02	k: 862	n:80000
WNK1   80000 perm   25 sec   (3263 perm/sec)   p_kst 1.077500e-02   p_cons 3.907875e-01   p_joint 2.088750e-02

Joint ci ratio: 8.916812e-02	ci left: 2.008402e-02	ci right 2.196925e-02	k: 1891	n:90000
Cons ci ratio: 1.631657e-02	ci left: 3.875326e-01	ci right 3.939189e-01	k: 35165	n:90000
KS ci ratio: 1.250526e-01	ci left: 1.012421e-02	ci right 1.148538e-02	k: 971	n:90000
WNK1   90000 perm   28 sec   (3203 perm/sec)   p_kst 1.078889e-02   p_cons 3.907222e-01   p_joint 2.101111e-02

Joint ci ratio: 1.181936e-01	ci left: 1.023655e-02	ci right 1.153206e-02	k: 1087	n:100000
Cons ci ratio: 1.548359e-02	ci left: 3.875643e-01	ci right 3.936220e-01	k: 39059	n:100000
KS ci ratio: 1.181936e-01	ci left: 1.023655e-02	ci right 1.153206e-02	k: 1087	n:100000
WNK1   100000 perm   32 sec   (3135 perm/sec)   p_kst 1.087000e-02   p_cons 3.905900e-01   p_joint 1.087000e-02

Joint ci ratio: 1.129703e-01	ci left: 1.021524e-02	ci right 1.144712e-02	k: 1190	n:110000
Cons ci ratio: 1.476387e-02	ci left: 3.876789e-01	ci right 3.934542e-01	k: 42962	n:110000
KS ci ratio: 1.129703e-01	ci left: 1.021524e-02	ci right 1.144712e-02	k: 1190	n:110000
WNK1   110000 perm   35 sec   (3103 perm/sec)   p_kst 1.081818e-02   p_cons 3.905636e-01   p_joint 1.081818e-02

Joint ci ratio: 1.083834e-01	ci left: 1.019854e-02	ci right 1.137528e-02	k: 1293	n:120000
Cons ci ratio: 1.412661e-02	ci left: 3.880961e-01	ci right 3.936259e-01	k: 46903	n:120000
KS ci ratio: 1.083834e-01	ci left: 1.019854e-02	ci right 1.137528e-02	k: 1293	n:120000
WNK1   120000 perm   39 sec   (3073 perm/sec)   p_kst 1.077500e-02   p_cons 3.908583e-01   p_joint 1.077500e-02

Joint ci ratio: 1.045026e-01	ci left: 1.014780e-02	ci right 1.127418e-02	k: 1391	n:130000
Cons ci ratio: 1.356028e-02	ci left: 3.886303e-01	ci right 3.939438e-01	k: 50867	n:130000
KS ci ratio: 1.045026e-01	ci left: 1.014780e-02	ci right 1.127418e-02	k: 1391	n:130000
WNK1   130000 perm   43 sec   (3043 perm/sec)   p_kst 1.070000e-02   p_cons 3.912846e-01   p_joint 1.070000e-02

Joint ci ratio: 1.002318e-01	ci left: 1.026515e-02	ci right 1.135525e-02	k: 1512	n:140000
Cons ci ratio: 1.349053e-02	ci left: 3.736615e-01	ci right 3.787437e-01	k: 52668	n:140000
KS ci ratio: 1.002318e-01	ci left: 1.026515e-02	ci right 1.135525e-02	k: 1512	n:140000
WNK1   140000 perm   46 sec   (3014 perm/sec)   p_kst 1.080000e-02   p_cons 3.762000e-01   p_joint 1.080000e-02

Joint ci ratio: 9.644510e-02	ci left: 1.036767e-02	ci right 1.142470e-02	k: 1633	n:150000
Cons ci ratio: 1.304830e-02	ci left: 3.732016e-01	ci right 3.781099e-01	k: 56348	n:150000
KS ci ratio: 9.644510e-02	ci left: 1.036767e-02	ci right 1.142470e-02	k: 1633	n:150000
WNK1   150000 perm   50 sec   (2984 perm/sec)   p_kst 1.088667e-02   p_cons 3.756533e-01   p_joint 1.088667e-02

Outputting figure to mutsig2_images.part000000000191/WNK1.2_8763_150000_0.010887_0.37565_0.010887.png
                gene_name: WNK1
               theta_stop: 0.096 
                    nperm: 150000 
                     p_ks: 0.011 
        ci_ks_bounds_left: 0.010 
       ci_ks_bounds_right: 0.011 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.011 
     ci_joint_bounds_left: 0.010 
    ci_joint_bounds_right: 0.011 

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.165.3896/
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/181708/iteration1/scatter.0000000191
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 191 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120357: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000192> was used as the working directory.
Started at Wed Oct 10 10:45:53 2012
Results reported at Wed Oct 10 10:47:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000192.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000192.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 192  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    131.03 sec.
    Max Memory :       911 MB
    Max Swap   :      3745 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.165.3896/
-whichjob
192
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 192: processing genes 17281 - 17370
Calculating significance of each gene.
Using projection method.
17281	XKR8	1
17282	XKR9	1
17283	XKRX	1
17284	XPA	1
17285	XPC	1.346203e-01
17286	XPNPEP1	1
17287	XPNPEP2	1
17288	XPNPEP3	1.975204e-01
17289	XPO1	4.029589e-01
17290	XPO4	1
17291	XPO5	1.359350e-01
17292	XPO6	1
17293	XPO7	2.856242e-01
17294	XPOT	1.997589e-01
17295	XPR1	3.080514e-04
17296	XRCC1	8.692786e-02
17297	XRCC2	1
17298	XRCC3	1
17299	XRCC4	1
17300	XRCC5	1
17301	XRCC6	1
17302	XRCC6BP1	1
17303	XRN1	1
17304	XRN2	1
17305	XRRA1	1
17306	XYLB	1
17307	XYLT1	2.748966e-01
17308	XYLT2	1
17309	YAF2	1
17310	YAP1	1.237916e-01
17311	YARS	1.448446e-01
17312	YARS2	1
17313	YBX1	1
17314	YBX2	1
17315	YDJC	1
17316	YEATS2	1
17317	YEATS4	1
17318	YES1	1
17319	YIF1A	1
17320	YIF1B	1
17321	YIPF1	5.830876e-02
17322	YIPF2	1
17323	YIPF3	1
17324	YIPF4	1
17325	YIPF5	1
17326	YIPF6	1.868898e-02
17327	YIPF7	1
17328	YJEFN3	1
17329	YKT6	1
17330	YLPM1	1
17331	YME1L1	1
17332	YOD1	1
17333	YPEL1	1
17334	YPEL2	1
17335	YPEL3	1
17336	YPEL4	1
17337	YPEL5	1
17338	YRDC	1
17339	YSK4	1
17340	YTHDC1	1
17341	YTHDC2	1
17342	YTHDF1	1
17343	YTHDF2	2.512256e-01
17344	YTHDF3	1
17345	YWHAB	3.872058e-02
17346	YWHAE	1
17347	YWHAG	1
17348	YWHAH	1
17349	YWHAQ	1
17350	YWHAZ	1
17351	YY1	1
17352	YY1AP1	2.771246e-01
17353	YY2	1
17354	ZACN	1
17355	ZADH2	1
17356	ZAK	1
17357	ZAN	1
17358	ZAP70	1
17359	ZAR1	1
17360	ZBBX	1
17361	ZBED1	1
17362	ZBED2	1
17363	ZBED4	1
17364	ZBP1	1.659405e-01
17365	ZBTB1	1
17366	ZBTB10	1
17367	ZBTB11	1.623465e-01
17368	ZBTB12	1
17369	ZBTB16	1
17370	ZBTB17	1
Done

Running MutSig 2:
Scatter job 192: processing genes 17281 - 17370
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
XPR1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.130420e-02	ci left: 4.639725e-01	ci right 4.836428e-01	k: 4738	n:10000
Cons ci ratio: 4.511523e-02	ci left: 4.203680e-01	ci right 4.398728e-01	k: 4301	n:10000
KS ci ratio: 6.211914e-02	ci left: 2.758690e-01	ci right 2.936566e-01	k: 2847	n:10000
XPR1   10000 perm   2 sec   (4502 perm/sec)   p_kst 2.847000e-01   p_cons 4.301000e-01   p_joint 4.738000e-01

Outputting figure to mutsig2_images.part000000000192/XPR1.5_2151_10000_0.2847_0.4301_0.4738.png
                gene_name: XPR1
               theta_stop: 0.062 
                    nperm: 10000 
                     p_ks: 0.28 
        ci_ks_bounds_left: 0.28 
       ci_ks_bounds_right: 0.29 
                   p_cons: 0.43 
      ci_cons_bounds_left: 0.42 
     ci_cons_bounds_right: 0.44 
                  p_joint: 0.47 
     ci_joint_bounds_left: 0.46 
    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.165.3896/
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/181708/iteration1/scatter.0000000192
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 192 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120360: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000193> was used as the working directory.
Started at Wed Oct 10 10:45:53 2012
Results reported at Wed Oct 10 10:49:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000193.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000193.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 193  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    210.61 sec.
    Max Memory :      1321 MB
    Max Swap   :      3915 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.165.3896/
-whichjob
193
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 193: processing genes 17371 - 17461
Calculating significance of each gene.
Using projection method.
17371	ZBTB2	1
17372	ZBTB20	1
17373	ZBTB22	1
17374	ZBTB24	1
17375	ZBTB25	1
17376	ZBTB26	1
17377	ZBTB3	1
17378	ZBTB32	9.706694e-02
17379	ZBTB33	1
17380	ZBTB34	1
17381	ZBTB37	1.443939e-03
17382	ZBTB38	1
17383	ZBTB39	1
17384	ZBTB4	1
17385	ZBTB40	2.056854e-01
17386	ZBTB41	1
17387	ZBTB43	1
17388	ZBTB44	1
17389	ZBTB45	1.632294e-01
17390	ZBTB46	1
17391	ZBTB47	1
17392	ZBTB48	2.979614e-01
17393	ZBTB49	9.373852e-02
17394	ZBTB5	1
17395	ZBTB6	1
17396	ZBTB7A	1
17397	ZBTB7B	1
17398	ZBTB7C	1
17399	ZBTB8A	1
17400	ZBTB8OS	1
17401	ZBTB9	1
17402	ZC3H10	1
17403	ZC3H11A	1
17404	ZC3H12A	1
17405	ZC3H12B	1.205683e-01
17406	ZC3H12C	2.000347e-01
17407	ZC3H12D	1
17408	ZC3H13	5.630673e-01
17409	ZC3H14	1
17410	ZC3H15	1
17411	ZC3H18	1
17412	ZC3H3	1
17413	ZC3H4	1
17414	ZC3H6	1
17415	ZC3H7A	3.286693e-01
17416	ZC3H7B	1
17417	ZC3H8	1
17418	ZC3HAV1	1
17419	ZC3HAV1L	1
17420	ZC3HC1	2.382255e-01
17421	ZC4H2	9.463546e-02
17422	ZCCHC10	1
17423	ZCCHC11	2.072473e-01
17424	ZCCHC12	1
17425	ZCCHC13	1
17426	ZCCHC14	3.597218e-01
17427	ZCCHC16	1
17428	ZCCHC17	1
17429	ZCCHC18	1
17430	ZCCHC2	1
17431	ZCCHC24	1
17432	ZCCHC3	1
17433	ZCCHC4	1
17434	ZCCHC5	1
17435	ZCCHC6	3.425249e-01
17436	ZCCHC7	1.957666e-01
17437	ZCCHC8	8.076570e-02
17438	ZCCHC9	1
17439	ZCRB1	1
17440	ZCWPW1	1
17441	ZCWPW2	1
17442	ZDBF2	4.672743e-01
17443	ZDHHC1	1.623295e-01
17444	ZDHHC11	1
17445	ZDHHC12	1
17446	ZDHHC13	1
17447	ZDHHC14	1
17448	ZDHHC15	1
17449	ZDHHC16	1
17450	ZDHHC17	1
17451	ZDHHC18	1
17452	ZDHHC19	1
17453	ZDHHC2	1
17454	ZDHHC20	1
17455	ZDHHC21	1
17456	ZDHHC22	4.405235e-02
17457	ZDHHC23	1
17458	ZDHHC24	1
17459	ZDHHC3	1
17460	ZDHHC4	1
17461	ZDHHC5	1
Done

Running MutSig 2:
Scatter job 193: processing genes 17371 - 17461
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZBTB37
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.088296e-02	ci left: 2.258292e-01	ci right 2.425259e-01	k: 2341	n:10000
Cons ci ratio: 5.651887e-02	ci left: 3.155244e-01	ci right 3.339778e-01	k: 3247	n:10000
KS ci ratio: 8.167954e-02	ci left: 1.794983e-01	ci right 1.948844e-01	k: 1871	n:10000
ZBTB37   10000 perm   2 sec   (5957 perm/sec)   p_kst 1.871000e-01   p_cons 3.247000e-01   p_joint 2.341000e-01

Outputting figure to mutsig2_images.part000000000193/ZBTB37.3_1587_10000_0.1871_0.3247_0.2341.png
                gene_name: ZBTB37
               theta_stop: 0.082 
                    nperm: 10000 
                     p_ks: 0.19 
        ci_ks_bounds_left: 0.18 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.32 
      ci_cons_bounds_left: 0.32 
     ci_cons_bounds_right: 0.33 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.24 

Current progress: 25 percent done.
ZCCHC11
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.607453e-01	ci left: 1.921493e-02	ci right 2.506805e-02	k: 220	n:10000
Cons ci ratio: 2.489961e-02	ci left: 7.035183e-01	ci right 7.213578e-01	k: 7125	n:10000
KS ci ratio: 4.846095e-01	ci left: 4.932166e-03	ci right 8.165407e-03	k: 64	n:10000
ZCCHC11   10000 perm   2 sec   (4982 perm/sec)   p_kst 6.400000e-03   p_cons 7.125000e-01   p_joint 2.200000e-02

Joint ci ratio: 2.652715e-01	ci left: 9.367279e-03	ci right 1.227757e-02	k: 215	n:20000
Cons ci ratio: 1.774898e-02	ci left: 7.028511e-01	ci right 7.154881e-01	k: 14184	n:20000
KS ci ratio: 3.567614e-01	ci left: 4.931479e-03	ci right 7.115892e-03	k: 119	n:20000
ZCCHC11   20000 perm   4 sec   (4487 perm/sec)   p_kst 5.950000e-03   p_cons 7.092000e-01   p_joint 1.075000e-02

Joint ci ratio: 1.892454e-01	ci left: 1.276459e-02	ci right 1.546404e-02	k: 422	n:30000
Cons ci ratio: 1.443005e-02	ci left: 7.058001e-01	ci right 7.160923e-01	k: 21329	n:30000
KS ci ratio: 3.006830e-01	ci left: 4.787072e-03	ci right 6.510790e-03	k: 168	n:30000
ZCCHC11   30000 perm   7 sec   (4308 perm/sec)   p_kst 5.600000e-03   p_cons 7.109667e-01   p_joint 1.406667e-02

Joint ci ratio: 2.250905e-01	ci left: 6.677907e-03	ci right 8.394749e-03	k: 300	n:40000
Cons ci ratio: 1.243656e-02	ci left: 7.084889e-01	ci right 7.173802e-01	k: 28518	n:40000
KS ci ratio: 2.600136e-01	ci left: 4.915659e-03	ci right 6.407485e-03	k: 225	n:40000
ZCCHC11   40000 perm   10 sec   (4169 perm/sec)   p_kst 5.625000e-03   p_cons 7.129500e-01   p_joint 7.500000e-03

Joint ci ratio: 2.336056e-01	ci left: 4.945911e-03	ci right 6.272480e-03	k: 279	n:50000
Cons ci ratio: 1.108151e-02	ci left: 7.105188e-01	ci right 7.184563e-01	k: 35725	n:50000
KS ci ratio: 2.370352e-01	ci left: 4.795300e-03	ci right 6.103127e-03	k: 271	n:50000
ZCCHC11   50000 perm   12 sec   (4064 perm/sec)   p_kst 5.420000e-03   p_cons 7.145000e-01   p_joint 5.580000e-03

Joint ci ratio: 1.549807e-01	ci left: 9.731866e-03	ci right 1.138266e-02	k: 632	n:60000
Cons ci ratio: 1.011807e-02	ci left: 7.107838e-01	ci right 7.180288e-01	k: 42865	n:60000
KS ci ratio: 2.004523e-01	ci left: 5.698378e-03	ci right 6.983408e-03	k: 379	n:60000
ZCCHC11   60000 perm   15 sec   (3982 perm/sec)   p_kst 6.316667e-03   p_cons 7.144167e-01   p_joint 1.053333e-02

Joint ci ratio: 1.536360e-01	ci left: 8.505988e-03	ci right 9.935138e-03	k: 644	n:70000
Cons ci ratio: 9.360366e-03	ci left: 7.113676e-01	ci right 7.180718e-01	k: 50031	n:70000
KS ci ratio: 1.858645e-01	ci left: 5.727263e-03	ci right 6.914219e-03	k: 441	n:70000
ZCCHC11   70000 perm   18 sec   (3898 perm/sec)   p_kst 6.300000e-03   p_cons 7.147286e-01   p_joint 9.200000e-03

Joint ci ratio: 1.283515e-01	ci left: 1.078479e-02	ci right 1.227595e-02	k: 921	n:80000
Cons ci ratio: 8.747853e-03	ci left: 7.119582e-01	ci right 7.182262e-01	k: 57208	n:80000
KS ci ratio: 1.731962e-01	ci left: 5.811277e-03	ci right 6.924976e-03	k: 508	n:80000
ZCCHC11   80000 perm   21 sec   (3834 perm/sec)   p_kst 6.350000e-03   p_cons 7.151000e-01   p_joint 1.151250e-02

Joint ci ratio: 1.075138e-01	ci left: 1.377241e-02	ci right 1.534800e-02	k: 1309	n:90000
Cons ci ratio: 8.254308e-03	ci left: 7.118043e-01	ci right 7.177152e-01	k: 64329	n:90000
KS ci ratio: 1.635248e-01	ci left: 5.825462e-03	ci right 6.873405e-03	k: 570	n:90000
ZCCHC11   90000 perm   24 sec   (3774 perm/sec)   p_kst 6.333333e-03   p_cons 7.147667e-01   p_joint 1.454444e-02

Joint ci ratio: 1.056489e-01	ci left: 1.286205e-02	ci right 1.430637e-02	k: 1357	n:100000
Cons ci ratio: 7.828551e-03	ci left: 7.120706e-01	ci right 7.176769e-01	k: 71488	n:100000
KS ci ratio: 1.540911e-01	ci left: 5.934346e-03	ci right 6.934606e-03	k: 642	n:100000
ZCCHC11   100000 perm   27 sec   (3719 perm/sec)   p_kst 6.420000e-03   p_cons 7.148800e-01   p_joint 1.357000e-02

Joint ci ratio: 1.033519e-01	ci left: 1.224147e-02	ci right 1.358439e-02	k: 1419	n:110000
Cons ci ratio: 7.463035e-03	ci left: 7.122675e-01	ci right 7.176121e-01	k: 78644	n:110000
KS ci ratio: 1.459165e-01	ci left: 6.042375e-03	ci right 7.002104e-03	k: 716	n:110000
ZCCHC11   110000 perm   30 sec   (3665 perm/sec)   p_kst 6.509091e-03   p_cons 7.149455e-01   p_joint 1.290000e-02

Joint ci ratio: 1.081724e-01	ci left: 1.023909e-02	ci right 1.141806e-02	k: 1298	n:120000
Cons ci ratio: 7.141437e-03	ci left: 7.126037e-01	ci right 7.177192e-01	k: 85820	n:120000
KS ci ratio: 1.379561e-01	ci left: 6.222076e-03	ci right 7.152005e-03	k: 801	n:120000
ZCCHC11   120000 perm   33 sec   (3612 perm/sec)   p_kst 6.675000e-03   p_cons 7.151667e-01   p_joint 1.081667e-02

Joint ci ratio: 9.776656e-02	ci left: 1.161781e-02	ci right 1.281948e-02	k: 1587	n:130000
Cons ci ratio: 6.865246e-03	ci left: 7.124681e-01	ci right 7.173839e-01	k: 92941	n:130000
KS ci ratio: 1.316947e-01	ci left: 6.323245e-03	ci right 7.222045e-03	k: 879	n:130000
ZCCHC11   130000 perm   36 sec   (3563 perm/sec)   p_kst 6.761538e-03   p_cons 7.149308e-01   p_joint 1.220769e-02

Joint ci ratio: 9.869361e-02	ci left: 1.059260e-02	ci right 1.169921e-02	k: 1559	n:140000
Cons ci ratio: 6.808425e-03	ci left: 7.006703e-01	ci right 7.054641e-01	k: 98430	n:140000
KS ci ratio: 1.261487e-01	ci left: 6.417696e-03	ci right 7.288632e-03	k: 958	n:140000
ZCCHC11   140000 perm   40 sec   (3511 perm/sec)   p_kst 6.842857e-03   p_cons 7.030714e-01   p_joint 1.113571e-02

Joint ci ratio: 9.588308e-02	ci left: 1.049132e-02	ci right 1.155438e-02	k: 1652	n:150000
Cons ci ratio: 6.402449e-03	ci left: 7.119196e-01	ci right 7.164988e-01	k: 107132	n:150000
KS ci ratio: 1.216034e-01	ci left: 6.461446e-03	ci right 7.304451e-03	k: 1031	n:150000
ZCCHC11   150000 perm   43 sec   (3457 perm/sec)   p_kst 6.873333e-03   p_cons 7.142133e-01   p_joint 1.101333e-02

Joint ci ratio: 9.028905e-02	ci left: 1.111773e-02	ci right 1.217507e-02	k: 1862	n:160000
Cons ci ratio: 6.194983e-03	ci left: 7.122674e-01	ci right 7.166998e-01	k: 114318	n:160000
KS ci ratio: 1.182733e-01	ci left: 6.415284e-03	ci right 7.227742e-03	k: 1090	n:160000
ZCCHC11   160000 perm   47 sec   (3402 perm/sec)   p_kst 6.812500e-03   p_cons 7.144875e-01   p_joint 1.163750e-02

Joint ci ratio: 8.145227e-02	ci left: 1.289338e-02	ci right 1.399389e-02	k: 2284	n:170000
Cons ci ratio: 6.012259e-03	ci left: 7.121814e-01	ci right 7.164819e-01	k: 121437	n:170000
KS ci ratio: 1.149512e-01	ci left: 6.403402e-03	ci right 7.190030e-03	k: 1154	n:170000
ZCCHC11   170000 perm   51 sec   (3344 perm/sec)   p_kst 6.788235e-03   p_cons 7.143353e-01   p_joint 1.343529e-02

Joint ci ratio: 7.519812e-02	ci left: 1.431264e-02	ci right 1.543639e-02	k: 2676	n:180000
Cons ci ratio: 5.840906e-03	ci left: 7.123795e-01	ci right 7.165581e-01	k: 128605	n:180000
KS ci ratio: 1.113437e-01	ci left: 6.457941e-03	ci right 7.224738e-03	k: 1230	n:180000
ZCCHC11   180000 perm   54 sec   (3305 perm/sec)   p_kst 6.833333e-03   p_cons 7.144722e-01   p_joint 1.486667e-02

Joint ci ratio: 7.320198e-02	ci left: 1.432384e-02	ci right 1.541735e-02	k: 2824	n:190000
Cons ci ratio: 5.689135e-03	ci left: 7.121468e-01	ci right 7.162151e-01	k: 135695	n:190000
KS ci ratio: 1.078070e-01	ci left: 6.537816e-03	ci right 7.287874e-03	k: 1312	n:190000
ZCCHC11   190000 perm   58 sec   (3267 perm/sec)   p_kst 6.905263e-03   p_cons 7.141842e-01   p_joint 1.486316e-02

Joint ci ratio: 7.631654e-02	ci left: 1.252285e-02	ci right 1.352134e-02	k: 2603	n:200000
Cons ci ratio: 5.542967e-03	ci left: 7.123547e-01	ci right 7.163191e-01	k: 142868	n:200000
KS ci ratio: 1.055049e-01	ci left: 6.493181e-03	ci right 7.221223e-03	k: 1370	n:200000
ZCCHC11   200000 perm   62 sec   (3228 perm/sec)   p_kst 6.850000e-03   p_cons 7.143400e-01   p_joint 1.301500e-02

Joint ci ratio: 8.168453e-02	ci left: 1.040430e-02	ci right 1.129499e-02	k: 2277	n:210000
Cons ci ratio: 5.410229e-03	ci left: 7.123387e-01	ci right 7.162078e-01	k: 149998	n:210000
KS ci ratio: 1.026950e-01	ci left: 6.536472e-03	ci right 7.248670e-03	k: 1446	n:210000
ZCCHC11   210000 perm   66 sec   (3185 perm/sec)   p_kst 6.885714e-03   p_cons 7.142762e-01   p_joint 1.084286e-02

Joint ci ratio: 8.539926e-02	ci left: 9.081057e-03	ci right 9.895582e-03	k: 2086	n:220000
Cons ci ratio: 5.288121e-03	ci left: 7.122068e-01	ci right 7.159875e-01	k: 157102	n:220000
KS ci ratio: 1.003974e-01	ci left: 6.536170e-03	ci right 7.231463e-03	k: 1513	n:220000
ZCCHC11   220000 perm   70 sec   (3150 perm/sec)   p_kst 6.877273e-03   p_cons 7.141000e-01   p_joint 9.481818e-03

Joint ci ratio: 8.416441e-02	ci left: 8.950052e-03	ci right 9.740648e-03	k: 2148	n:230000
Cons ci ratio: 5.173262e-03	ci left: 7.121396e-01	ci right 7.158376e-01	k: 164218	n:230000
KS ci ratio: 9.837286e-02	ci left: 6.519090e-03	ci right 7.197775e-03	k: 1576	n:230000
ZCCHC11   230000 perm   74 sec   (3115 perm/sec)   p_kst 6.852174e-03   p_cons 7.139913e-01   p_joint 9.339130e-03

Outputting figure to mutsig2_images.part000000000193/ZCCHC11.3_5054_230000_0.0068522_0.71399_0.0093391.png
                gene_name: ZCCHC11
               theta_stop: 0.098 
                    nperm: 230000 
                     p_ks: 0.0069 
        ci_ks_bounds_left: 0.0065 
       ci_ks_bounds_right: 0.0072 
                   p_cons: 0.71 
      ci_cons_bounds_left: 0.71 
     ci_cons_bounds_right: 0.72 
                  p_joint: 0.0093 
     ci_joint_bounds_left: 0.0090 
    ci_joint_bounds_right: 0.0097 

Current progress: 50 percent done.
ZBTB40
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.168825e-01	ci left: 9.516088e-02	ci right 1.070726e-01	k: 1010	n:10000
Cons ci ratio: 3.528161e-02	ci left: 5.425901e-01	ci right 5.621794e-01	k: 5524	n:10000
KS ci ratio: 2.870972e-01	ci left: 1.567108e-02	ci right 2.101476e-02	k: 182	n:10000
ZBTB40   10000 perm   2 sec   (5436 perm/sec)   p_kst 1.820000e-02   p_cons 5.524000e-01   p_joint 1.010000e-01

Joint ci ratio: 4.571055e-02	ci left: 2.626648e-01	ci right 2.750025e-01	k: 5376	n:20000
Cons ci ratio: 2.474832e-02	ci left: 5.494819e-01	ci right 5.633017e-01	k: 11128	n:20000
KS ci ratio: 1.968048e-01	ci left: 1.753359e-02	ci right 2.140790e-02	k: 388	n:20000
ZBTB40   20000 perm   4 sec   (4863 perm/sec)   p_kst 1.940000e-02   p_cons 5.564000e-01   p_joint 2.688000e-01

Joint ci ratio: 6.449605e-02	ci left: 1.060863e-01	ci right 1.131895e-01	k: 3288	n:30000
Cons ci ratio: 2.023601e-02	ci left: 5.500555e-01	ci right 5.613338e-01	k: 16671	n:30000
KS ci ratio: 1.651492e-01	ci left: 1.690934e-02	ci right 1.998493e-02	k: 552	n:30000
ZBTB40   30000 perm   6 sec   (4647 perm/sec)   p_kst 1.840000e-02   p_cons 5.557000e-01   p_joint 1.096000e-01

Joint ci ratio: 3.993114e-02	ci left: 1.902587e-01	ci right 1.980357e-01	k: 7765	n:40000
Cons ci ratio: 1.744007e-02	ci left: 5.532167e-01	ci right 5.629749e-01	k: 22324	n:40000
KS ci ratio: 1.431559e-01	ci left: 1.708140e-02	ci right 1.973917e-02	k: 735	n:40000
ZBTB40   40000 perm   9 sec   (4502 perm/sec)   p_kst 1.837500e-02   p_cons 5.581000e-01   p_joint 1.941250e-01

Joint ci ratio: 3.650979e-02	ci left: 1.839282e-01	ci right 1.907882e-01	k: 9367	n:50000
Cons ci ratio: 1.557811e-02	ci left: 5.543945e-01	ci right 5.631187e-01	k: 27938	n:50000
KS ci ratio: 1.272003e-01	ci left: 1.745314e-02	ci right 1.984321e-02	k: 931	n:50000
ZBTB40   50000 perm   11 sec   (4349 perm/sec)   p_kst 1.862000e-02   p_cons 5.587600e-01   p_joint 1.873400e-01

Joint ci ratio: 3.395963e-02	ci left: 1.786218e-01	ci right 1.848091e-01	k: 10902	n:60000
Cons ci ratio: 1.417267e-02	ci left: 5.564507e-01	ci right 5.644101e-01	k: 33626	n:60000
KS ci ratio: 1.166180e-01	ci left: 1.740441e-02	ci right 1.957585e-02	k: 1108	n:60000
ZBTB40   60000 perm   14 sec   (4271 perm/sec)   p_kst 1.846667e-02   p_cons 5.604333e-01   p_joint 1.817000e-01

Joint ci ratio: 3.039139e-02	ci left: 1.891021e-01	ci right 1.949521e-01	k: 13441	n:70000
Cons ci ratio: 1.312836e-02	ci left: 5.564848e-01	ci right 5.638531e-01	k: 39212	n:70000
KS ci ratio: 1.078331e-01	ci left: 1.752853e-02	ci right 1.954023e-02	k: 1296	n:70000
ZBTB40   70000 perm   17 sec   (4204 perm/sec)   p_kst 1.851429e-02   p_cons 5.601714e-01   p_joint 1.920143e-01

Joint ci ratio: 2.773692e-02	ci left: 1.970090e-01	ci right 2.025628e-01	k: 15982	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: 1.004307e-01	ci left: 1.774816e-02	ci right 1.963698e-02	k: 1494	n:80000
ZBTB40   80000 perm   19 sec   (4135 perm/sec)   p_kst 1.867500e-02   p_cons 5.608125e-01   p_joint 1.997750e-01

Joint ci ratio: 2.482967e-02	ci left: 2.141779e-01	ci right 2.195737e-01	k: 19518	n:90000
Cons ci ratio: 1.154751e-02	ci left: 5.582285e-01	ci right 5.647231e-01	k: 50533	n:90000
KS ci ratio: 9.462614e-02	ci left: 1.782497e-02	ci right 1.960624e-02	k: 1683	n:90000
ZBTB40   90000 perm   22 sec   (4067 perm/sec)   p_kst 1.870000e-02   p_cons 5.614778e-01   p_joint 2.168667e-01

Outputting figure to mutsig2_images.part000000000193/ZBTB40.2_3788_90000_0.0187_0.56148_0.21687.png
                gene_name: ZBTB40
               theta_stop: 0.095 
                    nperm: 90000 
                     p_ks: 0.019 
        ci_ks_bounds_left: 0.018 
       ci_ks_bounds_right: 0.020 
                   p_cons: 0.56 
      ci_cons_bounds_left: 0.56 
     ci_cons_bounds_right: 0.56 
                  p_joint: 0.22 
     ci_joint_bounds_left: 0.21 
    ci_joint_bounds_right: 0.22 

Current progress: 75 percent done.
ZCCHC14
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.153779e-02	ci left: 3.569465e-01	ci right 3.759313e-01	k: 3664	n:10000
Cons ci ratio: 2.012596e-02	ci left: 7.833022e-01	ci right 7.993277e-01	k: 7914	n:10000
KS ci ratio: 1.055514e-01	ci left: 1.147668e-01	ci right 1.276548e-01	k: 1211	n:10000
ZCCHC14   10000 perm   2 sec   (5605 perm/sec)   p_kst 1.211000e-01   p_cons 7.914000e-01   p_joint 3.664000e-01

Joint ci ratio: 2.783593e-02	ci left: 4.908963e-01	ci right 5.048043e-01	k: 9957	n:20000
Cons ci ratio: 1.470172e-02	ci left: 7.746476e-01	ci right 7.861708e-01	k: 15609	n:20000
KS ci ratio: 7.502540e-02	ci left: 1.155760e-01	ci right 1.246348e-01	k: 2401	n:20000
ZCCHC14   20000 perm   4 sec   (4988 perm/sec)   p_kst 1.200500e-01   p_cons 7.804500e-01   p_joint 4.978500e-01

Outputting figure to mutsig2_images.part000000000193/ZCCHC14.2_2902_20000_0.12005_0.78045_0.49785.png
                gene_name: ZCCHC14
               theta_stop: 0.075 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.12 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.50 
     ci_joint_bounds_left: 0.49 
    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.165.3896/
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/181708/iteration1/scatter.0000000193
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 193 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120363: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000194> was used as the working directory.
Started at Wed Oct 10 10:45:53 2012
Results reported at Wed Oct 10 10:48:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000194.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000194.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 194  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    198.94 sec.
    Max Memory :      1387 MB
    Max Swap   :      3889 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.165.3896/
-whichjob
194
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 194: processing genes 17462 - 17551
Calculating significance of each gene.
Using projection method.
17462	ZDHHC6	3.186505e-02
17463	ZDHHC7	1
17464	ZDHHC8	1
17465	ZDHHC9	1
17466	ZEB1	1
17467	ZEB2	1
17468	ZER1	1
17469	ZFAND1	1
17470	ZFAND2A	1
17471	ZFAND2B	1
17472	ZFAND3	1
17473	ZFAND5	1
17474	ZFAND6	1
17475	ZFAT	1
17476	ZFC3H1	1.799937e-01
17477	ZFHX3	1
17478	ZFHX4	5.370532e-01
17479	ZFP1	1
17480	ZFP106	1
17481	ZFP112	1
17482	ZFP14	1
17483	ZFP161	1
17484	ZFP2	1
17485	ZFP28	1
17486	ZFP3	1
17487	ZFP30	1
17488	ZFP36	1
17489	ZFP36L1	1.326829e-01
17490	ZFP36L2	1
17491	ZFP37	2.061425e-02
17492	ZFP41	1
17493	ZFP42	1
17494	ZFP57	3.012215e-03
17495	ZFP64	1
17496	ZFP82	1.506276e-01
17497	ZFP90	1
17498	ZFP91	1
17499	ZFPL1	1
17500	ZFPM1	4.194451e-02
17501	ZFPM2	4.133938e-01
17502	ZFR	1
17503	ZFR2	1
17504	ZFX	1
17505	ZFY	1
17506	ZFYVE1	1
17507	ZFYVE16	4.343772e-01
17508	ZFYVE19	1
17509	ZFYVE20	1.823125e-01
17510	ZFYVE21	1
17511	ZFYVE26	1
17512	ZFYVE27	1.993478e-01
17513	ZFYVE28	1
17514	ZFYVE9	1
17515	ZG16B	1
17516	ZGLP1	1
17517	ZGPAT	1
17518	ZHX1	1
17519	ZHX2	1.743230e-01
17520	ZHX3	2.565283e-01
17521	ZIC1	1.872833e-01
17522	ZIC2	1.072677e-01
17523	ZIC3	1.016832e-01
17524	ZIC4	1
17525	ZIC5	1
17526	ZIK1	1
17527	ZIM2	1
17528	ZIM3	8.931388e-02
17529	ZKSCAN1	1.944271e-01
17530	ZKSCAN2	1
17531	ZKSCAN3	1
17532	ZKSCAN4	1
17533	ZKSCAN5	1.600446e-01
17534	ZMAT1	9.741900e-02
17535	ZMAT2	1
17536	ZMAT3	1
17537	ZMAT4	1
17538	ZMAT5	1
17539	ZMIZ1	1
17540	ZMIZ2	1
17541	ZMPSTE24	1
17542	ZMYM1	1
17543	ZMYM2	5.071444e-01
17544	ZMYM3	1
17545	ZMYM4	1
17546	ZMYM5	1
17547	ZMYM6	1
17548	ZMYND10	1
17549	ZMYND11	1
17550	ZMYND12	1
17551	ZMYND15	1
Done

Running MutSig 2:
Scatter job 194: processing genes 17462 - 17551
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZFHX4
Processing conservation and coverage...
91% 
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.993788e-02	ci left: 4.807559e-01	ci right 5.004496e-01	k: 4906	n:10000
Cons ci ratio: 6.764274e-02	ci left: 2.428218e-01	ci right 2.599232e-01	k: 2513	n:10000
KS ci ratio: 4.118018e-02	ci left: 4.654705e-01	ci right 4.851439e-01	k: 4753	n:10000
ZFHX4   10000 perm   3 sec   (3095 perm/sec)   p_kst 4.753000e-01   p_cons 2.513000e-01   p_joint 4.906000e-01

Outputting figure to mutsig2_images.part000000000194/ZFHX4.4_10891_10000_0.4753_0.2513_0.4906.png
                gene_name: ZFHX4
               theta_stop: 0.068 
                    nperm: 10000 
                     p_ks: 0.48 
        ci_ks_bounds_left: 0.47 
       ci_ks_bounds_right: 0.49 
                   p_cons: 0.25 
      ci_cons_bounds_left: 0.24 
     ci_cons_bounds_right: 0.26 
                  p_joint: 0.49 
     ci_joint_bounds_left: 0.48 
    ci_joint_bounds_right: 0.50 

Current progress: 14 percent done.
ZFYVE9
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.648733e-01	ci left: 4.907401e-02	ci right 5.798834e-02	k: 534	n:10000
Cons ci ratio: 2.067321e-02	ci left: 7.741813e-01	ci right 7.904539e-01	k: 7824	n:10000
KS ci ratio: 2.831816e-01	ci left: 1.613586e-02	ci right 2.154960e-02	k: 187	n:10000
ZFYVE9   10000 perm   2 sec   (4939 perm/sec)   p_kst 1.870000e-02   p_cons 7.824000e-01   p_joint 5.340000e-02

Joint ci ratio: 1.142358e-01	ci left: 5.241537e-02	ci right 5.881460e-02	k: 1111	n:20000
Cons ci ratio: 1.421378e-02	ci left: 7.861057e-01	ci right 7.974093e-01	k: 15836	n:20000
KS ci ratio: 2.002444e-01	ci left: 1.691536e-02	ci right 2.072636e-02	k: 375	n:20000
ZFYVE9   20000 perm   4 sec   (4458 perm/sec)   p_kst 1.875000e-02   p_cons 7.918000e-01   p_joint 5.555000e-02

Joint ci ratio: 1.146049e-01	ci left: 3.537839e-02	ci right 3.971176e-02	k: 1125	n:30000
Cons ci ratio: 1.163712e-02	ci left: 7.862535e-01	ci right 7.954901e-01	k: 23727	n:30000
KS ci ratio: 1.673200e-01	ci left: 1.646177e-02	ci right 1.949927e-02	k: 538	n:30000
ZFYVE9   30000 perm   7 sec   (4287 perm/sec)   p_kst 1.793333e-02   p_cons 7.909000e-01   p_joint 3.750000e-02

Joint ci ratio: 7.866486e-02	ci left: 5.614612e-02	ci right 6.076824e-02	k: 2337	n:40000
Cons ci ratio: 1.031903e-02	ci left: 7.789024e-01	ci right 7.870065e-01	k: 31319	n:40000
KS ci ratio: 1.462216e-01	ci left: 1.635811e-02	ci right 1.896259e-02	k: 705	n:40000
ZFYVE9   40000 perm   10 sec   (4174 perm/sec)   p_kst 1.762500e-02   p_cons 7.829750e-01   p_joint 5.842500e-02

Joint ci ratio: 7.963542e-02	ci left: 4.437641e-02	ci right 4.807650e-02	k: 2310	n:50000
Cons ci ratio: 9.197968e-03	ci left: 7.805074e-01	ci right 7.877396e-01	k: 39207	n:50000
KS ci ratio: 1.346825e-01	ci left: 1.553690e-02	ci right 1.779972e-02	k: 832	n:50000
ZFYVE9   50000 perm   12 sec   (4082 perm/sec)   p_kst 1.664000e-02   p_cons 7.841400e-01   p_joint 4.620000e-02

Joint ci ratio: 7.901878e-02	ci left: 3.784098e-02	ci right 4.097044e-02	k: 2363	n:60000
Cons ci ratio: 8.360332e-03	ci left: 7.822940e-01	ci right 7.888783e-01	k: 47136	n:60000
KS ci ratio: 1.233628e-01	ci left: 1.552812e-02	ci right 1.758569e-02	k: 992	n:60000
ZFYVE9   60000 perm   15 sec   (4001 perm/sec)   p_kst 1.653333e-02   p_cons 7.856000e-01   p_joint 3.938333e-02

Joint ci ratio: 7.475168e-02	ci left: 3.638522e-02	ci right 3.922468e-02	k: 2645	n:70000
Cons ci ratio: 7.748693e-03	ci left: 7.821675e-01	ci right 7.882660e-01	k: 54966	n:70000
KS ci ratio: 1.142369e-01	ci left: 1.559702e-02	ci right 1.750050e-02	k: 1157	n:70000
ZFYVE9   70000 perm   18 sec   (3917 perm/sec)   p_kst 1.652857e-02   p_cons 7.852286e-01   p_joint 3.778571e-02

Joint ci ratio: 8.160065e-02	ci left: 2.689221e-02	ci right 2.919218e-02	k: 2242	n:80000
Cons ci ratio: 7.241597e-03	ci left: 7.826767e-01	ci right 7.883776e-01	k: 62843	n:80000
KS ci ratio: 1.069176e-01	ci left: 1.564075e-02	ci right 1.741956e-02	k: 1321	n:80000
ZFYVE9   80000 perm   21 sec   (3856 perm/sec)   p_kst 1.651250e-02   p_cons 7.855375e-01   p_joint 2.802500e-02

Joint ci ratio: 9.537924e-02	ci left: 1.754283e-02	ci right 1.931063e-02	k: 1657	n:90000
Cons ci ratio: 6.838556e-03	ci left: 7.822901e-01	ci right 7.876693e-01	k: 70649	n:90000
KS ci ratio: 1.008116e-01	ci left: 1.568864e-02	ci right 1.736496e-02	k: 1486	n:90000
ZFYVE9   90000 perm   24 sec   (3797 perm/sec)   p_kst 1.651111e-02   p_cons 7.849889e-01   p_joint 1.841111e-02

Joint ci ratio: 7.800752e-02	ci left: 2.366835e-02	ci right 2.559936e-02	k: 2462	n:100000
Cons ci ratio: 6.493366e-03	ci left: 7.821292e-01	ci right 7.872343e-01	k: 78469	n:100000
KS ci ratio: 9.576283e-02	ci left: 1.569021e-02	ci right 1.727802e-02	k: 1647	n:100000
ZFYVE9   100000 perm   27 sec   (3742 perm/sec)   p_kst 1.647000e-02   p_cons 7.846900e-01   p_joint 2.462000e-02

Outputting figure to mutsig2_images.part000000000194/ZFYVE9.4_4357_100000_0.01647_0.78469_0.02462.png
                gene_name: ZFYVE9
               theta_stop: 0.096 
                    nperm: 100000 
                     p_ks: 0.016 
        ci_ks_bounds_left: 0.016 
       ci_ks_bounds_right: 0.017 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.78 
     ci_cons_bounds_right: 0.79 
                  p_joint: 0.025 
     ci_joint_bounds_left: 0.024 
    ci_joint_bounds_right: 0.026 

Current progress: 29 percent done.
ZFP57
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.356648e-02	ci left: 5.671455e-01	ci right 5.866096e-01	k: 5769	n:10000
Cons ci ratio: 2.107936e-02	ci left: 7.673949e-01	ci right 7.838442e-01	k: 7757	n:10000
KS ci ratio: 5.208602e-02	ci left: 3.520751e-01	ci right 3.710056e-01	k: 3615	n:10000
ZFP57   10000 perm   2 sec   (5217 perm/sec)   p_kst 3.615000e-01   p_cons 7.757000e-01   p_joint 5.769000e-01

Outputting figure to mutsig2_images.part000000000194/ZFP57.3_1627_10000_0.3615_0.7757_0.5769.png
                gene_name: ZFP57
               theta_stop: 0.052 
                    nperm: 10000 
                     p_ks: 0.36 
        ci_ks_bounds_left: 0.35 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.78 
      ci_cons_bounds_left: 0.77 
     ci_cons_bounds_right: 0.78 
                  p_joint: 0.58 
     ci_joint_bounds_left: 0.57 
    ci_joint_bounds_right: 0.59 

Current progress: 43 percent done.
ZFC3H1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.711733e-02	ci left: 5.173580e-01	ci right 5.370262e-01	k: 5272	n:10000
Cons ci ratio: 1.432059e-02	ci left: 8.758224e-01	ci right 8.885540e-01	k: 8823	n:10000
KS ci ratio: 1.394779e-01	ci left: 6.807308e-02	ci right 7.837719e-02	k: 731	n:10000
ZFC3H1   10000 perm   2 sec   (4704 perm/sec)   p_kst 7.310000e-02   p_cons 8.823000e-01   p_joint 5.272000e-01

Joint ci ratio: 1.961764e-02	ci left: 6.596659e-01	ci right 6.727857e-01	k: 13325	n:20000
Cons ci ratio: 9.980774e-03	ci left: 8.807517e-01	ci right 8.896359e-01	k: 17705	n:20000
KS ci ratio: 9.962254e-02	ci left: 6.825964e-02	ci right 7.546543e-02	k: 1436	n:20000
ZFC3H1   20000 perm   5 sec   (4249 perm/sec)   p_kst 7.180000e-02   p_cons 8.852500e-01   p_joint 6.662500e-01

Outputting figure to mutsig2_images.part000000000194/ZFC3H1.2_6110_20000_0.0718_0.88525_0.66625.png
                gene_name: ZFC3H1
               theta_stop: 0.100 
                    nperm: 20000 
                     p_ks: 0.072 
        ci_ks_bounds_left: 0.068 
       ci_ks_bounds_right: 0.075 
                   p_cons: 0.89 
      ci_cons_bounds_left: 0.88 
     ci_cons_bounds_right: 0.89 
                  p_joint: 0.67 
     ci_joint_bounds_left: 0.66 
    ci_joint_bounds_right: 0.67 

Current progress: 57 percent done.
ZFP37
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.928552e-01	ci left: 1.502126e-02	ci right 2.026513e-02	k: 175	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: 5.204093e-02	ci left: 3.524727e-01	ci right 3.714078e-01	k: 3619	n:10000
ZFP37   10000 perm   2 sec   (6128 perm/sec)   p_kst 3.619000e-01   p_cons 2.620000e-02   p_joint 1.750000e-02

Joint ci ratio: 1.732762e-01	ci left: 2.278476e-02	ci right 2.715484e-02	k: 498	n:20000
Cons ci ratio: 1.693159e-01	ci left: 2.388659e-02	ci right 2.835263e-02	k: 521	n:20000
KS ci ratio: 3.630954e-02	ci left: 3.614603e-01	ci right 3.748780e-01	k: 7363	n:20000
ZFP37   20000 perm   4 sec   (5414 perm/sec)   p_kst 3.681500e-01   p_cons 2.605000e-02   p_joint 2.490000e-02

Joint ci ratio: 1.196653e-01	ci left: 3.246326e-02	ci right 3.662751e-02	k: 1035	n:30000
Cons ci ratio: 1.364677e-01	ci left: 2.493733e-02	ci right 2.862175e-02	k: 802	n:30000
KS ci ratio: 2.947951e-02	ci left: 3.653303e-01	ci right 3.762947e-01	k: 11124	n:30000
ZFP37   30000 perm   6 sec   (5035 perm/sec)   p_kst 3.708000e-01   p_cons 2.673333e-02   p_joint 3.450000e-02

Joint ci ratio: 1.052354e-01	ci left: 3.175807e-02	ci right 3.531007e-02	k: 1340	n:40000
Cons ci ratio: 1.197848e-01	ci left: 2.451102e-02	ci right 2.765829e-02	k: 1042	n:40000
KS ci ratio: 2.550720e-02	ci left: 3.664874e-01	ci right 3.759813e-01	k: 14849	n:40000
ZFP37   40000 perm   8 sec   (4831 perm/sec)   p_kst 3.712250e-01   p_cons 2.605000e-02   p_joint 3.350000e-02

Joint ci ratio: 9.318781e-02	ci left: 3.258498e-02	ci right 3.578940e-02	k: 1708	n:50000
Cons ci ratio: 1.078095e-01	ci left: 2.436954e-02	ci right 2.716589e-02	k: 1287	n:50000
KS ci ratio: 2.287455e-02	ci left: 3.657658e-01	ci right 3.742493e-01	k: 18500	n:50000
ZFP37   50000 perm   11 sec   (4694 perm/sec)   p_kst 3.700000e-01   p_cons 2.574000e-02   p_joint 3.416000e-02

Joint ci ratio: 6.959780e-02	ci left: 4.846627e-02	ci right 5.197740e-02	k: 3012	n:60000
Cons ci ratio: 9.846863e-02	ci left: 2.446476e-02	ci right 2.701472e-02	k: 1543	n:60000
KS ci ratio: 2.084364e-02	ci left: 3.669830e-01	ci right 3.747295e-01	k: 22251	n:60000
ZFP37   60000 perm   13 sec   (4617 perm/sec)   p_kst 3.708500e-01   p_cons 2.571667e-02   p_joint 5.020000e-02

Outputting figure to mutsig2_images.part000000000194/ZFP37.2_1909_60000_0.37085_0.025717_0.0502.png
                gene_name: ZFP37
               theta_stop: 0.098 
                    nperm: 60000 
                     p_ks: 0.37 
        ci_ks_bounds_left: 0.37 
       ci_ks_bounds_right: 0.37 
                   p_cons: 0.026 
      ci_cons_bounds_left: 0.024 
     ci_cons_bounds_right: 0.027 
                  p_joint: 0.050 
     ci_joint_bounds_left: 0.048 
    ci_joint_bounds_right: 0.052 

Current progress: 71 percent done.
ZMAT1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.829005e-02	ci left: 6.481042e-01	ci right 6.668040e-01	k: 6575	n:10000
Cons ci ratio: 6.985136e-02	ci left: 2.310633e-01	ci right 2.478887e-01	k: 2394	n:10000
KS ci ratio: 1.862795e-02	ci left: 8.080607e-01	ci right 8.233550e-01	k: 8158	n:10000
ZMAT1   10000 perm   2 sec   (5825 perm/sec)   p_kst 8.158000e-01   p_cons 2.394000e-01   p_joint 6.575000e-01

Outputting figure to mutsig2_images.part000000000194/ZMAT1.2_1941_10000_0.8158_0.2394_0.6575.png
                gene_name: ZMAT1
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.82 
        ci_ks_bounds_left: 0.81 
       ci_ks_bounds_right: 0.82 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.66 
     ci_joint_bounds_left: 0.65 
    ci_joint_bounds_right: 0.67 

Current progress: 86 percent done.
ZMYM2
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 9.683164e-02	ci left: 1.339403e-01	ci right 1.476696e-01	k: 1407	n:10000
Cons ci ratio: 1.502819e-02	ci left: 8.651913e-01	ci right 8.783912e-01	k: 8719	n:10000
KS ci ratio: 2.676375e-01	ci left: 1.818649e-02	ci right 2.389730e-02	k: 209	n:10000
ZMYM2   10000 perm   2 sec   (5406 perm/sec)   p_kst 2.090000e-02   p_cons 8.719000e-01   p_joint 1.407000e-01

Joint ci ratio: 8.137980e-02	ci left: 9.970398e-02	ci right 1.082116e-01	k: 2078	n:20000
Cons ci ratio: 1.118686e-02	ci left: 8.550631e-01	ci right 8.647321e-01	k: 17199	n:20000
KS ci ratio: 1.843791e-01	ci left: 2.005956e-02	ci right 2.418100e-02	k: 441	n:20000
ZMYM2   20000 perm   4 sec   (4829 perm/sec)   p_kst 2.205000e-02   p_cons 8.599500e-01   p_joint 1.039000e-01

Joint ci ratio: 5.971460e-02	ci left: 1.218368e-01	ci right 1.293692e-01	k: 3767	n:30000
Cons ci ratio: 9.148337e-03	ci left: 8.555836e-01	ci right 8.634799e-01	k: 25787	n:30000
KS ci ratio: 1.525583e-01	ci left: 1.988850e-02	ci right 2.320506e-02	k: 645	n:30000
ZMYM2   30000 perm   6 sec   (4626 perm/sec)   p_kst 2.150000e-02   p_cons 8.595667e-01   p_joint 1.255667e-01

Joint ci ratio: 4.341181e-02	ci left: 1.656365e-01	ci right 1.730116e-01	k: 6772	n:40000
Cons ci ratio: 7.946913e-03	ci left: 8.553741e-01	ci right 8.622237e-01	k: 34353	n:40000
KS ci ratio: 1.306041e-01	ci left: 2.058481e-02	ci right 2.348516e-02	k: 880	n:40000
ZMYM2   40000 perm   9 sec   (4429 perm/sec)   p_kst 2.200000e-02   p_cons 8.588250e-01   p_joint 1.693000e-01

Joint ci ratio: 4.090681e-02	ci left: 1.519767e-01	ci right 1.583434e-01	k: 7757	n:50000
Cons ci ratio: 7.101581e-03	ci left: 8.559590e-01	ci right 8.620792e-01	k: 42952	n:50000
KS ci ratio: 1.165594e-01	ci left: 2.082924e-02	ci right 2.342666e-02	k: 1105	n:50000
ZMYM2   50000 perm   12 sec   (4333 perm/sec)   p_kst 2.210000e-02   p_cons 8.590400e-01   p_joint 1.551400e-01

Joint ci ratio: 3.663853e-02	ci left: 1.572733e-01	ci right 1.631596e-01	k: 9612	n:60000
Cons ci ratio: 6.486096e-03	ci left: 8.561056e-01	ci right 8.616930e-01	k: 51535	n:60000
KS ci ratio: 1.057216e-01	ci left: 2.121451e-02	ci right 2.359867e-02	k: 1343	n:60000
ZMYM2   60000 perm   14 sec   (4252 perm/sec)   p_kst 2.238333e-02   p_cons 8.589167e-01   p_joint 1.602000e-01

Joint ci ratio: 3.534871e-02	ci left: 1.467808e-01	ci right 1.520769e-01	k: 10459	n:70000
Cons ci ratio: 6.021974e-03	ci left: 8.556226e-01	ci right 8.608048e-01	k: 60076	n:70000
KS ci ratio: 9.836160e-02	ci left: 2.109337e-02	ci right 2.328934e-02	k: 1552	n:70000
ZMYM2   70000 perm   17 sec   (4159 perm/sec)   p_kst 2.217143e-02   p_cons 8.582286e-01   p_joint 1.494143e-01

Outputting figure to mutsig2_images.part000000000194/ZMYM2.2_4226_70000_0.022171_0.85823_0.14941.png
                gene_name: ZMYM2
               theta_stop: 0.098 
                    nperm: 70000 
                     p_ks: 0.022 
        ci_ks_bounds_left: 0.021 
       ci_ks_bounds_right: 0.023 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.86 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.15 
    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.165.3896/
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/181708/iteration1/scatter.0000000194
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 194 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120366: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000195> was used as the working directory.
Started at Wed Oct 10 10:45:53 2012
Results reported at Wed Oct 10 10:49:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000195.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000195.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 195  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    257.95 sec.
    Max Memory :      1160 MB
    Max Swap   :      3910 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.165.3896/
-whichjob
195
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 195: processing genes 17552 - 17642
Calculating significance of each gene.
Using projection method.
17552	ZMYND17	1
17553	ZMYND19	9.590901e-02
17554	ZMYND8	4.559438e-01
17555	ZNF10	1
17556	ZNF100	1
17557	ZNF101	1
17558	ZNF107	1
17559	ZNF114	1
17560	ZNF117	1
17561	ZNF12	1
17562	ZNF121	1
17563	ZNF124	1.056761e-01
17564	ZNF131	1
17565	ZNF132	1
17566	ZNF133	5.190055e-02
17567	ZNF134	1
17568	ZNF135	1
17569	ZNF136	1
17570	ZNF138	1
17571	ZNF14	1
17572	ZNF140	1
17573	ZNF141	1
17574	ZNF142	1
17575	ZNF143	1
17576	ZNF146	5.547996e-02
17577	ZNF148	1
17578	ZNF154	1
17579	ZNF155	1
17580	ZNF157	1
17581	ZNF16	8.528417e-02
17582	ZNF160	5.051952e-02
17583	ZNF165	2.273406e-01
17584	ZNF167	2.607553e-01
17585	ZNF169	1
17586	ZNF17	1.727052e-01
17587	ZNF174	1
17588	ZNF175	1
17589	ZNF177	1
17590	ZNF18	1
17591	ZNF180	2.449243e-01
17592	ZNF181	1
17593	ZNF182	1
17594	ZNF184	2.390653e-01
17595	ZNF185	1
17596	ZNF187	1
17597	ZNF189	1.964232e-01
17598	ZNF19	1
17599	ZNF192	1
17600	ZNF193	1
17601	ZNF195	1
17602	ZNF197	1
17603	ZNF2	1
17604	ZNF20	1
17605	ZNF200	9.506516e-02
17606	ZNF202	1
17607	ZNF205	5.200754e-03
17608	ZNF207	1.413374e-02
17609	ZNF208	1.687455e-01
17610	ZNF211	6.640178e-02
17611	ZNF212	1
17612	ZNF213	1
17613	ZNF214	4.693042e-02
17614	ZNF215	1
17615	ZNF217	2.162577e-01
17616	ZNF219	1
17617	ZNF22	1
17618	ZNF221	9.796687e-02
17619	ZNF222	1.299284e-01
17620	ZNF223	1
17621	ZNF224	1.278376e-01
17622	ZNF225	1
17623	ZNF226	1
17624	ZNF227	3.620134e-01
17625	ZNF229	1
17626	ZNF23	1.968679e-01
17627	ZNF230	4.309347e-02
17628	ZNF232	1
17629	ZNF233	1
17630	ZNF234	1
17631	ZNF235	1
17632	ZNF236	4.014914e-01
17633	ZNF238	1
17634	ZNF239	2.135439e-01
17635	ZNF24	1
17636	ZNF248	1
17637	ZNF25	5.604254e-02
17638	ZNF250	1
17639	ZNF251	1
17640	ZNF253	1
17641	ZNF254	1
17642	ZNF256	1
Done

Running MutSig 2:
Scatter job 195: processing genes 17552 - 17642
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF200
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.301551e-01	ci left: 1.160595e-02	ci right 1.628351e-02	k: 138	n:10000
Cons ci ratio: 1.620383e-02	ci left: 8.470282e-01	ci right 8.609649e-01	k: 8541	n:10000
KS ci ratio: 6.521239e-01	ci left: 2.439052e-03	ci right 4.864323e-03	k: 35	n:10000
ZNF200   10000 perm   2 sec   (5340 perm/sec)   p_kst 3.500000e-03   p_cons 8.541000e-01   p_joint 1.380000e-02

Joint ci ratio: 2.089046e-01	ci left: 1.549097e-02	ci right 1.915129e-02	k: 345	n:20000
Cons ci ratio: 1.068018e-02	ci left: 8.660217e-01	ci right 8.753702e-01	k: 17415	n:20000
KS ci ratio: 4.892032e-01	ci left: 2.421370e-03	ci right 4.028444e-03	k: 63	n:20000
ZNF200   20000 perm   7 sec   (2848 perm/sec)   p_kst 3.150000e-03   p_cons 8.707500e-01   p_joint 1.725000e-02

Joint ci ratio: 1.005334e-01	ci left: 4.580345e-02	ci right 5.068451e-02	k: 1446	n:30000
Cons ci ratio: 8.737490e-03	ci left: 8.664456e-01	ci right 8.740825e-01	k: 26109	n:30000
KS ci ratio: 3.800645e-01	ci left: 2.863519e-03	ci right 4.235401e-03	k: 105	n:30000
ZNF200   30000 perm   9 sec   (3204 perm/sec)   p_kst 3.500000e-03   p_cons 8.703000e-01   p_joint 4.820000e-02

Joint ci ratio: 1.105500e-01	ci left: 2.878783e-02	ci right 3.218078e-02	k: 1218	n:40000
Cons ci ratio: 7.571802e-03	ci left: 8.668165e-01	ci right 8.734296e-01	k: 34806	n:40000
KS ci ratio: 3.083131e-01	ci left: 3.405185e-03	ci right 4.668493e-03	k: 160	n:40000
ZNF200   40000 perm   12 sec   (3386 perm/sec)   p_kst 4.000000e-03   p_cons 8.701500e-01   p_joint 3.045000e-02

Joint ci ratio: 9.742943e-02	ci left: 2.983005e-02	ci right 3.290468e-02	k: 1567	n:50000
Cons ci ratio: 6.781652e-03	ci left: 8.668592e-01	ci right 8.727778e-01	k: 43492	n:50000
KS ci ratio: 2.766282e-01	ci left: 3.447092e-03	ci right 4.571698e-03	k: 199	n:50000
ZNF200   50000 perm   14 sec   (3505 perm/sec)   p_kst 3.980000e-03   p_cons 8.698400e-01   p_joint 3.134000e-02

Joint ci ratio: 9.363168e-02	ci left: 2.705279e-02	ci right 2.972642e-02	k: 1702	n:60000
Cons ci ratio: 6.194107e-03	ci left: 8.669970e-01	ci right 8.724005e-01	k: 52183	n:60000
KS ci ratio: 2.509563e-01	ci left: 3.541977e-03	ci right 4.573571e-03	k: 242	n:60000
ZNF200   60000 perm   17 sec   (3596 perm/sec)   p_kst 4.033333e-03   p_cons 8.697167e-01   p_joint 2.836667e-02

Joint ci ratio: 8.331189e-02	ci left: 2.937845e-02	ci right 3.194636e-02	k: 2145	n:70000
Cons ci ratio: 5.709698e-03	ci left: 8.681919e-01	ci right 8.731774e-01	k: 60949	n:70000
KS ci ratio: 2.146256e-01	ci left: 4.233849e-03	ci right 5.265007e-03	k: 331	n:70000
ZNF200   70000 perm   19 sec   (3650 perm/sec)   p_kst 4.728571e-03   p_cons 8.707000e-01   p_joint 3.064286e-02

Joint ci ratio: 8.014199e-02	ci left: 2.787255e-02	ci right 3.021177e-02	k: 2322	n:80000
Cons ci ratio: 5.350104e-03	ci left: 8.679648e-01	ci right 8.726333e-01	k: 69625	n:80000
KS ci ratio: 2.016817e-01	ci left: 4.225968e-03	ci right 5.185494e-03	k: 375	n:80000
ZNF200   80000 perm   22 sec   (3682 perm/sec)   p_kst 4.687500e-03   p_cons 8.703125e-01   p_joint 2.902500e-02

Joint ci ratio: 7.089308e-02	ci left: 3.168955e-02	ci right 3.402957e-02	k: 2956	n:90000
Cons ci ratio: 5.042158e-03	ci left: 8.681882e-01	ci right 8.725879e-01	k: 78336	n:90000
KS ci ratio: 1.894736e-01	ci left: 4.284801e-03	ci right 5.192019e-03	k: 425	n:90000
ZNF200   90000 perm   24 sec   (3690 perm/sec)   p_kst 4.722222e-03   p_cons 8.704000e-01   p_joint 3.284444e-02

Joint ci ratio: 6.569529e-02	ci left: 3.324939e-02	ci right 3.551772e-02	k: 3437	n:100000
Cons ci ratio: 4.786793e-03	ci left: 8.681415e-01	ci right 8.723170e-01	k: 87024	n:100000
KS ci ratio: 1.786790e-01	ci left: 4.361931e-03	ci right 5.227177e-03	k: 478	n:100000
ZNF200   100000 perm   27 sec   (3685 perm/sec)   p_kst 4.780000e-03   p_cons 8.702400e-01   p_joint 3.437000e-02

Joint ci ratio: 6.463658e-02	ci left: 3.130777e-02	ci right 3.340789e-02	k: 3558	n:110000
Cons ci ratio: 4.568502e-03	ci left: 8.680166e-01	ci right 8.720002e-01	k: 95702	n:110000
KS ci ratio: 1.708369e-01	ci left: 4.356593e-03	ci right 5.178944e-03	k: 523	n:110000
ZNF200   110000 perm   30 sec   (3669 perm/sec)   p_kst 4.754545e-03   p_cons 8.700182e-01   p_joint 3.234545e-02

Joint ci ratio: 5.740248e-02	ci left: 3.633349e-02	ci right 3.848894e-02	k: 4488	n:120000
Cons ci ratio: 4.367422e-03	ci left: 8.684447e-01	ci right 8.722541e-01	k: 104443	n:120000
KS ci ratio: 1.626567e-01	ci left: 4.424785e-03	ci right 5.216104e-03	k: 577	n:120000
ZNF200   120000 perm   33 sec   (3646 perm/sec)   p_kst 4.808333e-03   p_cons 8.703583e-01   p_joint 3.740000e-02

Joint ci ratio: 5.714628e-02	ci left: 3.393165e-02	ci right 3.593531e-02	k: 4540	n:130000
Cons ci ratio: 4.464413e-03	ci left: 8.537935e-01	ci right 8.576214e-01	k: 111243	n:130000
KS ci ratio: 1.571819e-01	ci left: 4.387175e-03	ci right 5.142869e-03	k: 618	n:130000
ZNF200   130000 perm   36 sec   (3618 perm/sec)   p_kst 4.753846e-03   p_cons 8.557154e-01   p_joint 3.492308e-02

Joint ci ratio: 5.278507e-02	ci left: 3.689869e-02	ci right 3.890622e-02	k: 5305	n:140000
Cons ci ratio: 4.300663e-03	ci left: 8.539417e-01	ci right 8.576292e-01	k: 119811	n:140000
KS ci ratio: 1.510795e-01	ci left: 4.424051e-03	ci right 5.153835e-03	k: 669	n:140000
ZNF200   140000 perm   39 sec   (3585 perm/sec)   p_kst 4.778571e-03   p_cons 8.557929e-01   p_joint 3.789286e-02

Joint ci ratio: 5.366701e-02	ci left: 3.342413e-02	ci right 3.527392e-02	k: 5151	n:150000
Cons ci ratio: 4.156059e-03	ci left: 8.539316e-01	ci right 8.574946e-01	k: 128358	n:150000
KS ci ratio: 1.465587e-01	ci left: 4.398684e-03	ci right 5.100670e-03	k: 711	n:150000
ZNF200   150000 perm   42 sec   (3539 perm/sec)   p_kst 4.740000e-03   p_cons 8.557200e-01   p_joint 3.434000e-02

Joint ci ratio: 5.421237e-02	ci left: 3.078522e-02	ci right 3.250680e-02	k: 5062	n:160000
Cons ci ratio: 4.027567e-03	ci left: 8.537739e-01	ci right 8.572257e-01	k: 136881	n:160000
KS ci ratio: 1.419487e-01	ci left: 4.406917e-03	ci right 5.086221e-03	k: 758	n:160000
ZNF200   160000 perm   46 sec   (3458 perm/sec)   p_kst 4.737500e-03   p_cons 8.555063e-01   p_joint 3.163750e-02

Joint ci ratio: 5.452026e-02	ci left: 2.870657e-02	ci right 3.032129e-02	k: 5016	n:170000
Cons ci ratio: 3.910292e-03	ci left: 8.536364e-01	ci right 8.569867e-01	k: 145404	n:170000
KS ci ratio: 1.385272e-01	ci left: 4.363366e-03	ci right 5.018407e-03	k: 796	n:170000
ZNF200   170000 perm   50 sec   (3420 perm/sec)   p_kst 4.682353e-03   p_cons 8.553176e-01   p_joint 2.950588e-02

Joint ci ratio: 5.399333e-02	ci left: 2.768130e-02	ci right 2.922283e-02	k: 5120	n:180000
Cons ci ratio: 3.804057e-03	ci left: 8.534263e-01	ci right 8.566845e-01	k: 153911	n:180000
KS ci ratio: 1.338995e-01	ci left: 4.421477e-03	ci right 5.061301e-03	k: 852	n:180000
ZNF200   180000 perm   53 sec   (3383 perm/sec)   p_kst 4.733333e-03   p_cons 8.550611e-01   p_joint 2.844444e-02

Joint ci ratio: 5.134143e-02	ci left: 2.900361e-02	ci right 3.053710e-02	k: 5655	n:190000
Cons ci ratio: 3.704687e-03	ci left: 8.533294e-01	ci right 8.565018e-01	k: 162435	n:190000
KS ci ratio: 1.308688e-01	ci left: 4.392317e-03	ci right 5.012417e-03	k: 892	n:190000
ZNF200   190000 perm   57 sec   (3347 perm/sec)   p_kst 4.694737e-03   p_cons 8.549211e-01   p_joint 2.976316e-02

Joint ci ratio: 5.042545e-02	ci left: 2.858991e-02	ci right 3.007377e-02	k: 5865	n:200000
Cons ci ratio: 3.612207e-03	ci left: 8.532785e-01	ci right 8.563712e-01	k: 170966	n:200000
KS ci ratio: 1.278287e-01	ci left: 4.380743e-03	ci right 4.983752e-03	k: 935	n:200000
ZNF200   200000 perm   60 sec   (3308 perm/sec)   p_kst 4.675000e-03   p_cons 8.548300e-01   p_joint 2.932500e-02

Joint ci ratio: 4.898657e-02	ci left: 2.886513e-02	ci right 3.031932e-02	k: 6213	n:210000
Cons ci ratio: 3.522466e-03	ci left: 8.535059e-01	ci right 8.565224e-01	k: 179554	n:210000
KS ci ratio: 1.234177e-01	ci left: 4.485786e-03	ci right 5.080391e-03	k: 1003	n:210000
ZNF200   210000 perm   64 sec   (3264 perm/sec)   p_kst 4.776190e-03   p_cons 8.550190e-01   p_joint 2.958571e-02

Joint ci ratio: 4.861543e-02	ci left: 2.800626e-02	ci right 2.940619e-02	k: 6314	n:220000
Cons ci ratio: 3.439786e-03	ci left: 8.536632e-01	ci right 8.566092e-01	k: 188131	n:220000
KS ci ratio: 1.203968e-01	ci left: 4.506639e-03	ci right 5.088345e-03	k: 1054	n:220000
ZNF200   220000 perm   68 sec   (3228 perm/sec)   p_kst 4.790909e-03   p_cons 8.551409e-01   p_joint 2.870000e-02

Joint ci ratio: 4.818572e-02	ci left: 2.729519e-02	ci right 2.864717e-02	k: 6432	n:230000
Cons ci ratio: 3.364083e-03	ci left: 8.537028e-01	ci right 8.565839e-01	k: 196684	n:230000
KS ci ratio: 1.172682e-01	ci left: 4.551164e-03	ci right 5.122294e-03	k: 1111	n:230000
ZNF200   230000 perm   72 sec   (3191 perm/sec)   p_kst 4.830435e-03   p_cons 8.551478e-01   p_joint 2.796522e-02

Joint ci ratio: 4.707996e-02	ci left: 2.741363e-02	ci right 2.873947e-02	k: 6737	n:240000
Cons ci ratio: 3.291726e-03	ci left: 8.538485e-01	ci right 8.566679e-01	k: 205263	n:240000
KS ci ratio: 1.151661e-01	ci left: 4.527396e-03	ci right 5.084666e-03	k: 1152	n:240000
ZNF200   240000 perm   76 sec   (3155 perm/sec)   p_kst 4.800000e-03   p_cons 8.552625e-01   p_joint 2.807083e-02

Joint ci ratio: 4.613806e-02	ci left: 2.741612e-02	ci right 2.871485e-02	k: 7015	n:250000
Cons ci ratio: 3.222959e-03	ci left: 8.540514e-01	ci right 8.568124e-01	k: 213859	n:250000
KS ci ratio: 1.123256e-01	ci left: 4.575593e-03	ci right 5.123984e-03	k: 1211	n:250000
ZNF200   250000 perm   80 sec   (3120 perm/sec)   p_kst 4.844000e-03   p_cons 8.554360e-01   p_joint 2.806000e-02

Joint ci ratio: 4.499412e-02	ci left: 2.772679e-02	ci right 2.900683e-02	k: 7374	n:260000
Cons ci ratio: 3.164761e-03	ci left: 8.537334e-01	ci right 8.564433e-01	k: 222324	n:260000
KS ci ratio: 1.103857e-01	ci left: 4.560384e-03	ci right 5.096899e-03	k: 1254	n:260000
ZNF200   260000 perm   84 sec   (3078 perm/sec)   p_kst 4.823077e-03   p_cons 8.550923e-01   p_joint 2.836154e-02

Joint ci ratio: 4.317825e-02	ci left: 2.898225e-02	ci right 3.026491e-02	k: 7997	n:270000
Cons ci ratio: 3.103322e-03	ci left: 8.539413e-01	ci right 8.565992e-01	k: 230924	n:270000
KS ci ratio: 1.088382e-01	ci left: 4.521154e-03	ci right 5.045119e-03	k: 1290	n:270000
ZNF200   270000 perm   89 sec   (3041 perm/sec)   p_kst 4.777778e-03   p_cons 8.552741e-01   p_joint 2.961852e-02

Joint ci ratio: 4.040795e-02	ci left: 3.186040e-02	ci right 3.317787e-02	k: 9104	n:280000
Cons ci ratio: 3.050511e-03	ci left: 8.537119e-01	ci right 8.563236e-01	k: 239406	n:280000
KS ci ratio: 1.067495e-01	ci left: 4.536918e-03	ci right 5.051985e-03	k: 1341	n:280000
ZNF200   280000 perm   93 sec   (3003 perm/sec)   p_kst 4.789286e-03   p_cons 8.550214e-01   p_joint 3.251429e-02

Joint ci ratio: 4.000246e-02	ci left: 3.141020e-02	ci right 3.269572e-02	k: 9294	n:290000
Cons ci ratio: 2.999964e-03	ci left: 8.535263e-01	ci right 8.560941e-01	k: 247896	n:290000
KS ci ratio: 1.048522e-01	ci left: 4.544968e-03	ci right 5.051213e-03	k: 1390	n:290000
ZNF200   290000 perm   98 sec   (2967 perm/sec)   p_kst 4.793103e-03   p_cons 8.548138e-01   p_joint 3.204828e-02

Joint ci ratio: 3.935658e-02	ci left: 3.137966e-02	ci right 3.264273e-02	k: 9602	n:300000
Cons ci ratio: 2.947644e-03	ci left: 8.537082e-01	ci right 8.562316e-01	k: 256492	n:300000
KS ci ratio: 1.034505e-01	ci left: 4.516833e-03	ci right 5.012808e-03	k: 1428	n:300000
ZNF200   300000 perm   102 sec   (2934 perm/sec)   p_kst 4.760000e-03   p_cons 8.549733e-01   p_joint 3.200667e-02

Joint ci ratio: 3.884437e-02	ci left: 3.118828e-02	ci right 3.242694e-02	k: 9859	n:310000
Cons ci ratio: 2.900984e-03	ci left: 8.536196e-01	ci right 8.561028e-01	k: 265008	n:310000
KS ci ratio: 1.017555e-01	ci left: 4.521994e-03	ci right 5.009915e-03	k: 1476	n:310000
ZNF200   310000 perm   107 sec   (2898 perm/sec)   p_kst 4.761290e-03   p_cons 8.548645e-01   p_joint 3.180323e-02

Joint ci ratio: 3.813416e-02	ci left: 3.135573e-02	ci right 3.257777e-02	k: 10228	n:320000
Cons ci ratio: 2.856541e-03	ci left: 8.535307e-01	ci right 8.559754e-01	k: 273522	n:320000
KS ci ratio: 1.002404e-01	ci left: 4.517754e-03	ci right 4.997532e-03	k: 1521	n:320000
ZNF200   320000 perm   112 sec   (2864 perm/sec)   p_kst 4.753125e-03   p_cons 8.547562e-01   p_joint 3.196250e-02

Joint ci ratio: 3.748893e-02	ci left: 3.146817e-02	ci right 3.267340e-02	k: 10582	n:330000
Cons ci ratio: 2.812706e-03	ci left: 8.535690e-01	ci right 8.559762e-01	k: 282076	n:330000
KS ci ratio: 9.904535e-02	ci left: 4.490176e-03	ci right 4.961010e-03	k: 1558	n:330000
ZNF200   330000 perm   117 sec   (2830 perm/sec)   p_kst 4.721212e-03   p_cons 8.547758e-01   p_joint 3.206667e-02

Outputting figure to mutsig2_images.part000000000195/ZNF200.3_1204_330000_0.0047212_0.85478_0.032067.png
                gene_name: ZNF200
               theta_stop: 0.099 
                    nperm: 330000 
                     p_ks: 0.0047 
        ci_ks_bounds_left: 0.0045 
       ci_ks_bounds_right: 0.0050 
                   p_cons: 0.85 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.032 
     ci_joint_bounds_left: 0.031 
    ci_joint_bounds_right: 0.033 

Current progress: 25 percent done.
ZNF160
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.974662e-02	ci left: 4.831544e-01	ci right 5.028497e-01	k: 4930	n:10000
Cons ci ratio: 1.579881e-02	ci left: 8.533504e-01	ci right 8.670391e-01	k: 8603	n:10000
KS ci ratio: 1.250251e-01	ci left: 8.387799e-02	ci right 9.516246e-02	k: 894	n:10000
ZNF160   10000 perm   2 sec   (5473 perm/sec)   p_kst 8.940000e-02   p_cons 8.603000e-01   p_joint 4.930000e-01

Joint ci ratio: 2.087831e-02	ci left: 6.312950e-01	ci right 6.446649e-01	k: 12760	n:20000
Cons ci ratio: 1.120775e-02	ci left: 8.546067e-01	ci right 8.642886e-01	k: 17190	n:20000
KS ci ratio: 8.674154e-02	ci left: 8.861709e-02	ci right 9.670178e-02	k: 1852	n:20000
ZNF160   20000 perm   4 sec   (4885 perm/sec)   p_kst 9.260000e-02   p_cons 8.595000e-01   p_joint 6.380000e-01

Outputting figure to mutsig2_images.part000000000195/ZNF160.2_2473_20000_0.0926_0.8595_0.638.png
                gene_name: ZNF160
               theta_stop: 0.087 
                    nperm: 20000 
                     p_ks: 0.093 
        ci_ks_bounds_left: 0.089 
       ci_ks_bounds_right: 0.097 
                   p_cons: 0.86 
      ci_cons_bounds_left: 0.85 
     ci_cons_bounds_right: 0.86 
                  p_joint: 0.64 
     ci_joint_bounds_left: 0.63 
    ci_joint_bounds_right: 0.64 

Current progress: 50 percent done.
ZNF205
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.012596e-02	ci left: 7.833022e-01	ci right 7.993277e-01	k: 7914	n:10000
Cons ci ratio: 3.942995e-02	ci left: 4.871524e-01	ci right 5.068493e-01	k: 4970	n:10000
KS ci ratio: 3.979435e-02	ci left: 4.825547e-01	ci right 5.022497e-01	k: 4924	n:10000
ZNF205   10000 perm   2 sec   (5051 perm/sec)   p_kst 4.924000e-01   p_cons 4.970000e-01   p_joint 7.914000e-01

Outputting figure to mutsig2_images.part000000000195/ZNF205.2_1689_10000_0.4924_0.497_0.7914.png
                gene_name: ZNF205
               theta_stop: 0.040 
                    nperm: 10000 
                     p_ks: 0.49 
        ci_ks_bounds_left: 0.48 
       ci_ks_bounds_right: 0.50 
                   p_cons: 0.50 
      ci_cons_bounds_left: 0.49 
     ci_cons_bounds_right: 0.51 
                  p_joint: 0.79 
     ci_joint_bounds_left: 0.78 
    ci_joint_bounds_right: 0.80 

Current progress: 75 percent done.
ZNF207
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.771708e-02	ci left: 8.228987e-01	ci right 8.377084e-01	k: 8304	n:10000
Cons ci ratio: 4.060676e-02	ci left: 4.724627e-01	ci right 4.921476e-01	k: 4823	n:10000
KS ci ratio: 9.028637e-02	ci left: 1.513922e-01	ci right 1.658072e-01	k: 1585	n:10000
ZNF207   10000 perm   2 sec   (6162 perm/sec)   p_kst 1.585000e-01   p_cons 4.823000e-01   p_joint 8.304000e-01

Outputting figure to mutsig2_images.part000000000195/ZNF207.2_1533_10000_0.1585_0.4823_0.8304.png
                gene_name: ZNF207
               theta_stop: 0.090 
                    nperm: 10000 
                     p_ks: 0.16 
        ci_ks_bounds_left: 0.15 
       ci_ks_bounds_right: 0.17 
                   p_cons: 0.48 
      ci_cons_bounds_left: 0.47 
     ci_cons_bounds_right: 0.49 
                  p_joint: 0.83 
     ci_joint_bounds_left: 0.82 
    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.165.3896/
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/181708/iteration1/scatter.0000000195
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 195 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1539>
Subject: Job 1120369: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1539>, 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/181708/iteration1/scatter.0000000196> was used as the working directory.
Started at Wed Oct 10 10:45:55 2012
Results reported at Wed Oct 10 10:47:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000196.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000196.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 196  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    138.62 sec.
    Max Memory :      1051 MB
    Max Swap   :      3757 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.165.3896/
-whichjob
196
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 196: processing genes 17643 - 17732
Calculating significance of each gene.
Using projection method.
17643	ZNF257	1
17644	ZNF259	1
17645	ZNF260	1
17646	ZNF263	3.736129e-03
17647	ZNF264	1
17648	ZNF266	1
17649	ZNF267	1
17650	ZNF268	1
17651	ZNF273	1.398610e-01
17652	ZNF274	1
17653	ZNF275	4.312011e-02
17654	ZNF276	1
17655	ZNF277	1
17656	ZNF28	1
17657	ZNF280A	2.398081e-01
17658	ZNF280B	1
17659	ZNF280C	1
17660	ZNF280D	1
17661	ZNF281	1
17662	ZNF282	5.324014e-02
17663	ZNF283	1.346767e-01
17664	ZNF284	1
17665	ZNF285	1
17666	ZNF286A	1
17667	ZNF286B	1
17668	ZNF287	1
17669	ZNF292	5.252959e-01
17670	ZNF295	1
17671	ZNF296	8.381144e-02
17672	ZNF3	1
17673	ZNF30	1
17674	ZNF300	1
17675	ZNF302	1
17676	ZNF304	1
17677	ZNF311	1
17678	ZNF317	4.169017e-02
17679	ZNF318	1
17680	ZNF319	1.531028e-01
17681	ZNF32	1
17682	ZNF320	1
17683	ZNF321	1
17684	ZNF322A	1
17685	ZNF322B	1
17686	ZNF323	1
17687	ZNF324	1.745867e-01
17688	ZNF324B	1
17689	ZNF326	1
17690	ZNF329	1
17691	ZNF330	8.044774e-02
17692	ZNF331	1
17693	ZNF333	1
17694	ZNF334	1
17695	ZNF335	3.141943e-02
17696	ZNF337	1
17697	ZNF33A	1
17698	ZNF33B	1
17699	ZNF34	1
17700	ZNF341	1
17701	ZNF343	1
17702	ZNF345	1
17703	ZNF346	1
17704	ZNF347	1
17705	ZNF35	1
17706	ZNF350	1
17707	ZNF354A	1
17708	ZNF354B	1.909148e-01
17709	ZNF354C	9.825971e-03
17710	ZNF358	1
17711	ZNF362	1
17712	ZNF365	3.200371e-01
17713	ZNF366	1
17714	ZNF367	1
17715	ZNF37A	1
17716	ZNF382	1
17717	ZNF383	1
17718	ZNF384	6.363006e-02
17719	ZNF385A	1
17720	ZNF385B	1
17721	ZNF385D	1
17722	ZNF391	1
17723	ZNF394	1.655669e-01
17724	ZNF395	2.371681e-01
17725	ZNF396	1
17726	ZNF397	1
17727	ZNF397OS	2.485771e-01
17728	ZNF398	1
17729	ZNF404	9.495279e-02
17730	ZNF407	1
17731	ZNF408	1
17732	ZNF41	1
Done

Running MutSig 2:
Scatter job 196: processing genes 17643 - 17732
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF263
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.229471e-02	ci left: 2.189190e-01	ci right 2.354402e-01	k: 2271	n:10000
Cons ci ratio: 2.929540e-02	ci left: 6.321112e-01	ci right 6.510063e-01	k: 6416	n:10000
KS ci ratio: 1.650363e-01	ci left: 4.897794e-02	ci right 5.788448e-02	k: 533	n:10000
ZNF263   10000 perm   2 sec   (5124 perm/sec)   p_kst 5.330000e-02   p_cons 6.416000e-01   p_joint 2.271000e-01

Joint ci ratio: 7.090811e-02	ci left: 1.278300e-01	ci right 1.372771e-01	k: 2650	n:20000
Cons ci ratio: 2.065738e-02	ci left: 6.362141e-01	ci right 6.495443e-01	k: 12858	n:20000
KS ci ratio: 1.163560e-01	ci left: 5.056727e-02	ci right 5.686327e-02	k: 1073	n:20000
ZNF263   20000 perm   7 sec   (2775 perm/sec)   p_kst 5.365000e-02   p_cons 6.429000e-01   p_joint 1.325000e-01

Joint ci ratio: 5.819639e-02	ci left: 1.275304e-01	ci right 1.352078e-01	k: 3940	n:30000
Cons ci ratio: 1.683266e-02	ci left: 6.383842e-01	ci right 6.492546e-01	k: 19315	n:30000
KS ci ratio: 9.438741e-02	ci left: 5.179491e-02	ci right 5.695849e-02	k: 1630	n:30000
ZNF263   30000 perm   10 sec   (3119 perm/sec)   p_kst 5.433333e-02   p_cons 6.438333e-01   p_joint 1.313333e-01

Outputting figure to mutsig2_images.part000000000196/ZNF263.3_2076_30000_0.054333_0.64383_0.13133.png
                gene_name: ZNF263
               theta_stop: 0.094 
                    nperm: 30000 
                     p_ks: 0.054 
        ci_ks_bounds_left: 0.052 
       ci_ks_bounds_right: 0.057 
                   p_cons: 0.64 
      ci_cons_bounds_left: 0.64 
     ci_cons_bounds_right: 0.65 
                  p_joint: 0.13 
     ci_joint_bounds_left: 0.13 
    ci_joint_bounds_right: 0.14 

Current progress: 33 percent done.
ZNF335
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.583828e-02	ci left: 6.879873e-01	ci right 7.060978e-01	k: 6971	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: 2.781424e-02	ci left: 6.557528e-01	ci right 6.743510e-01	k: 6651	n:10000
ZNF335   10000 perm   2 sec   (4727 perm/sec)   p_kst 6.651000e-01   p_cons 3.932000e-01   p_joint 6.971000e-01

Outputting figure to mutsig2_images.part000000000196/ZNF335.3_4137_10000_0.6651_0.3932_0.6971.png
                gene_name: ZNF335
               theta_stop: 0.049 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.39 
      ci_cons_bounds_left: 0.38 
     ci_cons_bounds_right: 0.40 
                  p_joint: 0.70 
     ci_joint_bounds_left: 0.69 
    ci_joint_bounds_right: 0.71 

Current progress: 67 percent done.
ZNF354C
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.604643e-02	ci left: 6.845600e-01	ci right 7.027271e-01	k: 6937	n:10000
Cons ci ratio: 3.136703e-02	ci left: 5.999577e-01	ci right 6.191784e-01	k: 6096	n:10000
KS ci ratio: 2.468101e-02	ci left: 7.071507e-01	ci right 7.249233e-01	k: 7161	n:10000
ZNF354C   10000 perm   2 sec   (5998 perm/sec)   p_kst 7.161000e-01   p_cons 6.096000e-01   p_joint 6.937000e-01

Outputting figure to mutsig2_images.part000000000196/ZNF354C.2_1681_10000_0.7161_0.6096_0.6937.png
                gene_name: ZNF354C
               theta_stop: 0.031 
                    nperm: 10000 
                     p_ks: 0.72 
        ci_ks_bounds_left: 0.71 
       ci_ks_bounds_right: 0.72 
                   p_cons: 0.61 
      ci_cons_bounds_left: 0.60 
     ci_cons_bounds_right: 0.62 
                  p_joint: 0.69 
     ci_joint_bounds_left: 0.68 
    ci_joint_bounds_right: 0.70 

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.165.3896/
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/181708/iteration1/scatter.0000000196
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 196 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120373: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000197> was used as the working directory.
Started at Wed Oct 10 10:45:59 2012
Results reported at Wed Oct 10 10:48:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000197.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000197.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 197  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    210.96 sec.
    Max Memory :      1314 MB
    Max Swap   :      3821 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.165.3896/
-whichjob
197
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 197: processing genes 17733 - 17823
Calculating significance of each gene.
Using projection method.
17733	ZNF410	1.062212e-01
17734	ZNF414	1
17735	ZNF415	4.571642e-02
17736	ZNF416	1
17737	ZNF417	1
17738	ZNF418	3.972578e-02
17739	ZNF419	1.405036e-01
17740	ZNF420	1
17741	ZNF423	2.053816e-01
17742	ZNF425	1
17743	ZNF426	1
17744	ZNF428	1
17745	ZNF429	1
17746	ZNF43	1
17747	ZNF430	1
17748	ZNF431	1
17749	ZNF432	1
17750	ZNF433	1
17751	ZNF434	1
17752	ZNF436	1
17753	ZNF438	7.546357e-02
17754	ZNF439	1
17755	ZNF44	1
17756	ZNF440	1
17757	ZNF441	2.505593e-01
17758	ZNF442	1
17759	ZNF443	1
17760	ZNF445	1
17761	ZNF446	1
17762	ZNF449	1
17763	ZNF45	1
17764	ZNF451	1
17765	ZNF454	1
17766	ZNF460	1.863955e-01
17767	ZNF461	1.646573e-02
17768	ZNF462	7.460272e-01
17769	ZNF467	1
17770	ZNF468	1
17771	ZNF470	1
17772	ZNF471	2.197107e-01
17773	ZNF473	1
17774	ZNF474	1
17775	ZNF479	1
17776	ZNF48	1
17777	ZNF480	1
17778	ZNF483	1
17779	ZNF484	1
17780	ZNF485	1
17781	ZNF486	1
17782	ZNF488	1
17783	ZNF490	1
17784	ZNF491	1
17785	ZNF492	1
17786	ZNF493	2.335529e-01
17787	ZNF496	1
17788	ZNF497	1
17789	ZNF498	1
17790	ZNF500	1
17791	ZNF501	1
17792	ZNF502	1
17793	ZNF503	1
17794	ZNF506	1
17795	ZNF507	1.130004e-01
17796	ZNF510	2.582289e-01
17797	ZNF511	1
17798	ZNF512	9.063674e-02
17799	ZNF512B	1
17800	ZNF513	1.409932e-01
17801	ZNF514	1.873532e-01
17802	ZNF516	2.445265e-01
17803	ZNF517	1
17804	ZNF518A	4.632276e-02
17805	ZNF518B	1
17806	ZNF519	1.916418e-01
17807	ZNF521	1.826364e-01
17808	ZNF524	1
17809	ZNF526	1
17810	ZNF527	1.624062e-01
17811	ZNF528	1
17812	ZNF529	1
17813	ZNF530	1
17814	ZNF532	1.531762e-01
17815	ZNF534	1
17816	ZNF536	1.321573e-01
17817	ZNF540	1
17818	ZNF543	1
17819	ZNF544	2.916043e-01
17820	ZNF546	1
17821	ZNF547	1
17822	ZNF548	1
17823	ZNF549	1
Done

Running MutSig 2:
Scatter job 197: processing genes 17733 - 17823
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF418
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 7.100173e-02	ci left: 2.252368e-01	ci right 2.419187e-01	k: 2335	n:10000
Cons ci ratio: 8.173326e-02	ci left: 1.793015e-01	ci right 1.946813e-01	k: 1869	n:10000
KS ci ratio: 1.028651e-01	ci left: 1.202398e-01	ci right 1.333784e-01	k: 1267	n:10000
ZNF418   10000 perm   2 sec   (5277 perm/sec)   p_kst 1.267000e-01   p_cons 1.869000e-01   p_joint 2.335000e-01

Joint ci ratio: 4.380678e-02	ci left: 2.795947e-01	ci right 2.921676e-01	k: 5717	n:20000
Cons ci ratio: 5.669738e-02	ci left: 1.874020e-01	ci right 1.983874e-01	k: 3857	n:20000
KS ci ratio: 7.340230e-02	ci left: 1.202003e-01	ci right 1.294091e-01	k: 2495	n:20000
ZNF418   20000 perm   7 sec   (2897 perm/sec)   p_kst 1.247500e-01   p_cons 1.928500e-01   p_joint 2.858500e-01

Outputting figure to mutsig2_images.part000000000197/ZNF418.2_2043_20000_0.12475_0.19285_0.28585.png
                gene_name: ZNF418
               theta_stop: 0.073 
                    nperm: 20000 
                     p_ks: 0.12 
        ci_ks_bounds_left: 0.12 
       ci_ks_bounds_right: 0.13 
                   p_cons: 0.19 
      ci_cons_bounds_left: 0.19 
     ci_cons_bounds_right: 0.20 
                  p_joint: 0.29 
     ci_joint_bounds_left: 0.28 
    ci_joint_bounds_right: 0.29 

Current progress: 25 percent done.
ZNF461
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.753408e-02	ci left: 3.950588e-01	ci right 4.143968e-01	k: 4047	n:10000
Cons ci ratio: 4.198116e-02	ci left: 4.558845e-01	ci right 4.755355e-01	k: 4657	n:10000
KS ci ratio: 8.363681e-02	ci left: 1.725141e-01	ci right 1.876728e-01	k: 1800	n:10000
ZNF461   10000 perm   2 sec   (5712 perm/sec)   p_kst 1.800000e-01   p_cons 4.657000e-01   p_joint 4.047000e-01

Outputting figure to mutsig2_images.part000000000197/ZNF461.2_1712_10000_0.18_0.4657_0.4047.png
                gene_name: ZNF461
               theta_stop: 0.084 
                    nperm: 10000 
                     p_ks: 0.18 
        ci_ks_bounds_left: 0.17 
       ci_ks_bounds_right: 0.19 
                   p_cons: 0.47 
      ci_cons_bounds_left: 0.46 
     ci_cons_bounds_right: 0.48 
                  p_joint: 0.40 
     ci_joint_bounds_left: 0.40 
    ci_joint_bounds_right: 0.41 

Current progress: 50 percent done.
ZNF518A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.220289e-01	ci left: 1.224928e-02	ci right 1.703957e-02	k: 145	n:10000
Cons ci ratio: 1.595841e-01	ci left: 5.234307e-02	ci right 6.151717e-02	k: 568	n:10000
KS ci ratio: 2.173503e-01	ci left: 2.806894e-02	ci right 3.500749e-02	k: 314	n:10000
ZNF518A   10000 perm   2 sec   (4508 perm/sec)   p_kst 3.140000e-02   p_cons 5.680000e-02   p_joint 1.450000e-02

Joint ci ratio: 1.622704e-01	ci left: 2.604555e-02	ci right 3.069292e-02	k: 566	n:20000
Cons ci ratio: 1.131092e-01	ci left: 5.343714e-02	ci right 5.989251e-02	k: 1132	n:20000
KS ci ratio: 1.534422e-01	ci left: 2.917075e-02	ci right 3.406667e-02	k: 631	n:20000
ZNF518A   20000 perm   5 sec   (4127 perm/sec)   p_kst 3.155000e-02   p_cons 5.660000e-02   p_joint 2.830000e-02

Joint ci ratio: 1.363805e-01	ci left: 2.496955e-02	ci right 2.865619e-02	k: 803	n:30000
Cons ci ratio: 9.236837e-02	ci left: 5.401154e-02	ci right 5.927474e-02	k: 1698	n:30000
KS ci ratio: 1.244079e-01	ci left: 3.003717e-02	ci right 3.405413e-02	k: 960	n:30000
ZNF518A   30000 perm   8 sec   (3854 perm/sec)   p_kst 3.200000e-02   p_cons 5.660000e-02   p_joint 2.676667e-02

Joint ci ratio: 2.491573e-01	ci left: 5.383925e-03	ci right 6.939080e-03	k: 245	n:40000
Cons ci ratio: 8.550099e-02	ci left: 4.778644e-02	ci right 5.207920e-02	k: 1996	n:40000
KS ci ratio: 1.056026e-01	ci left: 3.153881e-02	ci right 3.507936e-02	k: 1331	n:40000
ZNF518A   40000 perm   11 sec   (3749 perm/sec)   p_kst 3.327500e-02   p_cons 4.990000e-02   p_joint 6.125000e-03

Joint ci ratio: 2.064334e-01	ci left: 6.420729e-03	ci right 7.917347e-03	k: 357	n:50000
Cons ci ratio: 7.615800e-02	ci left: 4.840040e-02	ci right 5.225203e-02	k: 2515	n:50000
KS ci ratio: 9.510600e-02	ci left: 3.129505e-02	ci right 3.443949e-02	k: 1642	n:50000
ZNF518A   50000 perm   14 sec   (3579 perm/sec)   p_kst 3.284000e-02   p_cons 5.030000e-02   p_joint 7.140000e-03

Joint ci ratio: 1.906042e-01	ci left: 6.332616e-03	ci right 7.682398e-03	k: 419	n:60000
Cons ci ratio: 6.582974e-02	ci left: 5.396015e-02	ci right 5.764963e-02	k: 3347	n:60000
KS ci ratio: 8.653865e-02	ci left: 3.163388e-02	ci right 3.451152e-02	k: 1983	n:60000
ZNF518A   60000 perm   17 sec   (3521 perm/sec)   p_kst 3.305000e-02   p_cons 5.578333e-02   p_joint 6.983333e-03

Joint ci ratio: 1.867166e-01	ci left: 5.672770e-03	ci right 6.854433e-03	k: 437	n:70000
Cons ci ratio: 6.094656e-02	ci left: 5.409683e-02	ci right 5.751154e-02	k: 3905	n:70000
KS ci ratio: 7.989943e-02	ci left: 3.191305e-02	ci right 3.458296e-02	k: 2326	n:70000
ZNF518A   70000 perm   20 sec   (3479 perm/sec)   p_kst 3.322857e-02   p_cons 5.578571e-02   p_joint 6.242857e-03

Joint ci ratio: 1.687490e-01	ci left: 6.134420e-03	ci right 7.276795e-03	k: 535	n:80000
Cons ci ratio: 5.715285e-02	ci left: 5.394802e-02	ci right 5.713431e-02	k: 4442	n:80000
KS ci ratio: 7.486193e-02	ci left: 3.189558e-02	ci right 3.438843e-02	k: 2650	n:80000
ZNF518A   80000 perm   24 sec   (3388 perm/sec)   p_kst 3.312500e-02   p_cons 5.552500e-02   p_joint 6.687500e-03

Joint ci ratio: 1.468458e-01	ci left: 7.278431e-03	ci right 8.442515e-03	k: 706	n:90000
Cons ci ratio: 5.389210e-02	ci left: 5.402396e-02	ci right 5.702700e-02	k: 4996	n:90000
KS ci ratio: 7.067098e-02	ci left: 3.188613e-02	ci right 3.423298e-02	k: 2974	n:90000
ZNF518A   90000 perm   27 sec   (3327 perm/sec)   p_kst 3.304444e-02   p_cons 5.551111e-02   p_joint 7.844444e-03

Joint ci ratio: 1.558075e-01	ci left: 5.799743e-03	ci right 6.789221e-03	k: 628	n:100000
Cons ci ratio: 5.106438e-02	ci left: 5.422718e-02	ci right 5.707866e-02	k: 5564	n:100000
KS ci ratio: 6.736709e-02	ci left: 3.164561e-02	ci right 3.386160e-02	k: 3274	n:100000
ZNF518A   100000 perm   30 sec   (3279 perm/sec)   p_kst 3.274000e-02   p_cons 5.564000e-02   p_joint 6.280000e-03

Joint ci ratio: 1.467428e-01	ci left: 5.972295e-03	ci right 6.926735e-03	k: 708	n:110000
Cons ci ratio: 4.874494e-02	ci left: 5.417216e-02	ci right 5.688770e-02	k: 6107	n:110000
KS ci ratio: 6.451491e-02	ci left: 3.142410e-02	ci right 3.352792e-02	k: 3571	n:110000
ZNF518A   110000 perm   34 sec   (3243 perm/sec)   p_kst 3.246364e-02   p_cons 5.551818e-02   p_joint 6.436364e-03

Joint ci ratio: 1.131178e-01	ci left: 9.347539e-03	ci right 1.047634e-02	k: 1188	n:120000
Cons ci ratio: 4.673391e-02	ci left: 5.408756e-02	ci right 5.668398e-02	k: 6645	n:120000
KS ci ratio: 6.192230e-02	ci left: 3.131506e-02	ci right 3.332429e-02	k: 3877	n:120000
ZNF518A   120000 perm   38 sec   (3190 perm/sec)   p_kst 3.230833e-02   p_cons 5.537500e-02   p_joint 9.900000e-03

Joint ci ratio: 1.094153e-01	ci left: 9.241685e-03	ci right 1.031881e-02	k: 1270	n:130000
Cons ci ratio: 4.510925e-02	ci left: 5.366025e-02	ci right 5.614427e-02	k: 7136	n:130000
KS ci ratio: 5.969278e-02	ci left: 3.114843e-02	ci right 3.307252e-02	k: 4173	n:130000
ZNF518A   130000 perm   41 sec   (3151 perm/sec)   p_kst 3.210000e-02   p_cons 5.489231e-02   p_joint 9.769231e-03

Joint ci ratio: 1.007718e-01	ci left: 1.015371e-02	ci right 1.123813e-02	k: 1496	n:140000
Cons ci ratio: 4.339971e-02	ci left: 5.386800e-02	ci right 5.626476e-02	k: 7708	n:140000
KS ci ratio: 5.742959e-02	ci left: 3.128142e-02	ci right 3.313802e-02	k: 4508	n:140000
ZNF518A   140000 perm   45 sec   (3121 perm/sec)   p_kst 3.220000e-02   p_cons 5.505714e-02   p_joint 1.068571e-02

Joint ci ratio: 1.018090e-01	ci left: 9.288150e-03	ci right 1.029093e-02	k: 1467	n:150000
Cons ci ratio: 4.200254e-02	ci left: 5.372615e-02	ci right 5.603776e-02	k: 8231	n:150000
KS ci ratio: 5.532315e-02	ci left: 3.148995e-02	ci right 3.328818e-02	k: 4857	n:150000
ZNF518A   150000 perm   49 sec   (3090 perm/sec)   p_kst 3.238000e-02   p_cons 5.487333e-02   p_joint 9.780000e-03

Joint ci ratio: 9.812987e-02	ci left: 9.390165e-03	ci right 1.036522e-02	k: 1579	n:160000
Cons ci ratio: 4.070510e-02	ci left: 5.367121e-02	ci right 5.590746e-02	k: 8765	n:160000
KS ci ratio: 5.357639e-02	ci left: 3.150693e-02	ci right 3.324757e-02	k: 5179	n:160000
ZNF518A   160000 perm   52 sec   (3058 perm/sec)   p_kst 3.236875e-02   p_cons 5.478125e-02   p_joint 9.868750e-03

Outputting figure to mutsig2_images.part000000000197/ZNF518A.2_4455_160000_0.032369_0.054781_0.0098688.png
                gene_name: ZNF518A
               theta_stop: 0.098 
                    nperm: 160000 
                     p_ks: 0.032 
        ci_ks_bounds_left: 0.032 
       ci_ks_bounds_right: 0.033 
                   p_cons: 0.055 
      ci_cons_bounds_left: 0.054 
     ci_cons_bounds_right: 0.056 
                  p_joint: 0.0099 
     ci_joint_bounds_left: 0.0094 
    ci_joint_bounds_right: 0.010 

Current progress: 75 percent done.
ZNF536
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.524022e-02	ci left: 6.978692e-01	ci right 7.158101e-01	k: 7069	n:10000
Cons ci ratio: 6.448821e-02	ci left: 2.610197e-01	ci right 2.785146e-01	k: 2697	n:10000
KS ci ratio: 6.553540e-02	ci left: 2.547867e-01	ci right 2.721513e-01	k: 2634	n:10000
ZNF536   10000 perm   2 sec   (5256 perm/sec)   p_kst 2.634000e-01   p_cons 2.697000e-01   p_joint 7.069000e-01

Outputting figure to mutsig2_images.part000000000197/ZNF536.2_3919_10000_0.2634_0.2697_0.7069.png
                gene_name: ZNF536
               theta_stop: 0.066 
                    nperm: 10000 
                     p_ks: 0.26 
        ci_ks_bounds_left: 0.25 
       ci_ks_bounds_right: 0.27 
                   p_cons: 0.27 
      ci_cons_bounds_left: 0.26 
     ci_cons_bounds_right: 0.28 
                  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.165.3896/
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/181708/iteration1/scatter.0000000197
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 197 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1531>
Subject: Job 1120377: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1531>, 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/181708/iteration1/scatter.0000000198> was used as the working directory.
Started at Wed Oct 10 10:45:59 2012
Results reported at Wed Oct 10 10:48:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000198.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000198.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 198  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    131.23 sec.
    Max Memory :      1312 MB
    Max Swap   :      3838 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.165.3896/
-whichjob
198
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 198: processing genes 17824 - 17913
Calculating significance of each gene.
Using projection method.
17824	ZNF550	1
17825	ZNF551	1
17826	ZNF552	1
17827	ZNF554	1
17828	ZNF555	1.827696e-03
17829	ZNF556	1
17830	ZNF557	1
17831	ZNF558	1
17832	ZNF559	1
17833	ZNF560	1
17834	ZNF561	1
17835	ZNF562	1.962876e-01
17836	ZNF563	1
17837	ZNF564	1
17838	ZNF565	1
17839	ZNF566	1
17840	ZNF567	9.877190e-02
17841	ZNF568	1
17842	ZNF569	2.152139e-01
17843	ZNF57	1.902316e-01
17844	ZNF570	1
17845	ZNF571	1
17846	ZNF572	1
17847	ZNF573	9.458922e-02
17848	ZNF574	1
17849	ZNF575	5.488274e-02
17850	ZNF576	1
17851	ZNF577	1
17852	ZNF578	1
17853	ZNF581	1
17854	ZNF582	1.740814e-01
17855	ZNF583	1
17856	ZNF584	1
17857	ZNF585A	1
17858	ZNF585B	1
17859	ZNF586	1
17860	ZNF587	1
17861	ZNF589	1
17862	ZNF592	1
17863	ZNF593	1
17864	ZNF594	7.305974e-02
17865	ZNF595	8.602646e-02
17866	ZNF596	1
17867	ZNF597	4.108662e-02
17868	ZNF598	1
17869	ZNF599	1
17870	ZNF600	1
17871	ZNF605	1
17872	ZNF606	1.223948e-01
17873	ZNF607	7.581605e-02
17874	ZNF608	3.566289e-01
17875	ZNF609	3.460197e-01
17876	ZNF610	1
17877	ZNF611	1
17878	ZNF613	4.307857e-02
17879	ZNF614	1
17880	ZNF615	1
17881	ZNF616	2.060321e-01
17882	ZNF618	1
17883	ZNF619	1
17884	ZNF620	2.096097e-01
17885	ZNF621	1
17886	ZNF622	1
17887	ZNF623	1
17888	ZNF624	1
17889	ZNF625	1
17890	ZNF626	1
17891	ZNF627	1
17892	ZNF628	1
17893	ZNF629	9.752041e-02
17894	ZNF630	1
17895	ZNF638	3.930002e-01
17896	ZNF639	6.510780e-02
17897	ZNF641	1.655852e-01
17898	ZNF642	1
17899	ZNF643	1
17900	ZNF644	1.119595e-01
17901	ZNF645	1
17902	ZNF646	1
17903	ZNF648	1
17904	ZNF649	1
17905	ZNF652	1
17906	ZNF653	1
17907	ZNF654	1
17908	ZNF655	1
17909	ZNF658	1
17910	ZNF660	1
17911	ZNF662	1
17912	ZNF664	1
17913	ZNF665	1
Done

Running MutSig 2:
Scatter job 198: processing genes 17824 - 17913
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF555
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 2.475992e-02	ci left: 7.058389e-01	ci right 7.236358e-01	k: 7148	n:10000
Cons ci ratio: 1.719903e-02	ci left: 8.312409e-01	ci right 8.457613e-01	k: 8386	n:10000
KS ci ratio: 3.874217e-02	ci left: 4.959503e-01	ci right 5.156463e-01	k: 5058	n:10000
ZNF555   10000 perm   2 sec   (4998 perm/sec)   p_kst 5.058000e-01   p_cons 8.386000e-01   p_joint 7.148000e-01

Outputting figure to mutsig2_images.part000000000198/ZNF555.3_1903_10000_0.5058_0.8386_0.7148.png
                gene_name: ZNF555
               theta_stop: 0.039 
                    nperm: 10000 
                     p_ks: 0.51 
        ci_ks_bounds_left: 0.50 
       ci_ks_bounds_right: 0.52 
                   p_cons: 0.84 
      ci_cons_bounds_left: 0.83 
     ci_cons_bounds_right: 0.85 
                  p_joint: 0.71 
     ci_joint_bounds_left: 0.71 
    ci_joint_bounds_right: 0.72 

Current progress: 25 percent done.
ZNF594
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.104297e-01	ci left: 1.056875e-01	ci right 1.181396e-01	k: 1118	n:10000
Cons ci ratio: 1.544678e-01	ci left: 5.580941e-02	ci right 6.524862e-02	k: 604	n:10000
KS ci ratio: 3.166431e-02	ci left: 5.954396e-01	ci right 6.146991e-01	k: 6051	n:10000
ZNF594   10000 perm   2 sec   (5005 perm/sec)   p_kst 6.051000e-01   p_cons 6.040000e-02   p_joint 1.118000e-01

Joint ci ratio: 8.702652e-02	ci left: 8.807791e-02	ci right 9.614113e-02	k: 1841	n:20000
Cons ci ratio: 1.085607e-01	ci left: 5.786828e-02	ci right 6.455999e-02	k: 1223	n:20000
KS ci ratio: 2.237250e-02	ci left: 5.986866e-01	ci right 6.122828e-01	k: 12110	n:20000
ZNF594   20000 perm   4 sec   (4782 perm/sec)   p_kst 6.055000e-01   p_cons 6.115000e-02   p_joint 9.205000e-02

Joint ci ratio: 4.067541e-02	ci left: 2.315682e-01	ci right 2.412163e-01	k: 7091	n:30000
Cons ci ratio: 8.825665e-02	ci left: 5.897053e-02	ci right 6.444807e-02	k: 1850	n:30000
KS ci ratio: 1.820246e-02	ci left: 6.016468e-01	ci right 6.127324e-01	k: 18216	n:30000
ZNF594   30000 perm   6 sec   (4689 perm/sec)   p_kst 6.072000e-01   p_cons 6.166667e-02   p_joint 2.363667e-01

Outputting figure to mutsig2_images.part000000000198/ZNF594.2_2428_30000_0.6072_0.061667_0.23637.png
                gene_name: ZNF594
               theta_stop: 0.088 
                    nperm: 30000 
                     p_ks: 0.61 
        ci_ks_bounds_left: 0.60 
       ci_ks_bounds_right: 0.61 
                   p_cons: 0.062 
      ci_cons_bounds_left: 0.059 
     ci_cons_bounds_right: 0.064 
                  p_joint: 0.24 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.24 

Current progress: 50 percent done.
ZNF644
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.614730e-02	ci left: 3.184024e-01	ci right 3.368981e-01	k: 3276	n:10000
Cons ci ratio: 2.657465e-02	ci left: 6.758935e-01	ci right 6.941986e-01	k: 6851	n:10000
KS ci ratio: 9.371625e-02	ci left: 1.418777e-01	ci right 1.559275e-01	k: 1488	n:10000
ZNF644   10000 perm   2 sec   (4230 perm/sec)   p_kst 1.488000e-01   p_cons 6.851000e-01   p_joint 3.276000e-01

Outputting figure to mutsig2_images.part000000000198/ZNF644.2_4004_10000_0.1488_0.6851_0.3276.png
                gene_name: ZNF644
               theta_stop: 0.094 
                    nperm: 10000 
                     p_ks: 0.15 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.16 
                   p_cons: 0.69 
      ci_cons_bounds_left: 0.68 
     ci_cons_bounds_right: 0.69 
                  p_joint: 0.33 
     ci_joint_bounds_left: 0.32 
    ci_joint_bounds_right: 0.34 

Current progress: 75 percent done.
ZNF655
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: 2.894603e-02	ci left: 6.376421e-01	ci right 6.564722e-01	k: 6471	n:10000
KS ci ratio: 3.316256e-02	ci left: 5.730625e-01	ci right 5.924892e-01	k: 5828	n:10000
ZNF655   10000 perm   2 sec   (5938 perm/sec)   p_kst 5.828000e-01   p_cons 6.471000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000198/ZNF655.2_2015_10000_0.5828_0.6471_1.png
                gene_name: ZNF655
               theta_stop: 0.033 
                    nperm: 10000 
                     p_ks: 0.58 
        ci_ks_bounds_left: 0.57 
       ci_ks_bounds_right: 0.59 
                   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.165.3896/
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/181708/iteration1/scatter.0000000198
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 198 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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@node1532>
Subject: Job 1120380: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1532>, 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/181708/iteration1/scatter.0000000199> was used as the working directory.
Started at Wed Oct 10 10:45:59 2012
Results reported at Wed Oct 10 10:48:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000199.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000199.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 199  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :    141.65 sec.
    Max Memory :      1346 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.165.3896/
-whichjob
199
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 199: processing genes 17914 - 18004
Calculating significance of each gene.
Using projection method.
17914	ZNF667	1
17915	ZNF668	7.635000e-02
17916	ZNF669	1
17917	ZNF670	1
17918	ZNF671	2.688975e-02
17919	ZNF672	1
17920	ZNF673	1
17921	ZNF674	1
17922	ZNF675	1
17923	ZNF676	1
17924	ZNF677	1.808362e-01
17925	ZNF678	1
17926	ZNF679	1
17927	ZNF680	1
17928	ZNF681	2.375795e-01
17929	ZNF682	1
17930	ZNF683	1
17931	ZNF684	1
17932	ZNF687	1
17933	ZNF688	1
17934	ZNF689	2.132564e-01
17935	ZNF69	1
17936	ZNF691	1
17937	ZNF692	1
17938	ZNF695	2.051530e-01
17939	ZNF696	1
17940	ZNF697	1
17941	ZNF699	1
17942	ZNF7	2.964502e-01
17943	ZNF70	1.152089e-01
17944	ZNF700	1
17945	ZNF701	1
17946	ZNF704	1
17947	ZNF705A	1
17948	ZNF705D	1
17949	ZNF706	1
17950	ZNF707	1
17951	ZNF708	1
17952	ZNF709	1
17953	ZNF71	1
17954	ZNF710	2.496512e-02
17955	ZNF711	1
17956	ZNF713	2.006179e-01
17957	ZNF714	3.645001e-02
17958	ZNF716	1
17959	ZNF718	1
17960	ZNF720	1
17961	ZNF721	1
17962	ZNF727	1.225767e-01
17963	ZNF732	1
17964	ZNF735	5.997485e-02
17965	ZNF736	1
17966	ZNF737	2.202836e-01
17967	ZNF74	1.802891e-01
17968	ZNF740	1
17969	ZNF746	1
17970	ZNF747	1
17971	ZNF749	1
17972	ZNF750	1
17973	ZNF75A	1
17974	ZNF75D	7.523871e-03
17975	ZNF76	1
17976	ZNF761	1
17977	ZNF763	1
17978	ZNF764	1
17979	ZNF765	1.288450e-01
17980	ZNF766	1
17981	ZNF768	9.437421e-02
17982	ZNF77	1
17983	ZNF770	1
17984	ZNF772	1
17985	ZNF773	1
17986	ZNF774	1
17987	ZNF775	1
17988	ZNF776	1
17989	ZNF777	1.113646e-01
17990	ZNF778	1
17991	ZNF780A	2.143983e-01
17992	ZNF780B	1
17993	ZNF781	1
17994	ZNF782	1
17995	ZNF784	1
17996	ZNF785	1
17997	ZNF786	1
17998	ZNF787	1
17999	ZNF789	1
18000/18094 18000	ZNF79	1
18001	ZNF790	1.986408e-01
18002	ZNF791	1
18003	ZNF792	1
18004	ZNF793	1.613449e-01
Done

Running MutSig 2:
Scatter job 199: processing genes 17914 - 18004
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF671
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.904642e-02	ci left: 3.801249e-01	ci right 3.993394e-01	k: 3897	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: 7.021762e-02	ci left: 2.291867e-01	ci right 2.459664e-01	k: 2375	n:10000
ZNF671   10000 perm   2 sec   (4622 perm/sec)   p_kst 2.375000e-01   p_cons 5.982000e-01   p_joint 3.897000e-01

Outputting figure to mutsig2_images.part000000000199/ZNF671.3_1621_10000_0.2375_0.5982_0.3897.png
                gene_name: ZNF671
               theta_stop: 0.070 
                    nperm: 10000 
                     p_ks: 0.24 
        ci_ks_bounds_left: 0.23 
       ci_ks_bounds_right: 0.25 
                   p_cons: 0.60 
      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: 25 percent done.
ZNF681
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: 1.178264e-02	ci left: 9.116264e-01	ci right 9.225292e-01	k: 9172	n:10000
ZNF681   10000 perm   2 sec   (6143 perm/sec)   p_kst 9.172000e-01   p_cons 8.254000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000199/ZNF681.3_1954_10000_0.9172_0.8254_1.png
                gene_name: ZNF681
               theta_stop: 0.018 
                    nperm: 10000 
                     p_ks: 0.92 
        ci_ks_bounds_left: 0.91 
       ci_ks_bounds_right: 0.92 
                   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.
ZNF710
Processing conservation and coverage...
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: 1.927855e-01	ci left: 3.586235e-02	ci right 4.360871e-02	k: 396	n:10000
KS ci ratio: 9.780389e-02	ci left: 1.315900e-01	ci right 1.452214e-01	k: 1383	n:10000
ZNF710   10000 perm   2 sec   (5797 perm/sec)   p_kst 1.383000e-01   p_cons 3.960000e-02   p_joint 4.085000e-01

Joint ci ratio: 4.616244e-02	ci left: 2.588434e-01	ci right 2.711250e-01	k: 5299	n:20000
Cons ci ratio: 1.387992e-01	ci left: 3.568248e-02	ci right 4.105279e-02	k: 766	n:20000
KS ci ratio: 6.855648e-02	ci left: 1.356621e-01	ci right 1.453426e-01	k: 2809	n:20000
ZNF710   20000 perm   4 sec   (5127 perm/sec)   p_kst 1.404500e-01   p_cons 3.830000e-02   p_joint 2.649500e-01

Joint ci ratio: 7.645430e-02	ci left: 7.747815e-02	ci right 8.367003e-02	k: 2416	n:30000
Cons ci ratio: 1.150301e-01	ci left: 3.511911e-02	ci right 3.943776e-02	k: 1117	n:30000
KS ci ratio: 5.608486e-02	ci left: 1.360919e-01	ci right 1.439780e-01	k: 4200	n:30000
ZNF710   30000 perm   6 sec   (4778 perm/sec)   p_kst 1.400000e-01   p_cons 3.723333e-02   p_joint 8.053333e-02

Joint ci ratio: 3.562077e-02	ci left: 2.282431e-01	ci right 2.365458e-01	k: 9295	n:40000
Cons ci ratio: 9.971205e-02	ci left: 3.534213e-02	ci right 3.907544e-02	k: 1487	n:40000
KS ci ratio: 4.852741e-02	ci left: 1.368360e-01	ci right 1.436663e-01	k: 5609	n:40000
ZNF710   40000 perm   9 sec   (4605 perm/sec)   p_kst 1.402250e-01   p_cons 3.717500e-02   p_joint 2.323750e-01

Outputting figure to mutsig2_images.part000000000199/ZNF710.2_2011_40000_0.14022_0.037175_0.23237.png
                gene_name: ZNF710
               theta_stop: 0.100 
                    nperm: 40000 
                     p_ks: 0.14 
        ci_ks_bounds_left: 0.14 
       ci_ks_bounds_right: 0.14 
                   p_cons: 0.037 
      ci_cons_bounds_left: 0.035 
     ci_cons_bounds_right: 0.039 
                  p_joint: 0.23 
     ci_joint_bounds_left: 0.23 
    ci_joint_bounds_right: 0.24 

Current progress: 75 percent done.
ZNF75D
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: 1.269826e-01	ci left: 8.144990e-02	ci right 9.259206e-02	k: 869	n:10000
KS ci ratio: 2.409930e-02	ci left: 7.168405e-01	ci right 7.344279e-01	k: 7257	n:10000
ZNF75D   10000 perm   2 sec   (6000 perm/sec)   p_kst 7.257000e-01   p_cons 8.690000e-02   p_joint 1.027000e-01

Joint ci ratio: 8.784308e-02	ci left: 8.655862e-02	ci right 9.456088e-02	k: 1810	n:20000
Cons ci ratio: 9.268048e-02	ci left: 7.828247e-02	ci right 8.593954e-02	k: 1641	n:20000
KS ci ratio: 1.687853e-02	ci left: 7.232855e-01	ci right 7.356477e-01	k: 14590	n:20000
ZNF75D   20000 perm   4 sec   (5247 perm/sec)   p_kst 7.295000e-01   p_cons 8.205000e-02   p_joint 9.050000e-02

Outputting figure to mutsig2_images.part000000000199/ZNF75D.2_1553_20000_0.7295_0.08205_0.0905.png
                gene_name: ZNF75D
               theta_stop: 0.093 
                    nperm: 20000 
                     p_ks: 0.73 
        ci_ks_bounds_left: 0.72 
       ci_ks_bounds_right: 0.74 
                   p_cons: 0.082 
      ci_cons_bounds_left: 0.078 
     ci_cons_bounds_right: 0.086 
                  p_joint: 0.090 
     ci_joint_bounds_left: 0.087 
    ci_joint_bounds_right: 0.095 

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.165.3896/
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/181708/iteration1/scatter.0000000199
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 199 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 1120384: <scatter_181708> Done

Job <scatter_181708> was submitted from host <node439> 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/181708/iteration1/scatter.0000000200> was used as the working directory.
Started at Wed Oct 10 10:46:08 2012
Results reported at Wed Oct 10 13:41:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000200.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/181708/iteration1/scatter.0000000200.tries
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/run_matlab.py --with-display /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 200  -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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/181708/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   :  10662.68 sec.
    Max Memory :      1545 MB
    Max Swap   :      3924 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.165.3896/
-whichjob
200
-i
BLCA
-maf
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
-ppr
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
-cov
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
-cat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt
-pat
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
-genes
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
-b
hg19
-genesets
/xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
-cosmic
/xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
-refseq
/xchip/cga1/annotation/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: './BLCA.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 "BLCA"
Loading coverage... 

The following 768 genes have very low coverage and are being omitted:
    'A2LD1'            [     0]
    'AG2'              [     0]
    'AGAP4'            [     0]
    'AGBL3'            [     0]
    'AMY1A'            [0.1465]
    'AMY1B'            [0.1465]
    'AMY1C'            [0.1465]
    'ANKRD18A'         [0.1322]
    'ANKRD20A2'        [0.0827]
    'ANKRD20A3'        [0.1556]
    'ANKRD31'          [     0]
    'ANKRD33B'         [     0]
    'ANKRD34C'         [     0]
    'ANKRD43'          [0.2170]
    'ANKRD58'          [0.1089]
    'ANKRD9'           [0.1052]
    'ANXA8'            [     0]
    'ANXA8L1'          [     0]
    'ANXA8L2'          [0.0618]
    'APLN'             [     0]
    'ARHGAP23'         [     0]
    'ARHGAP40'         [     0]
    'ARHGAP42'         [     0]
    'ARHGEF33'         [     0]
    'ARL17A'           [     0]
    'ARL17B'           [     0]
    'ARL5C'            [     0]
    'ARX'              [0.1451]
    'ASAH2B'           [0.1714]
    'ASCL2'            [     0]
    'ATXN1L'           [     0]
    'ATXN7L1'          [0.1738]
    'ATXN7L3B'         [     0]
    'B3GALT6'          [0.1710]
    'BBC3'             [0.2352]
    'BCORL2'           [     0]
    'BEAN'             [     0]
    'BET3L'            [     0]
    'BHLHA15'          [     0]
    'BHLHA9'           [     0]
    '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]
    'C10orf95'         [0.2253]
    'C11orf21'         [     0]
    'C11orf34'         [     0]
    'C11orf86'         [     0]
    'C11orf90'         [     0]
    'C11orf91'         [     0]
    'C11orf93'         [     0]
    'C11orf95'         [     0]
    'C12orf70'         [     0]
    'C12orf73'         [     0]
    'C12orf75'         [     0]
    'C13orf38'         [     0]
    'C14orf176'        [     0]
    'C14orf38'         [     0]
    'C14orf80'         [0.2261]
    'C15orf61'         [     0]
    'C15orf62'         [     0]
    'C16orf52'         [     0]
    'C16orf74'         [0.1301]
    'C17orf105'        [     0]
    'C17orf106'        [     0]
    'C17orf107'        [     0]
    'C17orf51'         [     0]
    'C17orf72'         [     0]
    'C17orf89'         [0.1434]
    'C17orf96'         [     0]
    'C17orf97'         [     0]
    'C17orf99'         [     0]
    'C19orf20'         [0.0867]
    'C19orf24'         [0.0102]
    'C19orf25'         [0.0677]
    'C19orf38'         [     0]
    'C19orf69'         [     0]
    'C19orf71'         [     0]
    'C19orf76'         [0.1647]
    'C19orf77'         [     0]
    'C1orf185'         [     0]
    'C1orf204'         [     0]
    'C1orf212'         [0.1886]
    'C1orf223'         [     0]
    'C1orf228'         [     0]
    'C1orf229'         [     0]
    'C1orf230'         [     0]
    'C1orf68'          [     0]
    'C1orf70'          [     0]
    'C20orf123'        [     0]
    'C20orf144'        [0.2483]
    'C20orf173'        [     0]
    'C20orf201'        [0.1997]
    'C20orf202'        [     0]
    'C20orf203'        [     0]
    'C22orf26'         [     0]
    'C22orf30'         [0.1178]
    'C22orf41'         [     0]
    'C22orf46'         [     0]
    'C2CD4A'           [0.2369]
    'C2CD4B'           [0.0360]
    'C2CD4C'           [     0]
    'C2CD4D'           [     0]
    'C2orf27A'         [0.0532]
    'C2orf27B'         [0.0796]
    'C2orf72'          [     0]
    'C2orf74'          [     0]
    'C2orf81'          [     0]
    'C2orf82'          [     0]
    'C3orf16'          [     0]
    'C3orf77'          [     0]
    'C3orf78'          [     0]
    'C4A'              [0.1166]
    'C4B'              [0.1166]
    'C4orf47'          [     0]
    'C4orf48'          [     0]
    'C4orf52'          [     0]
    'C5orf47'          [     0]
    'C5orf52'          [     0]
    'C5orf60'          [     0]
    'C6orf103'         [     0]
    'C6orf132'         [     0]
    'C6orf141'         [     0]
    'C6orf163'         [     0]
    'C6orf52'          [     0]
    'C6orf94'          [     0]
    'C7orf71'          [     0]
    'C7orf72'          [     0]
    'C8orf30A'         [0.0462]
    'C8orf48'          [     0]
    'C8orf55'          [0.1784]
    'C8orf83'          [     0]
    'C9orf144B'        [     0]
    'C9orf169'         [     0]
    'C9orf57'          [     0]
    'CALHM3'           [     0]
    'CAPN14'           [     0]
    'CAPN8'            [     0]
    'CBWD3'            [0.1719]
    'CBWD5'            [0.2317]
    'CBY3'             [     0]
    'CCDC152'          [     0]
    'CCDC154'          [     0]
    'CCDC160'          [0.2425]
    'CCDC42B'          [     0]
    'CCDC79'           [     0]
    'CCDC85B'          [0.1473]
    'CCDC85C'          [     0]
    'CCL3L1'           [     0]
    'CCL3L3'           [     0]
    'CCL4L1'           [0.1631]
    'CCL4L2'           [0.1631]
    'CD24'             [     0]
    'CDC42EP5'         [     0]
    'CDHR4'            [0.1755]
    'CDKN1C'           [0.1404]
    'CDR2L'            [0.2434]
    'CDY1'             [     0]
    'CDY1B'            [     0]
    'CDY2A'            [     0]
    'CDY2B'            [     0]
    'CEBPA'            [0.2355]
    'CFC1'             [0.1323]
    'CFC1B'            [0.1323]
    'CHADL'            [0.0136]
    'CHIC1'            [0.1768]
    'CHST7'            [0.2278]
    'CISD3'            [     0]
    'CITED4'           [     0]
    'CLDN23'           [0.2442]
    'CLDN24'           [     0]
    'CLEC2A'           [     0]
    'CPSF4L'           [     0]
    'CSAG2'            [     0]
    'CSAG3'            [     0]
    'CT45A1'           [0.1069]
    'CT45A2'           [     0]
    'CT45A3'           [     0]
    'CT45A4'           [     0]
    'CT45A6'           [     0]
    'CT47A1'           [0.0036]
    'CT47A10'          [     0]
    'CT47A11'          [     0]
    'CT47A2'           [     0]
    'CT47A3'           [     0]
    'CT47A4'           [     0]
    'CT47A5'           [     0]
    'CT47A6'           [0.0288]
    'CT47A7'           [     0]
    'CT47A8'           [     0]
    'CT47A9'           [     0]
    'CTAG1A'           [     0]
    'CTAG1B'           [     0]
    'CTAGE4'           [0.1429]
    'CTF1'             [0.2166]
    'CTRB1'            [0.2405]
    'CTRB2'            [0.2440]
    'CTU1'             [0.0465]
    'CTXN2'            [     0]
    'CXorf30'          [     0]
    'CXorf49'          [     0]
    'CXorf49B'         [     0]
    'CXorf51'          [     0]
    'CXorf64'          [     0]
    'CYS1'             [0.1406]
    'DACT2'            [     0]
    'DACT3'            [0.1383]
    'DAZ1'             [     0]
    'DAZ2'             [0.0385]
    'DAZ3'             [0.0505]
    'DAZ4'             [0.0282]
    'DDT'              [0.2144]
    'DEFB103A'         [     0]
    'DEFB103B'         [     0]
    'DEFB105A'         [0.1872]
    'DEFB105B'         [0.1872]
    'DEFB107A'         [0.0812]
    'DEFB107B'         [0.0812]
    'DEFB130'          [     0]
    'DEFB133'          [     0]
    'DKFZP781G0119'    [     0]
    'DMRTC1'           [0.0780]
    'DMRTC1B'          [0.0780]
    'DNAH12'           [0.1440]
    'DNAH14'           [0.0512]
    'DNAH6'            [0.1047]
    'DOC2B'            [     0]
    'DPCR1'            [0.2040]
    'DTHD1'            [     0]
    'DUX4'             [     0]
    'EBF4'             [0.0262]
    'EFCAB9'           [     0]
    'EFR3B'            [     0]
    'EIF3C'            [0.0751]
    'EIF3CL'           [0.0751]
    'ELFN1'            [0.0086]
    'EML6'             [     0]
    'EXOSC6'           [0.0969]
    'EYS'              [0.1907]
    'F8A1'             [     0]
    'F8A2'             [0.0508]
    'F8A3'             [     0]
    'FAM149B1'         [     0]
    'FAM156A'          [     0]
    'FAM156B'          [     0]
    'FAM157A'          [     0]
    'FAM157B'          [     0]
    'FAM159B'          [     0]
    'FAM160A1'         [     0]
    'FAM163B'          [0.0348]
    'FAM170B'          [     0]
    'FAM171A2'         [     0]
    'FAM178B'          [0.1866]
    'FAM180B'          [     0]
    'FAM184B'          [     0]
    'FAM185A'          [     0]
    'FAM186A'          [     0]
    'FAM189A1'         [     0]
    'FAM194B'          [     0]
    'FAM196B'          [     0]
    'FAM198A'          [     0]
    'FAM200A'          [0.1236]
    'FAM200B'          [     0]
    'FAM20C'           [0.2175]
    'FAM22A'           [0.1885]
    'FAM22D'           [0.2396]
    'FAM23A'           [0.0708]
    'FAM25A'           [     0]
    'FAM25B'           [     0]
    'FAM25C'           [     0]
    'FAM25G'           [     0]
    'FAM38A'           [     0]
    'FAM38B'           [0.2081]
    'FAM47E'           [     0]
    'FAM59B'           [     0]
    'FAM71E2'          [     0]
    'FAM75A1'          [0.2031]
    'FAM75A2'          [0.2031]
    'FAM75A3'          [0.1100]
    'FAM75A5'          [0.0563]
    'FAM75A7'          [0.0563]
    'FAM90A10'         [     0]
    'FAM90A13'         [     0]
    'FAM90A14'         [     0]
    'FAM90A18'         [     0]
    'FAM90A19'         [     0]
    'FAM90A20'         [     0]
    'FAM90A5'          [     0]
    'FAM90A7'          [     0]
    'FAM90A8'          [     0]
    'FAM90A9'          [     0]
    'FBRSL1'           [     0]
    'FHAD1'            [     0]
    'FIGNL2'           [0.0944]
    'FLJ25363'         [     0]
    'FLJ36031'         [0.2384]
    'FLJ43859'         [0.1773]
    'FLJ44082'         [0.1383]
    'FLJ44606'         [     0]
    'FOXD1'            [0.2451]
    'FOXD4L2'          [     0]
    'FOXD4L4'          [     0]
    'FOXD4L6'          [0.0824]
    'FOXI2'            [0.2108]
    'FOXI3'            [0.1168]
    'FRAT1'            [0.1826]
    'FRAT2'            [0.0872]
    'FREM3'            [     0]
    'FRG2'             [0.1030]
    'FRG2C'            [     0]
    'FSD1L'            [     0]
    'FSIP2'            [0.2296]
    'GAGE12B'          [     0]
    'GAGE12C'          [     0]
    'GAGE12D'          [     0]
    'GAGE12E'          [     0]
    'GAGE12F'          [     0]
    'GAGE12G'          [     0]
    'GAGE12H'          [     0]
    'GAGE12I'          [     0]
    'GAGE12J'          [0.2325]
    'GAGE2A'           [0.0769]
    'GAGE2B'           [0.2044]
    'GAGE2C'           [0.0511]
    'GAGE2D'           [     0]
    'GAGE2E'           [0.1746]
    'GAGE4'            [     0]
    'GAGE5'            [     0]
    'GAGE6'            [     0]
    'GAGE7'            [     0]
    'GAGE8'            [0.1735]
    'GATSL1'           [     0]
    'GATSL2'           [0.0769]
    'GCNT7'            [     0]
    'GDF1'             [0.0536]
    'GFRA4'            [0.1477]
    'GIYD1'            [0.1495]
    'GIYD2'            [0.1495]
    'GJD3'             [0.1864]
    'GLTSCR1'          [0.2387]
    'GLYATL3'          [     0]
    'GOLGA6B'          [0.2211]
    'GOLGA6L1'         [0.0230]
    'GOLGA6L10'        [0.0080]
    'GOLGA6L6'         [0.0141]
    'GOLGA6L9'         [     0]
    'GOLGA8A'          [0.1538]
    'GOLGA8B'          [0.1561]
    'GP1BB'            [0.0230]
    'GPR144'           [     0]
    'GPR44'            [0.2469]
    'GPR89C'           [     0]
    'GRAPL'            [     0]
    'GREB1L'           [     0]
    'GRID2IP'          [     0]
    'GRRP1'            [0.1683]
    'GSC'              [0.2185]
    'GSC2'             [0.2007]
    'GSTT1'            [     0]
    'GSTT2'            [0.2303]
    'GSTT2B'           [0.1582]
    'GTF2H2'           [0.1208]
    'H2AFB2'           [     0]
    'H2BFM'            [0.0371]
    'HBZ'              [0.2255]
    'HEATR7A'          [0.2401]
    'HES2'             [0.2026]
    '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]
    'HSFX1'            [     0]
    'HSFX2'            [     0]
    'HSFY1'            [     0]
    'HSFY2'            [     0]
    'HSPB6'            [     0]
    'ID4'              [0.1637]
    'IFFO2'            [0.0875]
    'IGFN1'            [0.2418]
    'IKBKG'            [0.1908]
    'IL11'             [0.2364]
    'IQCF5'            [     0]
    'IQCF6'            [     0]
    'IRGM'             [     0]
    'KBTBD11'          [     0]
    'KBTBD13'          [0.1745]
    'KCP'              [     0]
    'KIAA0040'         [     0]
    'KIAA1107'         [     0]
    'KIAA1239'         [     0]
    'KIAA1671'         [     0]
    'KIAA1731'         [0.0125]
    'KIF26A'           [0.2171]
    'KILLIN'           [     0]
    'KISS1R'           [0.1465]
    'KLF2'             [0.2024]
    'KLHL29'           [     0]
    'KLHL33'           [     0]
    'KPNA7'            [     0]
    'KRTAP2-1'         [     0]
    'KRTAP2-2'         [     0]
    'KRTAP2-4'         [     0]
    'KRTAP20-3'        [     0]
    'KRTAP21-3'        [     0]
    'KRTAP22-2'        [     0]
    'KRTAP25-1'        [     0]
    'KRTAP7-1'         [     0]
    'LCE3B'            [     0]
    'LCE3C'            [     0]
    'LCE6A'            [     0]
    'LEUTX'            [     0]
    'LIMS3'            [     0]
    'LIPM'             [0.1090]
    'LIPT2'            [     0]
    'LOC100128071'     [     0]
    'LOC100128542'     [0.0631]
    'LOC100130274'     [     0]
    'LOC100130933'     [     0]
    'LOC100131801'     [     0]
    'LOC100132247'     [0.2157]
    'LOC100132963'     [     0]
    'LOC100133893'     [     0]
    'LOC100287428'     [     0]
    'LOC100287718'     [     0]
    'LOC100288797'     [     0]
    'LOC200030'        [0.0489]
    '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'        [0.1608]
    'LOC401097'        [     0]
    'LOC401387'        [     0]
    'LOC402778'        [     0]
    'LOC441056'        [     0]
    'LOC441294'        [     0]
    'LOC441869'        [     0]
    'LOC642597'        [     0]
    'LOC643008'        [     0]
    'LOC643596'        [     0]
    'LOC643677'        [     0]
    'LOC644538'        [     0]
    'LOC646627'        [     0]
    'LOC646851'        [     0]
    'LOC647309'        [     0]
    'LOC653543'        [     0]
    'LOC653544'        [0.0284]
    'LOC653545'        [0.0284]
    'LOC653548'        [0.0284]
    'LOC728392'        [     0]
    'LOC728410'        [0.0320]
    'LOC729991'        [     0]
    'LOC730755'        [     0]
    'LOR'              [0.1839]
    'LOXHD1'           [     0]
    'LRRC10B'          [     0]
    'LRRC26'           [0.0094]
    'LRRC37A'          [0.0734]
    'LRRC69'           [     0]
    'LUZP6'            [     0]
    'LYL1'             [0.1564]
    'MAFA'             [0.1939]
    'MAGEA2'           [     0]
    'MAGEA2B'          [     0]
    'MAGEA9'           [0.0599]
    'MAGEA9B'          [0.0599]
    'MAGED4'           [     0]
    'MAGED4B'          [     0]
    'MAP6D1'           [0.2085]
    'MARVELD1'         [     0]
    'MBD3L2'           [     0]
    'MBD3L3'           [     0]
    'MBD3L4'           [     0]
    'MBD3L5'           [0.0708]
    'MBOAT4'           [     0]
    'MESP1'            [0.1584]
    'METTL11B'         [     0]
    'MMP23B'           [     0]
    'MORN2'            [     0]
    'MRC1'             [0.2025]
    'MRC1L1'           [0.2025]
    'MRGPRG'           [     0]
    'MUC12'            [     0]
    'MYADML2'          [     0]
    'NACAD'            [     0]
    'NAIP'             [0.1527]
    'NANOS1'           [0.1994]
    'NAT14'            [0.0538]
    'NBPF11'           [0.0489]
    'NBPF4'            [     0]
    'NBPF6'            [0.0522]
    'NEURL1B'          [     0]
    'NHSL1'            [     0]
    'NKX1-2'           [     0]
    'NKX2-4'           [0.2466]
    'NKX2-6'           [     0]
    'NKX2-8'           [0.0814]
    'NOTO'             [     0]
    'NPIPL3'           [0.1178]
    'NXF2'             [0.1241]
    'NXF2B'            [0.1241]
    'NYX'              [0.2245]
    'OLIG1'            [0.2112]
    'ONECUT3'          [0.0559]
    'OR2T35'           [0.2095]
    'OR4C45'           [0.0656]
    'OR4F16'           [     0]
    'OR4F21'           [     0]
    'OR4F29'           [     0]
    'OR4F3'            [     0]
    'OR6P1'            [     0]
    'OST4'             [     0]
    'OTUD1'            [     0]
    'PABPC1L2A'        [0.0370]
    'PABPC1L2B'        [     0]
    'PABPC4L'          [     0]
    'PALM3'            [     0]
    'PARG'             [0.1731]
    'PATE3'            [     0]
    'PATE4'            [     0]
    'PATL2'            [     0]
    'PCSK1N'           [0.0576]
    'PDF'              [0.2385]
    'PET117'           [     0]
    'PGA4'             [     0]
    'PHGR1'            [     0]
    'PHOX2A'           [0.2313]
    'PKD1L3'           [     0]
    'PL-5283'          [     0]
    'PLGLB1'           [0.2025]
    'PLGLB2'           [0.2025]
    'PNMA6A'           [     0]
    'PNRC2'            [0.0755]
    'POLR2J3'          [0.1507]
    'POM121L2'         [     0]
    'POTEB'            [0.1701]
    'POTED'            [0.0383]
    'PPIAL4A'          [0.1259]
    'PPIAL4B'          [0.1259]
    'PPIAL4C'          [     0]
    'PPIAL4D'          [     0]
    'PPIAL4F'          [     0]
    'PPP1R3G'          [     0]
    'PRAMEF15'         [     0]
    'PRAMEF20'         [0.1230]
    'PRAMEF21'         [0.1230]
    'PRAMEF22'         [0.1880]
    'PRAMEF3'          [     0]
    'PRAMEF5'          [0.0218]
    'PRAMEF6'          [0.1714]
    'PRAMEF7'          [0.2290]
    'PRAMEF8'          [0.1527]
    'PRAMEF9'          [     0]
    'PRDM6'            [     0]
    'PRR20A'           [     0]
    'PRR20B'           [     0]
    'PRR20C'           [     0]
    'PRR20D'           [     0]
    'PRR20E'           [     0]
    'PRR24'            [     0]
    'PRRT4'            [     0]
    'PRSS41'           [     0]
    'PRY'              [     0]
    'PRY2'             [     0]
    'PSMG4'            [     0]
    'PTGER1'           [0.2206]
    'PTPN20A'          [0.0800]
    'PTPN20B'          [0.0800]
    'PTPRQ'            [     0]
    'R3HCC1'           [     0]
    'RAD21L1'          [     0]
    'RASA4'            [0.1290]
    'RBM20'            [     0]
    'RBMXL3'           [     0]
    'RBMY1A1'          [0.0866]
    'RBMY1B'           [0.1001]
    'RBMY1D'           [0.1001]
    'RBMY1E'           [0.0821]
    'RBMY1F'           [0.0338]
    'RBMY1J'           [0.0338]
    'RESP18'           [     0]
    'REXO1L1'          [0.0688]
    'RFPL4A'           [     0]
    'RFX8'             [     0]
    'RGPD1'            [0.1513]
    'RGPD2'            [0.1507]
    'RGPD5'            [0.1699]
    'RGPD6'            [     0]
    'RGS9BP'           [0.2378]
    'RGSL1'            [     0]
    'RHOXF2'           [0.2245]
    'RHOXF2B'          [0.2245]
    'RIMBP3'           [0.2263]
    'RIMBP3B'          [0.0159]
    'RIMBP3C'          [0.0159]
    'RNF187'           [     0]
    'RNF222'           [     0]
    'RPS17'            [     0]
    'RTL1'             [0.2459]
    'SAP25'            [     0]
    'SCAND1'           [0.2228]
    'SCT'              [     0]
    'SCXA'             [     0]
    'SCXB'             [     0]
    'SDHAF1'           [     0]
    'SERF1A'           [     0]
    'SERF1B'           [     0]
    'SETD1B'           [     0]
    'SFRS13A'          [0.1052]
    'SFT2D3'           [     0]
    'SH3D20'           [0.1272]
    'SHISA6'           [     0]
    'SHISA7'           [     0]
    'SHISA9'           [     0]
    'SLC15A5'          [     0]
    'SLC22A18AS'       [     0]
    'SLC22A24'         [0.1937]
    'SLC25A29'         [0.1678]
    'SLFN14'           [     0]
    'SMN1'             [0.0303]
    'SMN2'             [0.0297]
    'SP9'              [0.1041]
    'SPACA5'           [0.1035]
    'SPACA5B'          [0.1035]
    'SPANXA1'          [     0]
    'SPANXA2'          [     0]
    'SPANXB1'          [     0]
    'SPANXB2'          [     0]
    'SPANXF1'          [     0]
    'SPATA24'          [     0]
    'SPATA3'           [     0]
    'SPDYE2'           [0.1155]
    'SPDYE2L'          [0.1155]
    'SPINT3'           [     0]
    'SPRN'             [     0]
    'SRRM5'            [0.0844]
    'SSC5D'            [     0]
    'SSX2'             [     0]
    'SSX2B'            [     0]
    'SSX4'             [0.0953]
    'SSX4B'            [0.0953]
    'STAG3L1'          [0.0744]
    'STAG3L3'          [0.2030]
    'STARD9'           [     0]
    'SULT1A3'          [0.0151]
    'SULT1A4'          [0.0151]
    'SYCE1L'           [     0]
    'TARM1'            [     0]
    'TBC1D3'           [0.1582]
    'TBC1D3C'          [     0]
    'TBC1D3F'          [0.1582]
    'TBC1D3G'          [0.2444]
    'TBC1D3H'          [0.0106]
    'TCF15'            [0.0129]
    'TDRD12'           [     0]
    'TEX28'            [     0]
    'TIGD1'            [     0]
    'TLCD2'            [     0]
    'TMEM114'          [     0]
    'TMEM121'          [0.2149]
    'TMEM129'          [0.1997]
    'TMEM132C'         [0.0776]
    'TMEM151B'         [     0]
    'TMEM158'          [     0]
    'TMEM160'          [0.1794]
    'TMEM194B'         [     0]
    'TMEM212'          [     0]
    'TMEM229A'         [     0]
    'TMEM232'          [     0]
    'TMEM233'          [     0]
    'TMEM88B'          [     0]
    'TMPRSS11BNL'      [     0]
    'TOMM6'            [     0]
    'TP53TG3'          [     0]
    'TP53TG3B'         [     0]
    'TRIM43B'          [     0]
    'TRIM49L'          [0.0207]
    'TRIM64'           [     0]
    'TRIM64B'          [     0]
    'TRIM66'           [     0]
    'TRIM77'           [     0]
    'TRNP1'            [     0]
    'TSPY3'            [0.0755]
    'TSPY4'            [0.0931]
    'TSTD1'            [     0]
    'TTC28'            [     0]
    'TUSC1'            [     0]
    'TXNRD3'           [     0]
    'UBE2QL1'          [     0]
    'UNC80'            [0.0867]
    'UPF0639'          [     0]
    'UPK3BL'           [     0]
    'URB1'             [     0]
    'USP17'            [0.0322]
    'USP27X'           [0.1217]
    'UTF1'             [     0]
    'VCY'              [     0]
    'VCY1B'            [     0]
    'VSIG10L'          [     0]
    'VSTM2B'           [     0]
    'VWA5B1'           [     0]
    'VWA5B2'           [     0]
    'VWDE'             [     0]
    'WASH1'            [0.1258]
    'WDFY4'            [     0]
    'WDR87'            [     0]
    'XAGE1A'           [     0]
    'XAGE1B'           [     0]
    'XAGE1C'           [     0]
    'XAGE1D'           [     0]
    'XAGE1E'           [     0]
    'XAGE2'            [     0]
    'XAGE2B'           [     0]
    'XKRY'             [     0]
    'XKRY2'            [     0]
    'ZAR1L'            [     0]
    'ZBED3'            [     0]
    'ZBED5'            [     0]
    'ZBED6'            [     0]
    'ZBTB42'           [     0]
    'ZBTB8B'           [     0]
    'ZFP62'            [0.0092]
    'ZFP92'            [     0]
    'ZG16'             [     0]
    'ZNF26'            [     0]
    'ZNF389'           [0.1426]
    'ZNF444'           [0.1924]
    'ZNF469'           [     0]
    'ZNF541'           [     0]
    'ZNF579'           [0.2304]
    'ZNF580'           [0.2121]
    'ZNF703'           [0.2233]
    'ZNF705G'          [     0]
    'ZNF717'           [     0]
    'ZNF771'           [0.1636]
    'ZNF826'           [     0]
    'ZNF837'           [     0]
    'ZNF84'            [     0]
    'ZNF843'           [     0]
    'ZNF853'           [     0]
    'ZNF879'           [0.0757]
    'ZSCAN23'          [0.2283]
    'ZSWIM6'           [     0]
    'ZYG11A'           [     0]

The above 768 genes have very low coverage and are being omitted.
Loading gene list... 

The following 768 genes are being omittted because coverage is zero/redacted:
    'A2LD1'
    'AG2'
    'AGAP4'
    'AGBL3'
    'AMY1A'
    'AMY1B'
    'AMY1C'
    'ANKRD18A'
    'ANKRD20A2'
    'ANKRD20A3'
    'ANKRD31'
    'ANKRD33B'
    'ANKRD34C'
    'ANKRD43'
    'ANKRD58'
    'ANKRD9'
    'ANXA8'
    'ANXA8L1'
    'ANXA8L2'
    'APLN'
    'ARHGAP23'
    'ARHGAP40'
    'ARHGAP42'
    'ARHGEF33'
    'ARL17A'
    'ARL17B'
    'ARL5C'
    'ARX'
    'ASAH2B'
    'ASCL2'
    'ATXN1L'
    'ATXN7L1'
    'ATXN7L3B'
    'B3GALT6'
    'BBC3'
    'BCORL2'
    'BEAN'
    'BET3L'
    'BHLHA15'
    'BHLHA9'
    'BOLA2'
    'BOLA2B'
    'BOP1'
    'BPY2'
    'BPY2B'
    'BPY2C'
    'BSPH1'
    'BTBD18'
    'BTBD19'
    'C10orf105'
    'C10orf122'
    'C10orf131'
    'C10orf95'
    'C11orf21'
    'C11orf34'
    'C11orf86'
    'C11orf90'
    'C11orf91'
    'C11orf93'
    'C11orf95'
    'C12orf70'
    'C12orf73'
    'C12orf75'
    'C13orf38'
    'C14orf176'
    'C14orf38'
    'C14orf80'
    'C15orf61'
    'C15orf62'
    'C16orf52'
    'C16orf74'
    'C17orf105'
    'C17orf106'
    'C17orf107'
    'C17orf51'
    'C17orf72'
    'C17orf89'
    'C17orf96'
    'C17orf97'
    'C17orf99'
    'C19orf20'
    'C19orf24'
    'C19orf25'
    'C19orf38'
    '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'
    'C5orf47'
    'C5orf52'
    'C5orf60'
    'C6orf103'
    'C6orf132'
    'C6orf141'
    'C6orf163'
    'C6orf52'
    'C6orf94'
    'C7orf71'
    'C7orf72'
    'C8orf30A'
    'C8orf48'
    'C8orf55'
    'C8orf83'
    'C9orf144B'
    'C9orf169'
    'C9orf57'
    'CALHM3'
    'CAPN14'
    'CAPN8'
    'CBWD3'
    'CBWD5'
    'CBY3'
    'CCDC152'
    'CCDC154'
    'CCDC160'
    'CCDC42B'
    'CCDC79'
    'CCDC85B'
    'CCDC85C'
    'CCL3L1'
    'CCL3L3'
    'CCL4L1'
    'CCL4L2'
    'CD24'
    'CDC42EP5'
    'CDHR4'
    'CDKN1C'
    'CDR2L'
    'CDY1'
    'CDY1B'
    'CDY2A'
    'CDY2B'
    'CEBPA'
    'CFC1'
    'CFC1B'
    'CHADL'
    'CHIC1'
    'CHST7'
    'CISD3'
    'CITED4'
    'CLDN23'
    'CLDN24'
    'CLEC2A'
    'CPSF4L'
    'CSAG2'
    'CSAG3'
    'CT45A1'
    'CT45A2'
    'CT45A3'
    'CT45A4'
    'CT45A6'
    'CT47A1'
    'CT47A10'
    'CT47A11'
    'CT47A2'
    'CT47A3'
    'CT47A4'
    'CT47A5'
    'CT47A6'
    'CT47A7'
    'CT47A8'
    'CT47A9'
    'CTAG1A'
    'CTAG1B'
    'CTAGE4'
    'CTF1'
    'CTRB1'
    'CTRB2'
    'CTU1'
    'CTXN2'
    'CXorf30'
    'CXorf49'
    'CXorf49B'
    'CXorf51'
    'CXorf64'
    'CYS1'
    'DACT2'
    'DACT3'
    'DAZ1'
    'DAZ2'
    'DAZ3'
    'DAZ4'
    'DDT'
    'DEFB103A'
    'DEFB103B'
    'DEFB105A'
    'DEFB105B'
    'DEFB107A'
    'DEFB107B'
    'DEFB130'
    'DEFB133'
    'DKFZP781G0119'
    'DMRTC1'
    'DMRTC1B'
    'DNAH12'
    'DNAH14'
    'DNAH6'
    'DOC2B'
    'DPCR1'
    'DTHD1'
    'DUX4'
    'EBF4'
    'EFCAB9'
    'EFR3B'
    'EIF3C'
    'EIF3CL'
    'ELFN1'
    'EML6'
    'EXOSC6'
    'EYS'
    'F8A1'
    'F8A2'
    'F8A3'
    'FAM149B1'
    'FAM156A'
    'FAM156B'
    'FAM157A'
    'FAM157B'
    'FAM159B'
    'FAM160A1'
    'FAM163B'
    'FAM170B'
    'FAM171A2'
    'FAM178B'
    'FAM180B'
    'FAM184B'
    'FAM185A'
    'FAM186A'
    'FAM189A1'
    'FAM194B'
    'FAM196B'
    'FAM198A'
    'FAM200A'
    'FAM200B'
    'FAM20C'
    'FAM22A'
    'FAM22D'
    'FAM23A'
    'FAM25A'
    'FAM25B'
    'FAM25C'
    'FAM25G'
    'FAM38A'
    'FAM38B'
    'FAM47E'
    'FAM59B'
    'FAM71E2'
    'FAM75A1'
    'FAM75A2'
    'FAM75A3'
    'FAM75A5'
    'FAM75A7'
    'FAM90A10'
    'FAM90A13'
    'FAM90A14'
    'FAM90A18'
    'FAM90A19'
    'FAM90A20'
    'FAM90A5'
    'FAM90A7'
    'FAM90A8'
    'FAM90A9'
    'FBRSL1'
    'FHAD1'
    'FIGNL2'
    'FLJ25363'
    'FLJ36031'
    'FLJ43859'
    'FLJ44082'
    'FLJ44606'
    'FOXD1'
    'FOXD4L2'
    'FOXD4L4'
    'FOXD4L6'
    'FOXI2'
    'FOXI3'
    'FRAT1'
    'FRAT2'
    'FREM3'
    'FRG2'
    'FRG2C'
    'FSD1L'
    'FSIP2'
    'GAGE12B'
    'GAGE12C'
    'GAGE12D'
    'GAGE12E'
    'GAGE12F'
    'GAGE12G'
    'GAGE12H'
    'GAGE12I'
    'GAGE12J'
    'GAGE2A'
    'GAGE2B'
    'GAGE2C'
    'GAGE2D'
    'GAGE2E'
    'GAGE4'
    'GAGE5'
    'GAGE6'
    'GAGE7'
    'GAGE8'
    'GATSL1'
    'GATSL2'
    'GCNT7'
    'GDF1'
    'GFRA4'
    'GIYD1'
    'GIYD2'
    'GJD3'
    'GLTSCR1'
    'GLYATL3'
    'GOLGA6B'
    'GOLGA6L1'
    'GOLGA6L10'
    'GOLGA6L6'
    'GOLGA6L9'
    'GOLGA8A'
    'GOLGA8B'
    'GP1BB'
    'GPR144'
    'GPR44'
    'GPR89C'
    'GRAPL'
    'GREB1L'
    'GRID2IP'
    'GRRP1'
    'GSC'
    'GSC2'
    'GSTT1'
    'GSTT2'
    'GSTT2B'
    'GTF2H2'
    'H2AFB2'
    'H2BFM'
    'HBZ'
    'HEATR7A'
    'HES2'
    'HGC6.3'
    'HHLA1'
    'HIST2H2AA3'
    'HIST2H2AA4'
    'HIST2H3A'
    'HIST2H3C'
    'HIST2H4A'
    'HIST2H4B'
    'HMGXB3'
    'HRK'
    'HRNBP3'
    'HSBP1L1'
    'HSFX1'
    'HSFX2'
    'HSFY1'
    'HSFY2'
    'HSPB6'
    'ID4'
    'IFFO2'
    'IGFN1'
    'IKBKG'
    'IL11'
    'IQCF5'
    'IQCF6'
    'IRGM'
    'KBTBD11'
    'KBTBD13'
    'KCP'
    'KIAA0040'
    'KIAA1107'
    'KIAA1239'
    'KIAA1671'
    'KIAA1731'
    'KIF26A'
    'KILLIN'
    'KISS1R'
    'KLF2'
    'KLHL29'
    'KLHL33'
    'KPNA7'
    'KRTAP2-1'
    'KRTAP2-2'
    'KRTAP2-4'
    'KRTAP20-3'
    'KRTAP21-3'
    'KRTAP22-2'
    'KRTAP25-1'
    'KRTAP7-1'
    'LCE3B'
    'LCE3C'
    'LCE6A'
    'LEUTX'
    'LIMS3'
    'LIPM'
    'LIPT2'
    'LOC100128071'
    'LOC100128542'
    'LOC100130274'
    'LOC100130933'
    'LOC100131801'
    'LOC100132247'
    'LOC100132963'
    'LOC100133893'
    'LOC100287428'
    'LOC100287718'
    'LOC100288797'
    'LOC200030'
    'LOC221710'
    'LOC283999'
    'LOC339047'
    'LOC342346'
    'LOC360030'
    'LOC375190'
    'LOC388588'
    'LOC388946'
    'LOC389333'
    'LOC389493'
    'LOC390595'
    'LOC391322'
    'LOC400696'
    'LOC401097'
    'LOC401387'
    'LOC402778'
    'LOC441056'
    'LOC441294'
    'LOC441869'
    'LOC642597'
    'LOC643008'
    'LOC643596'
    'LOC643677'
    'LOC644538'
    'LOC646627'
    'LOC646851'
    'LOC647309'
    'LOC653543'
    'LOC653544'
    'LOC653545'
    'LOC653548'
    'LOC728392'
    'LOC728410'
    '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'
    'METTL11B'
    'MMP23B'
    'MORN2'
    'MRC1'
    'MRC1L1'
    'MRGPRG'
    'MUC12'
    'MYADML2'
    'NACAD'
    'NAIP'
    'NANOS1'
    'NAT14'
    'NBPF11'
    'NBPF4'
    'NBPF6'
    'NEURL1B'
    'NHSL1'
    'NKX1-2'
    'NKX2-4'
    'NKX2-6'
    'NKX2-8'
    'NOTO'
    'NPIPL3'
    'NXF2'
    'NXF2B'
    'NYX'
    'OLIG1'
    'ONECUT3'
    'OR2T35'
    'OR4C45'
    'OR4F16'
    'OR4F21'
    'OR4F29'
    'OR4F3'
    'OR6P1'
    'OST4'
    'OTUD1'
    'PABPC1L2A'
    'PABPC1L2B'
    'PABPC4L'
    'PALM3'
    'PARG'
    'PATE3'
    'PATE4'
    'PATL2'
    'PCSK1N'
    'PDF'
    'PET117'
    'PGA4'
    'PHGR1'
    'PHOX2A'
    'PKD1L3'
    'PL-5283'
    'PLGLB1'
    'PLGLB2'
    'PNMA6A'
    'PNRC2'
    'POLR2J3'
    'POM121L2'
    'POTEB'
    'POTED'
    'PPIAL4A'
    'PPIAL4B'
    'PPIAL4C'
    'PPIAL4D'
    'PPIAL4F'
    'PPP1R3G'
    'PRAMEF15'
    'PRAMEF20'
    'PRAMEF21'
    'PRAMEF22'
    'PRAMEF3'
    'PRAMEF5'
    'PRAMEF6'
    'PRAMEF7'
    'PRAMEF8'
    'PRAMEF9'
    'PRDM6'
    'PRR20A'
    'PRR20B'
    'PRR20C'
    'PRR20D'
    'PRR20E'
    'PRR24'
    'PRRT4'
    'PRSS41'
    'PRY'
    'PRY2'
    'PSMG4'
    'PTGER1'
    'PTPN20A'
    'PTPN20B'
    'PTPRQ'
    'R3HCC1'
    'RAD21L1'
    'RASA4'
    'RBM20'
    'RBMXL3'
    'RBMY1A1'
    'RBMY1B'
    'RBMY1D'
    'RBMY1E'
    'RBMY1F'
    'RBMY1J'
    'RESP18'
    'REXO1L1'
    'RFPL4A'
    'RFX8'
    'RGPD1'
    'RGPD2'
    'RGPD5'
    'RGPD6'
    'RGS9BP'
    'RGSL1'
    'RHOXF2'
    'RHOXF2B'
    'RIMBP3'
    'RIMBP3B'
    'RIMBP3C'
    'RNF187'
    'RNF222'
    'RPS17'
    'RTL1'
    'SAP25'
    'SCAND1'
    'SCT'
    'SCXA'
    'SCXB'
    'SDHAF1'
    'SERF1A'
    'SERF1B'
    'SETD1B'
    'SFRS13A'
    'SFT2D3'
    'SH3D20'
    'SHISA6'
    'SHISA7'
    'SHISA9'
    'SLC15A5'
    'SLC22A18AS'
    'SLC22A24'
    'SLC25A29'
    'SLFN14'
    'SMN1'
    'SMN2'
    'SP9'
    'SPACA5'
    'SPACA5B'
    'SPANXA1'
    'SPANXA2'
    'SPANXB1'
    'SPANXB2'
    'SPANXF1'
    'SPATA24'
    'SPATA3'
    'SPDYE2'
    'SPDYE2L'
    'SPINT3'
    'SPRN'
    'SRRM5'
    'SSC5D'
    'SSX2'
    'SSX2B'
    'SSX4'
    'SSX4B'
    'STAG3L1'
    'STAG3L3'
    'STARD9'
    'SULT1A3'
    'SULT1A4'
    'SYCE1L'
    'TARM1'
    'TBC1D3'
    'TBC1D3C'
    'TBC1D3F'
    'TBC1D3G'
    'TBC1D3H'
    'TCF15'
    'TDRD12'
    'TEX28'
    'TIGD1'
    'TLCD2'
    'TMEM114'
    'TMEM121'
    'TMEM129'
    'TMEM132C'
    'TMEM151B'
    'TMEM158'
    'TMEM160'
    'TMEM194B'
    'TMEM212'
    'TMEM229A'
    'TMEM232'
    'TMEM233'
    'TMEM88B'
    'TMPRSS11BNL'
    'TOMM6'
    'TP53TG3'
    'TP53TG3B'
    'TRIM43B'
    'TRIM49L'
    'TRIM64'
    'TRIM64B'
    'TRIM66'
    'TRIM77'
    'TRNP1'
    'TSPY3'
    'TSPY4'
    'TSTD1'
    'TTC28'
    'TUSC1'
    'TXNRD3'
    'UBE2QL1'
    'UNC80'
    'UPF0639'
    'UPK3BL'
    'URB1'
    'USP17'
    'USP27X'
    'UTF1'
    'VCY'
    'VCY1B'
    'VSIG10L'
    'VSTM2B'
    'VWA5B1'
    'VWA5B2'
    'VWDE'
    'WASH1'
    'WDFY4'
    'WDR87'
    'XAGE1A'
    'XAGE1B'
    'XAGE1C'
    'XAGE1D'
    'XAGE1E'
    'XAGE2'
    'XAGE2B'
    'XKRY'
    'XKRY2'
    'ZAR1L'
    'ZBED3'
    'ZBED5'
    'ZBED6'
    'ZBTB42'
    'ZBTB8B'
    'ZFP62'
    'ZFP92'
    'ZG16'
    'ZNF26'
    'ZNF389'
    'ZNF444'
    'ZNF469'
    'ZNF541'
    'ZNF579'
    'ZNF580'
    'ZNF703'
    'ZNF705G'
    'ZNF717'
    'ZNF771'
    'ZNF826'
    'ZNF837'
    'ZNF84'
    'ZNF843'
    'ZNF853'
    'ZNF879'
    'ZSCAN23'
    'ZSWIM6'
    'ZYG11A'

Loading patient list... 
Loading categories... 
Loading mutations... 
Assigning mutations to categories...
Designated 12 double-null mutations.
Removed assignments of their 12 partner-null mutations; these will be omitted from analysis.

                               0     1    2     3    4    5   6      TOTAL  
           Frame_Shift_Del     4     0    0     0    0   99   1        104  
           Frame_Shift_Ins     1     0    0     0    0   50   0         51  
              In_Frame_Del     0     0    0     0    0   29   0         29  
              In_Frame_Ins     0     0    0     0    0    5   0          5  
                  Missense     0     5    6    20    5    4   0         40  
         Missense_Mutation     0  2649  197  1241  639    0   0       4726  
         Nonsense_Mutation     6     0    0     0    0  409   9        424  
          Nonstop_Mutation     0     0    0     0    0    9   0          9  
                    Silent     0  1061   60   557  166    0   0       1844  
               Splice_Site     1     0    0     0    0  115   2        118  
    Translation_Start_Site     0     7    0     2    0    0   0          9  

                     TOTAL    12  3722  263  1820  810  720  12       7359  

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:
        ADAM21P1: [1]
            BCL8: [1]
         C10orf4: [1]
        C19orf34: [1]
         COL29A1: [1]
        CSNK2A1P: [1]
            CTF1: [1]
            CTU1: [1]
        CYP2D7P1: [1]
          DNAH14: [1]
         EP400NL: [1]
          FAM20C: [1]
          FAM23A: [1]
         FAM75A2: [1]
          FAM86D: [1]
        FLJ43950: [1]
         GOLGA6B: [1]
           GP1BA: [1]
          GTF2H2: [1]
          GUSBP1: [1]
         HERC2P2: [1]
           IGFN1: [1]
    LOC100132247: [1]
       LOC168474: [1]
       LOC200030: [1]
       LOC220429: [1]
       LOC648740: [1]
       LOC653544: [1]
       LOC728024: [1]
       LOC728989: [1]
          MST1P9: [1]
            NAIP: [1]
           OR3A4: [1]
         PCDHB18: [1]
         PI4KAP2: [1]
           PIPSL: [1]
           RASA4: [1]
           RGPD5: [1]
          RIMBP3: [1]
       RPL23AP32: [1]
         RPSAP58: [1]
         RUNDC2C: [1]
        SLC6A10P: [1]
        SLC7A5P2: [1]
          TBC1D3: [1]
          WASH3P: [1]
       ANKRD20A3: [2]
            BOP1: [2]
        C22orf30: [2]
            MRC1: [2]
          OR2L1P: [2]
          OR2T35: [2]
          PDIA3P: [2]
         PRAMEF6: [2]
          SDHAP1: [2]
          SDHAP2: [2]
            TRY6: [2]
          WASH2P: [3]
           DDX12: [5]
          TUBBP5: [5]
           FRG1B: [7]
         Unknown: [26]
       ----TOTAL: [114]
Categories not in categ set:
          NaN: [12]
    ----TOTAL: [12]
Mutations not in categ set:
       GOLGB1: [1]
         GPS2: [1]
        GRLF1: [1]
         HCN1: [1]
        MACF1: [1]
         MLL2: [1]
         MLL3: [1]
          RB1: [1]
        THADA: [1]
          TTN: [1]
       UNC13C: [1]
         URB2: [1]
    ----TOTAL: [12]

Mutations in this patient+gene+categ set: 7233/7359
	0 mutations not in patient set
	114 mutations not in gene set
	12 mutations not in categ set
		(Note: at least 12 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: 1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 
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)   2.38e-05   23.8/Mb  (relative = 3.67)  expected NS/S ratio = 3.0
            Tp*C->A   1.81e-06    1.8/Mb  (relative = 0.28)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.92e-06    3.9/Mb  (relative = 0.61)  expected NS/S ratio = 3.2
             A->mut   1.51e-06    1.5/Mb  (relative = 0.23)  expected NS/S ratio = 3.9
         indel+null   8.45e-07    0.8/Mb  (relative = 0.13)
        double_null   1.43e-08    0.0/Mb  (relative = 0.00)
              Total   6.47e-06    6.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5


Estimated SAMPLE-SPECIFIC nonsilent background mutation rates

BLCA-BL-A0C8
        Tp*C->(T/G)   1.19e-05   11.9/Mb  (relative = 2.51)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.08e-06    4.1/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   6.36e-07    0.6/Mb  (relative = 0.13)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13I
        Tp*C->(T/G)   1.11e-05   11.1/Mb  (relative = 3.28)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.15)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.31e-06    2.3/Mb  (relative = 0.68)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.34)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.38e-06    3.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BL-A13J
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.13)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.99e-06    4.0/Mb  (relative = 1.13)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   4.35e-07    0.4/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.55e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0S7
        Tp*C->(T/G)   7.57e-07    0.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.30)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 1.20)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   3.68e-07    0.4/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.71e-06    1.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A0YX
        Tp*C->(T/G)   1.10e-04  110.0/Mb  (relative = 5.66)  expected NS/S ratio = 3.0
            Tp*C->A   4.04e-06    4.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 0.26)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.06)  expected NS/S ratio = 3.9
         indel+null   1.87e-06    1.9/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   1.94e-05   19.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20J
        Tp*C->(T/G)   7.72e-05   77.2/Mb  (relative = 5.30)  expected NS/S ratio = 3.0
            Tp*C->A   3.28e-06    3.3/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   9.56e-07    1.0/Mb  (relative = 0.07)  expected NS/S ratio = 3.9
         indel+null   1.47e-06    1.5/Mb  (relative = 0.10)
        double_null   6.69e-08    0.1/Mb  (relative = 0.00)
              Total   1.46e-05   14.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20N
        Tp*C->(T/G)   1.66e-05   16.6/Mb  (relative = 1.94)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.50)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   7.46e-06    7.5/Mb  (relative = 0.87)  expected NS/S ratio = 3.2
             A->mut   4.10e-06    4.1/Mb  (relative = 0.48)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20O
        Tp*C->(T/G)   1.87e-05   18.7/Mb  (relative = 3.10)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.97e-06    5.0/Mb  (relative = 0.83)  expected NS/S ratio = 3.2
             A->mut   1.84e-06    1.8/Mb  (relative = 0.31)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.10)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.02e-06    6.0/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20P
        Tp*C->(T/G)   9.08e-06    9.1/Mb  (relative = 2.77)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.54)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.57e-06    2.6/Mb  (relative = 0.78)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.20)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.28e-06    3.3/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20Q
        Tp*C->(T/G)   1.01e-05   10.1/Mb  (relative = 3.05)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.23)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.24e-06    1.2/Mb  (relative = 0.38)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   8.70e-07    0.9/Mb  (relative = 0.26)
        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

BLCA-BT-A20T
        Tp*C->(T/G)   3.61e-05   36.1/Mb  (relative = 4.19)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.26)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.62e-06    4.6/Mb  (relative = 0.54)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.14)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.60e-06    8.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20U
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 4.44)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.40)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   1.60e-06    1.6/Mb  (relative = 0.50)  expected NS/S ratio = 3.2
             A->mut   2.73e-07    0.3/Mb  (relative = 0.09)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.13)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.18e-06    3.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20V
        Tp*C->(T/G)   7.32e-06    7.3/Mb  (relative = 2.04)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 0.99)  expected NS/S ratio = 3.2
             A->mut   1.16e-06    1.2/Mb  (relative = 0.32)  expected NS/S ratio = 3.9
         indel+null   6.02e-07    0.6/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.58e-06    3.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-BT-A20W
        Tp*C->(T/G)   7.57e-06    7.6/Mb  (relative = 2.15)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.14)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.55e-06    3.6/Mb  (relative = 1.01)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.41)  expected NS/S ratio = 3.9
         indel+null   4.02e-07    0.4/Mb  (relative = 0.11)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.51e-06    3.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0EZ
        Tp*C->(T/G)   1.41e-05   14.1/Mb  (relative = 2.41)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.22)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.68e-06    5.7/Mb  (relative = 0.97)  expected NS/S ratio = 3.2
             A->mut   1.43e-06    1.4/Mb  (relative = 0.24)  expected NS/S ratio = 3.9
         indel+null   9.71e-07    1.0/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   5.86e-06    5.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F0
        Tp*C->(T/G)   3.78e-06    3.8/Mb  (relative = 1.22)  expected NS/S ratio = 3.0
            Tp*C->A   5.05e-07    0.5/Mb  (relative = 0.16)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 1.06)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.39)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.23)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.11e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F1
        Tp*C->(T/G)   2.04e-05   20.4/Mb  (relative = 4.15)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.36)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.56)  expected NS/S ratio = 3.2
             A->mut   8.19e-07    0.8/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   5.02e-07    0.5/Mb  (relative = 0.10)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.92e-06    4.9/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F6
        Tp*C->(T/G)   2.62e-05   26.2/Mb  (relative = 3.94)  expected NS/S ratio = 3.0
            Tp*C->A   2.27e-06    2.3/Mb  (relative = 0.34)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.82e-06    3.8/Mb  (relative = 0.57)  expected NS/S ratio = 3.2
             A->mut   1.30e-06    1.3/Mb  (relative = 0.19)  expected NS/S ratio = 3.9
         indel+null   8.03e-07    0.8/Mb  (relative = 0.12)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   6.66e-06    6.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-C4-A0F7
        Tp*C->(T/G)   3.03e-06    3.0/Mb  (relative = 1.27)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.53)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.46e-06    3.5/Mb  (relative = 1.46)  expected NS/S ratio = 3.2
             A->mut   4.10e-07    0.4/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.68e-07    0.3/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   2.38e-06    2.4/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HR
        Tp*C->(T/G)   4.62e-05   46.2/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   2.02e-06    2.0/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.28e-06    3.3/Mb  (relative = 0.34)  expected NS/S ratio = 3.2
             A->mut   1.23e-06    1.2/Mb  (relative = 0.13)  expected NS/S ratio = 3.9
         indel+null   1.41e-06    1.4/Mb  (relative = 0.15)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   9.64e-06    9.6/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CF-A1HS
        Tp*C->(T/G)   3.30e-05   33.0/Mb  (relative = 3.49)  expected NS/S ratio = 3.0
            Tp*C->A   4.29e-06    4.3/Mb  (relative = 0.45)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   4.88e-06    4.9/Mb  (relative = 0.52)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.33)  expected NS/S ratio = 3.9
         indel+null   1.10e-06    1.1/Mb  (relative = 0.12)
        double_null   3.35e-08    0.0/Mb  (relative = 0.00)
              Total   9.47e-06    9.5/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YN
        Tp*C->(T/G)   5.55e-06    5.5/Mb  (relative = 1.18)  expected NS/S ratio = 3.0
            Tp*C->A   1.77e-06    1.8/Mb  (relative = 0.37)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   5.06e-06    5.1/Mb  (relative = 1.07)  expected NS/S ratio = 3.2
             A->mut   2.32e-06    2.3/Mb  (relative = 0.49)  expected NS/S ratio = 3.9
         indel+null   6.69e-07    0.7/Mb  (relative = 0.14)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   4.72e-06    4.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YO
        Tp*C->(T/G)   9.84e-06    9.8/Mb  (relative = 2.67)  expected NS/S ratio = 3.0
            Tp*C->A   7.57e-07    0.8/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.75)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.30)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.19)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.68e-06    3.7/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-CU-A0YR
        Tp*C->(T/G)   4.04e-06    4.0/Mb  (relative = 1.28)  expected NS/S ratio = 3.0
            Tp*C->A   1.01e-06    1.0/Mb  (relative = 0.32)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.04e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.2
             A->mut   2.05e-06    2.0/Mb  (relative = 0.65)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.22)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   3.15e-06    3.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A3
        Tp*C->(T/G)   8.43e-05   84.3/Mb  (relative = 4.48)  expected NS/S ratio = 3.0
            Tp*C->A   4.54e-06    4.5/Mb  (relative = 0.24)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   8.25e-06    8.3/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   3.14e-06    3.1/Mb  (relative = 0.17)  expected NS/S ratio = 3.9
         indel+null   2.28e-06    2.3/Mb  (relative = 0.12)
        double_null   1.00e-07    0.1/Mb  (relative = 0.01)
              Total   1.88e-05   18.8/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A5
        Tp*C->(T/G)   3.86e-05   38.6/Mb  (relative = 4.79)  expected NS/S ratio = 3.0
            Tp*C->A   3.03e-06    3.0/Mb  (relative = 0.38)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   3.37e-06    3.4/Mb  (relative = 0.42)  expected NS/S ratio = 3.2
             A->mut   1.09e-06    1.1/Mb  (relative = 0.14)  expected NS/S ratio = 3.9
         indel+null   7.36e-07    0.7/Mb  (relative = 0.09)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   8.07e-06    8.1/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1A7
        Tp*C->(T/G)   9.33e-06    9.3/Mb  (relative = 1.30)  expected NS/S ratio = 3.0
            Tp*C->A   1.51e-06    1.5/Mb  (relative = 0.21)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   6.39e-06    6.4/Mb  (relative = 0.89)  expected NS/S ratio = 3.2
             A->mut   4.30e-06    4.3/Mb  (relative = 0.60)  expected NS/S ratio = 3.9
         indel+null   1.20e-06    1.2/Mb  (relative = 0.17)
        double_null         00    0.0/Mb  (relative = 0.00)
              Total   7.16e-06    7.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

BLCA-DK-A1AB
        Tp*C->(T/G)   2.95e-05   29.5/Mb  (relative = 4.74)  expected NS/S ratio = 3.0
            Tp*C->A   1.26e-06    1.3/Mb  (relative = 0.20)  expected NS/S ratio = 4.0
    (A/C/G)p*C->mut   2.75e-06    2.8/Mb  (relative = 0.44)  expected NS/S ratio = 3.2
             A->mut   7.51e-07    0.8/Mb  (relative = 0.12)  expected NS/S ratio = 3.9
         indel+null   7.03e-07    0.7/Mb  (relative = 0.11)
        double_null   3.35e-08    0.0/Mb  (relative = 0.01)
              Total   6.22e-06    6.2/Mb  (relative = 1.00)  expected NS/S ratio = 3.5

Analyzing silent/nonsilent ratios
1000/18094 2000/18094 3000/18094 4000/18094 5000/18094 6000/18094 7000/18094 8000/18094 9000/18094 10000/18094 11000/18094 12000/18094 13000/18094 14000/18094 15000/18094 16000/18094 17000/18094 18000/18094 Done
estimate_nonsilent_passengers_from_silent

Running "classic" MutSig:
Scatter job 200: processing genes 18005 - 18094
Calculating significance of each gene.
Using projection method.
18005	ZNF799	1
18006	ZNF8	1
18007	ZNF80	1
18008	ZNF800	1
18009	ZNF804A	2.820866e-01
18010	ZNF804B	1
18011	ZNF805	1
18012	ZNF808	3.328076e-01
18013	ZNF81	1
18014	ZNF813	5.373218e-02
18015	ZNF814	1.495629e-03
18016	ZNF816A	4.518488e-02
18017	ZNF821	1
18018	ZNF823	1
18019	ZNF827	2.555500e-01
18020	ZNF828	1
18021	ZNF829	1.434557e-02
18022	ZNF83	1
18023	ZNF830	1.597081e-01
18024	ZNF831	1.869121e-01
18025	ZNF835	1
18026	ZNF836	1
18027	ZNF839	1
18028	ZNF841	1
18029	ZNF844	1
18030	ZNF845	7.644604e-02
18031	ZNF846	1
18032	ZNF85	1
18033	ZNF860	1
18034	ZNF862	1
18035	ZNF878	1
18036	ZNF880	1
18037	ZNF883	9.361955e-02
18038	ZNF90	1
18039	ZNF91	1
18040	ZNF92	1
18041	ZNF93	1
18042	ZNF98	1
18043	ZNF99	8.984837e-04
18044	ZNFX1	1
18045	ZNHIT1	1
18046	ZNHIT2	1
18047	ZNHIT3	1
18048	ZNHIT6	1
18049	ZNRD1	1
18050	ZNRF1	1
18051	ZNRF2	1
18052	ZNRF3	1
18053	ZNRF4	1
18054	ZP1	1
18055	ZP2	1
18056	ZP3	1
18057	ZP4	1
18058	ZPBP	1
18059	ZPBP2	1
18060	ZPLD1	1
18061	ZRANB1	2.784954e-01
18062	ZRANB2	1
18063	ZRANB3	1
18064	ZRSR2	1
18065	ZSCAN1	1.482997e-02
18066	ZSCAN10	1
18067	ZSCAN12	1
18068	ZSCAN16	1
18069	ZSCAN18	1
18070	ZSCAN2	1
18071	ZSCAN20	1
18072	ZSCAN21	1
18073	ZSCAN22	1
18074	ZSCAN29	1
18075	ZSCAN4	1
18076	ZSCAN5A	1.557373e-02
18077	ZSCAN5B	1
18078	ZSWIM1	1
18079	ZSWIM2	4.474809e-02
18080	ZSWIM3	1
18081	ZSWIM4	1
18082	ZSWIM5	4.102882e-01
18083	ZSWIM7	1
18084	ZUFSP	1
18085	ZW10	1
18086	ZWILCH	1
18087	ZWINT	1
18088	ZXDA	1
18089	ZXDB	1
18090	ZXDC	1
18091	ZYG11B	1
18092	ZYX	1
18093	ZZEF1	9.206581e-02
18094	ZZZ3	3.105454e-02
Done

Running MutSig 2:
Scatter job 200: processing genes 18005 - 18094
Running MutSig clustering v0.01 ;)
Sorting genes by total number of mutations....
Processing gene list...
ZNF814
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 4.449803e-01	ci left: 5.992474e-03	ci right 9.503426e-03	k: 76	n:10000
Cons ci ratio: 5.044745e-03	ci left: 9.811299e-01	ci right 9.861827e-01	k: 9838	n:10000
KS ci ratio: 2.771443e+00	ci left: 2.531778e-06	ci right 5.570370e-04	k: 1	n:10000
ZNF814   10000 perm   2 sec   (5686 perm/sec)   p_kst 1.000000e-04   p_cons 9.838000e-01   p_joint 7.600000e-03

Joint ci ratio: 3.890588e-01	ci left: 4.069996e-03	ci right 6.078049e-03	k: 100	n:20000
Cons ci ratio: 3.644720e-03	ci left: 9.811641e-01	ci right 9.847935e-01	k: 19661	n:20000
KS ci ratio: 2.771651e+00	ci left: 1.265890e-06	ci right 2.785503e-04	k: 1	n:20000
ZNF814   20000 perm   6 sec   (3375 perm/sec)   p_kst 5.000000e-05   p_cons 9.830500e-01   p_joint 5.000000e-03

Joint ci ratio: 3.498785e-01	ci left: 3.439032e-03	ci right 4.926184e-03	k: 124	n:30000
Cons ci ratio: 2.967109e-03	ci left: 9.816118e-01	ci right 9.845602e-01	k: 29494	n:30000
KS ci ratio: 2.771720e+00	ci left: 8.439266e-07	ci right 1.857073e-04	k: 1	n:30000
ZNF814   30000 perm   8 sec   (3714 perm/sec)   p_kst 3.333333e-05   p_cons 9.831333e-01   p_joint 4.133333e-03

Joint ci ratio: 3.857467e-01	ci left: 2.079684e-03	ci right 3.094681e-03	k: 102	n:40000
Cons ci ratio: 2.507069e-03	ci left: 9.826443e-01	ci right 9.851347e-01	k: 39357	n:40000
KS ci ratio: 2.263100e+00	ci left: 6.055289e-06	ci right 1.806054e-04	k: 2	n:40000
ZNF814   40000 perm   10 sec   (3894 perm/sec)   p_kst 5.000000e-05   p_cons 9.839250e-01   p_joint 2.550000e-03

Joint ci ratio: 4.750417e-01	ci left: 1.038628e-03	ci right 1.701445e-03	k: 67	n:50000
Cons ci ratio: 2.294236e-03	ci left: 9.820143e-01	ci right 9.842891e-01	k: 49159	n:50000
KS ci ratio: 2.771775e+00	ci left: 5.063560e-07	ci right 1.114278e-04	k: 1	n:50000
ZNF814   50000 perm   13 sec   (3990 perm/sec)   p_kst 2.000000e-05   p_cons 9.831800e-01   p_joint 1.340000e-03

Joint ci ratio: 4.554059e-01	ci left: 9.537900e-04	ci right 1.529536e-03	k: 73	n:60000
Cons ci ratio: 2.096045e-03	ci left: 9.820881e-01	ci right 9.841648e-01	k: 58989	n:60000
KS ci ratio: 2.771789e+00	ci left: 4.219634e-07	ci right 9.285719e-05	k: 1	n:60000
ZNF814   60000 perm   15 sec   (4036 perm/sec)   p_kst 1.666667e-05   p_cons 9.831500e-01   p_joint 1.216667e-03

Joint ci ratio: 5.016823e-01	ci left: 6.541521e-04	ci right 1.103177e-03	k: 60	n:70000
Cons ci ratio: 1.937505e-03	ci left: 9.822205e-01	ci right 9.841392e-01	k: 68824	n:70000
KS ci ratio: 2.771799e+00	ci left: 3.616829e-07	ci right 7.959231e-05	k: 1	n:70000
ZNF814   70000 perm   17 sec   (4050 perm/sec)   p_kst 1.428571e-05   p_cons 9.832000e-01   p_joint 8.571429e-04

Joint ci ratio: 5.236454e-01	ci left: 5.179598e-04	ci right 8.947830e-04	k: 55	n:80000
Cons ci ratio: 1.821168e-03	ci left: 9.821187e-01	ci right 9.839210e-01	k: 78643	n:80000
KS ci ratio: 2.771807e+00	ci left: 3.164725e-07	ci right 6.964355e-05	k: 1	n:80000
ZNF814   80000 perm   20 sec   (4045 perm/sec)   p_kst 1.250000e-05   p_cons 9.830375e-01   p_joint 6.875000e-04

Joint ci ratio: 5.190494e-01	ci left: 4.700531e-04	ci right 8.079322e-04	k: 56	n:90000
Cons ci ratio: 1.718877e-03	ci left: 9.821341e-01	ci right 9.838345e-01	k: 88470	n:90000
KS ci ratio: 2.771812e+00	ci left: 2.813089e-07	ci right 6.190558e-05	k: 1	n:90000
ZNF814   90000 perm   22 sec   (4028 perm/sec)   p_kst 1.111111e-05   p_cons 9.830000e-01   p_joint 6.222222e-04

Joint ci ratio: 5.017490e-01	ci left: 4.578935e-04	ci right 7.722524e-04	k: 60	n:100000
Cons ci ratio: 1.632569e-03	ci left: 9.821387e-01	ci right 9.837531e-01	k: 98296	n:100000
KS ci ratio: 2.771817e+00	ci left: 2.531780e-07	ci right 5.571516e-05	k: 1	n:100000
ZNF814   100000 perm   25 sec   (4004 perm/sec)   p_kst 1.000000e-05   p_cons 9.829600e-01   p_joint 6.000000e-04

Joint ci ratio: 4.898552e-01	ci left: 4.401266e-04	ci right 7.327083e-04	k: 63	n:110000
Cons ci ratio: 1.553428e-03	ci left: 9.822465e-01	ci right 9.837824e-01	k: 108133	n:110000
KS ci ratio: 2.771821e+00	ci left: 2.301619e-07	ci right 5.065025e-05	k: 1	n:110000
ZNF814   110000 perm   28 sec   (3971 perm/sec)   p_kst 9.090909e-06   p_cons 9.830273e-01   p_joint 5.727273e-04

Joint ci ratio: 4.650788e-01	ci left: 4.547643e-04	ci right 7.369499e-04	k: 70	n:120000
Cons ci ratio: 1.481414e-03	ci left: 9.824143e-01	ci right 9.838789e-01	k: 117979	n:120000
KS ci ratio: 2.771824e+00	ci left: 2.109817e-07	ci right 4.642948e-05	k: 1	n:120000
ZNF814   120000 perm   30 sec   (3935 perm/sec)   p_kst 8.333333e-06   p_cons 9.831583e-01   p_joint 5.833333e-04

Joint ci ratio: 5.102227e-01	ci left: 3.388002e-04	ci right 5.767196e-04	k: 58	n:130000
Cons ci ratio: 1.416509e-03	ci left: 9.826044e-01	ci right 9.840047e-01	k: 127831	n:130000
KS ci ratio: 2.771827e+00	ci left: 1.947524e-07	ci right 4.285804e-05	k: 1	n:130000
ZNF814   130000 perm   33 sec   (3896 perm/sec)   p_kst 7.692308e-06   p_cons 9.833154e-01   p_joint 4.461538e-04

Joint ci ratio: 5.017934e-01	ci left: 3.270606e-04	ci right 5.516224e-04	k: 60	n:140000
Cons ci ratio: 1.363224e-03	ci left: 9.826733e-01	ci right 9.840208e-01	k: 137670	n:140000
KS ci ratio: 2.771829e+00	ci left: 1.808415e-07	ci right 3.979680e-05	k: 1	n:140000
ZNF814   140000 perm   36 sec   (3856 perm/sec)   p_kst 7.142857e-06   p_cons 9.833571e-01   p_joint 4.285714e-04

Joint ci ratio: 4.466093e-01	ci left: 3.992158e-04	ci right 6.341285e-04	k: 76	n:150000
Cons ci ratio: 1.316331e-03	ci left: 9.827135e-01	ci right 9.840144e-01	k: 147506	n:150000
KS ci ratio: 2.771831e+00	ci left: 1.687854e-07	ci right 3.714372e-05	k: 1	n:150000
ZNF814   150000 perm   39 sec   (3814 perm/sec)   p_kst 6.666667e-06   p_cons 9.833733e-01   p_joint 5.066667e-04

Joint ci ratio: 4.466166e-01	ci left: 3.742637e-04	ci right 5.944978e-04	k: 76	n:160000
Cons ci ratio: 1.274452e-03	ci left: 9.827365e-01	ci right 9.839959e-01	k: 157340	n:160000
KS ci ratio: 2.263185e+00	ci left: 1.513812e-06	ci right 4.515356e-05	k: 2	n:160000
ZNF814   160000 perm   42 sec   (3772 perm/sec)   p_kst 1.250000e-05   p_cons 9.833750e-01   p_joint 4.750000e-04

Joint ci ratio: 4.824236e-01	ci left: 2.951039e-04	ci right 4.873146e-04	k: 65	n:170000
Cons ci ratio: 1.240550e-03	ci left: 9.826437e-01	ci right 9.838692e-01	k: 167155	n:170000
KS ci ratio: 2.263186e+00	ci left: 1.424764e-06	ci right 4.249751e-05	k: 2	n:170000
ZNF814   170000 perm   46 sec   (3729 perm/sec)   p_kst 1.176471e-05   p_cons 9.832647e-01   p_joint 3.823529e-04

Joint ci ratio: 5.977213e-01	ci left: 1.681712e-04	ci right 3.153859e-04	k: 42	n:180000
Cons ci ratio: 1.208360e-03	ci left: 9.825843e-01	ci right 9.837778e-01	k: 176974	n:180000
KS ci ratio: 2.263188e+00	ci left: 1.345610e-06	ci right 4.013657e-05	k: 2	n:180000
ZNF814   180000 perm   49 sec   (3686 perm/sec)   p_kst 1.111111e-05   p_cons 9.831889e-01   p_joint 2.333333e-04

Joint ci ratio: 5.842884e-01	ci left: 1.682705e-04	ci right 3.108716e-04	k: 44	n:190000
Cons ci ratio: 1.177411e-03	ci left: 9.825639e-01	ci right 9.837266e-01	k: 186799	n:190000
KS ci ratio: 2.263189e+00	ci left: 1.274788e-06	ci right 3.802415e-05	k: 2	n:190000
ZNF814   190000 perm   52 sec   (3643 perm/sec)   p_kst 1.052632e-05   p_cons 9.831526e-01   p_joint 2.315789e-04

Joint ci ratio: 5.779046e-01	ci left: 1.641211e-04	ci right 3.010563e-04	k: 45	n:200000
Cons ci ratio: 1.147335e-03	ci left: 9.825865e-01	ci right 9.837194e-01	k: 196632	n:200000
KS ci ratio: 2.263190e+00	ci left: 1.211049e-06	ci right 3.612297e-05	k: 2	n:200000
ZNF814   200000 perm   56 sec   (3594 perm/sec)   p_kst 1.000000e-05   p_cons 9.831600e-01   p_joint 2.250000e-04

Joint ci ratio: 5.717254e-01	ci left: 1.603747e-04	ci right 2.921681e-04	k: 46	n:210000
Cons ci ratio: 1.116388e-03	ci left: 9.826993e-01	ci right 9.838016e-01	k: 206484	n:210000
KS ci ratio: 2.771839e+00	ci left: 1.205610e-07	ci right 2.653135e-05	k: 1	n:210000
ZNF814   210000 perm   59 sec   (3548 perm/sec)   p_kst 4.761905e-06   p_cons 9.832571e-01   p_joint 2.190476e-04

Joint ci ratio: 6.121427e-01	ci left: 1.298967e-04	ci right 2.475766e-04	k: 40	n:220000
Cons ci ratio: 1.089595e-03	ci left: 9.827466e-01	ci right 9.838224e-01	k: 216324	n:220000
KS ci ratio: 2.263192e+00	ci left: 1.100953e-06	ci right 3.283910e-05	k: 2	n:220000
ZNF814   220000 perm   64 sec   (3462 perm/sec)   p_kst 9.090909e-06   p_cons 9.832909e-01   p_joint 1.818182e-04

Joint ci ratio: 5.909044e-01	ci left: 1.353046e-04	ci right 2.518210e-04	k: 43	n:230000
Cons ci ratio: 1.063651e-03	ci left: 9.828210e-01	ci right 9.838711e-01	k: 226171	n:230000
KS ci ratio: 2.263193e+00	ci left: 1.053086e-06	ci right 3.141133e-05	k: 2	n:230000
ZNF814   230000 perm   67 sec   (3420 perm/sec)   p_kst 8.695652e-06   p_cons 9.833522e-01   p_joint 1.869565e-04

Joint ci ratio: 5.717336e-01	ci left: 1.403274e-04	ci right 2.556483e-04	k: 46	n:240000
Cons ci ratio: 1.040657e-03	ci left: 9.828513e-01	ci right 9.838787e-01	k: 236009	n:240000
KS ci ratio: 1.959980e+00	ci left: 2.577808e-06	ci right 3.652987e-05	k: 3	n:240000
ZNF814   240000 perm   71 sec   (3381 perm/sec)   p_kst 1.250000e-05   p_cons 9.833708e-01   p_joint 1.916667e-04

Joint ci ratio: 5.909090e-01	ci left: 1.244800e-04	ci right 2.316760e-04	k: 43	n:250000
Cons ci ratio: 1.017844e-03	ci left: 9.829199e-01	ci right 9.839248e-01	k: 245857	n:250000
KS ci ratio: 1.959980e+00	ci left: 2.474695e-06	ci right 3.506869e-05	k: 3	n:250000
ZNF814   250000 perm   75 sec   (3341 perm/sec)   p_kst 1.200000e-05   p_cons 9.834280e-01   p_joint 1.720000e-04

Joint ci ratio: 6.048191e-01	ci left: 1.131650e-04	ci right 2.139214e-04	k: 41	n:260000
Cons ci ratio: 9.992834e-04	ci left: 9.828898e-01	ci right 9.838763e-01	k: 255681	n:260000
KS ci ratio: 1.959981e+00	ci left: 2.379514e-06	ci right 3.371991e-05	k: 3	n:260000
ZNF814   260000 perm   79 sec   (3304 perm/sec)   p_kst 1.153846e-05   p_cons 9.833885e-01   p_joint 1.576923e-04

Joint ci ratio: 6.197594e-01	ci left: 1.027161e-04	ci right 1.974551e-04	k: 39	n:270000
Cons ci ratio: 9.785844e-04	ci left: 9.829673e-01	ci right 9.839334e-01	k: 265533	n:270000
KS ci ratio: 1.959982e+00	ci left: 2.291384e-06	ci right 3.247103e-05	k: 3	n:270000
ZNF814   270000 perm   83 sec   (3265 perm/sec)   p_kst 1.111111e-05   p_cons 9.834556e-01   p_joint 1.444444e-04

Joint ci ratio: 6.197610e-01	ci left: 9.904757e-05	ci right 1.904033e-04	k: 39	n:280000
Cons ci ratio: 9.609003e-04	ci left: 9.829779e-01	ci right 9.839264e-01	k: 275368	n:280000
KS ci ratio: 1.959983e+00	ci left: 2.209549e-06	ci right 3.131137e-05	k: 3	n:280000
ZNF814   280000 perm   87 sec   (3226 perm/sec)   p_kst 1.071429e-05   p_cons 9.834571e-01   p_joint 1.392857e-04

Joint ci ratio: 6.197626e-01	ci left: 9.563208e-05	ci right 1.838378e-04	k: 39	n:290000
Cons ci ratio: 9.449416e-04	ci left: 9.829599e-01	ci right 9.838925e-01	k: 285195	n:290000
KS ci ratio: 1.959983e+00	ci left: 2.133357e-06	ci right 3.023168e-05	k: 3	n:290000
ZNF814   290000 perm   91 sec   (3189 perm/sec)   p_kst 1.034483e-05   p_cons 9.834310e-01   p_joint 1.344828e-04

Joint ci ratio: 6.197641e-01	ci left: 9.244429e-05	ci right 1.777100e-04	k: 39	n:300000
Cons ci ratio: 9.274692e-04	ci left: 9.830243e-01	ci right 9.839397e-01	k: 295046	n:300000
KS ci ratio: 1.959984e+00	ci left: 2.062245e-06	ci right 2.922396e-05	k: 3	n:300000
ZNF814   300000 perm   95 sec   (3153 perm/sec)   p_kst 1.000000e-05   p_cons 9.834867e-01   p_joint 1.300000e-04

Joint ci ratio: 6.929278e-01	ci left: 6.794613e-05	ci right 1.419390e-04	k: 31	n:310000
Cons ci ratio: 9.121913e-04	ci left: 9.830389e-01	ci right 9.839392e-01	k: 304883	n:310000
KS ci ratio: 1.959984e+00	ci left: 1.995721e-06	ci right 2.828126e-05	k: 3	n:310000
ZNF814   310000 perm   100 sec   (3100 perm/sec)   p_kst 9.677419e-06   p_cons 9.834935e-01   p_joint 1.000000e-04

Joint ci ratio: 6.823482e-01	ci left: 6.840090e-05	ci right 1.411673e-04	k: 32	n:320000
Cons ci ratio: 8.977307e-04	ci left: 9.830495e-01	ci right 9.839355e-01	k: 314719	n:320000
KS ci ratio: 1.959985e+00	ci left: 1.933355e-06	ci right 2.739748e-05	k: 3	n:320000
ZNF814   320000 perm   104 sec   (3066 perm/sec)   p_kst 9.375000e-06   p_cons 9.834969e-01   p_joint 1.000000e-04

Joint ci ratio: 7.040186e-01	ci left: 6.133680e-05	ci right 1.297759e-04	k: 30	n:330000
Cons ci ratio: 8.845140e-04	ci left: 9.830381e-01	ci right 9.839110e-01	k: 324548	n:330000
KS ci ratio: 1.959985e+00	ci left: 1.874768e-06	ci right 2.656726e-05	k: 3	n:330000
ZNF814   330000 perm   109 sec   (3034 perm/sec)   p_kst 9.090909e-06   p_cons 9.834788e-01   p_joint 9.090909e-05

Joint ci ratio: 6.929310e-01	ci left: 6.195080e-05	ci right 1.294152e-04	k: 31	n:340000
Cons ci ratio: 8.729663e-04	ci left: 9.829858e-01	ci right 9.838471e-01	k: 334363	n:340000
KS ci ratio: 1.959986e+00	ci left: 1.819628e-06	ci right 2.578588e-05	k: 3	n:340000
ZNF814   340000 perm   113 sec   (3003 perm/sec)   p_kst 8.823529e-06   p_cons 9.834206e-01   p_joint 9.117647e-05

Joint ci ratio: 6.823513e-01	ci left: 6.253789e-05	ci right 1.290674e-04	k: 32	n:350000
Cons ci ratio: 8.626017e-04	ci left: 9.829076e-01	ci right 9.837586e-01	k: 344168	n:350000
KS ci ratio: 1.959986e+00	ci left: 1.767638e-06	ci right 2.504915e-05	k: 3	n:350000
ZNF814   350000 perm   118 sec   (2972 perm/sec)   p_kst 8.571429e-06   p_cons 9.833371e-01   p_joint 9.142857e-05

Joint ci ratio: 6.823522e-01	ci left: 6.080070e-05	ci right 1.254823e-04	k: 32	n:360000
Cons ci ratio: 8.519301e-04	ci left: 9.828592e-01	ci right 9.836996e-01	k: 353982	n:360000
KS ci ratio: 1.959986e+00	ci left: 1.718537e-06	ci right 2.435334e-05	k: 3	n:360000
ZNF814   360000 perm   123 sec   (2932 perm/sec)   p_kst 8.333333e-06   p_cons 9.832833e-01   p_joint 8.888889e-05

Joint ci ratio: 6.823531e-01	ci left: 5.915742e-05	ci right 1.220909e-04	k: 32	n:370000
Cons ci ratio: 8.410849e-04	ci left: 9.828354e-01	ci right 9.836651e-01	k: 363804	n:370000
KS ci ratio: 1.959987e+00	ci left: 1.672090e-06	ci right 2.369515e-05	k: 3	n:370000
ZNF814   370000 perm   128 sec   (2885 perm/sec)   p_kst 8.108108e-06   p_cons 9.832541e-01   p_joint 8.648649e-05

Joint ci ratio: 7.156616e-01	ci left: 5.111046e-05	ci right 1.096004e-04	k: 29	n:380000
Cons ci ratio: 8.305088e-04	ci left: 9.828183e-01	ci right 9.836375e-01	k: 373628	n:380000
KS ci ratio: 1.959987e+00	ci left: 1.628087e-06	ci right 2.307160e-05	k: 3	n:380000
ZNF814   380000 perm   133 sec   (2854 perm/sec)   p_kst 7.894737e-06   p_cons 9.832316e-01   p_joint 7.631579e-05

Joint ci ratio: 7.156624e-01	ci left: 4.979992e-05	ci right 1.067902e-04	k: 29	n:390000
Cons ci ratio: 8.200656e-04	ci left: 9.828125e-01	ci right 9.836213e-01	k: 383456	n:390000
KS ci ratio: 1.959987e+00	ci left: 1.586342e-06	ci right 2.248002e-05	k: 3	n:390000
ZNF814   390000 perm   138 sec   (2821 perm/sec)   p_kst 7.692308e-06   p_cons 9.832205e-01   p_joint 7.435897e-05

Joint ci ratio: 6.929361e-01	ci left: 5.265808e-05	ci right 1.100033e-04	k: 31	n:400000
Cons ci ratio: 8.095770e-04	ci left: 9.828248e-01	ci right 9.836232e-01	k: 393291	n:400000
KS ci ratio: 1.959988e+00	ci left: 1.546683e-06	ci right 2.191802e-05	k: 3	n:400000
ZNF814   400000 perm   143 sec   (2789 perm/sec)   p_kst 7.500000e-06   p_cons 9.832275e-01   p_joint 7.750000e-05

Joint ci ratio: 6.722458e-01	ci left: 5.540473e-05	ci right 1.130330e-04	k: 33	n:410000
Cons ci ratio: 7.996580e-04	ci left: 9.828291e-01	ci right 9.836177e-01	k: 403123	n:410000
KS ci ratio: 1.959988e+00	ci left: 1.508959e-06	ci right 2.138344e-05	k: 3	n:410000
ZNF814   410000 perm   148 sec   (2763 perm/sec)   p_kst 7.317073e-06   p_cons 9.832268e-01   p_joint 8.048780e-05

Joint ci ratio: 6.929374e-01	ci left: 5.015052e-05	ci right 1.047651e-04	k: 31	n:420000
Cons ci ratio: 7.903230e-04	ci left: 9.828236e-01	ci right 9.836030e-01	k: 412951	n:420000
KS ci ratio: 1.959988e+00	ci left: 1.473031e-06	ci right 2.087432e-05	k: 3	n:420000
ZNF814   420000 perm   154 sec   (2734 perm/sec)   p_kst 7.142857e-06   p_cons 9.832167e-01   p_joint 7.380952e-05

Joint ci ratio: 6.048389e-01	ci left: 6.842481e-05	ci right 1.293493e-04	k: 41	n:430000
Cons ci ratio: 7.076247e-04	ci left: 9.858304e-01	ci right 9.865305e-01	k: 424059	n:430000
KS ci ratio: 1.959989e+00	ci left: 1.438775e-06	ci right 2.038887e-05	k: 3	n:430000
ZNF814   430000 perm   159 sec   (2709 perm/sec)   p_kst 6.976744e-06   p_cons 9.861837e-01   p_joint 9.534884e-05

Joint ci ratio: 6.048396e-01	ci left: 6.686969e-05	ci right 1.264096e-04	k: 41	n:440000
Cons ci ratio: 6.986510e-04	ci left: 9.858693e-01	ci right 9.865606e-01	k: 433936	n:440000
KS ci ratio: 1.959989e+00	ci left: 1.406075e-06	ci right 1.992549e-05	k: 3	n:440000
ZNF814   440000 perm   164 sec   (2681 perm/sec)   p_kst 6.818182e-06   p_cons 9.862182e-01   p_joint 9.318182e-05

Joint ci ratio: 6.048402e-01	ci left: 6.538367e-05	ci right 1.236005e-04	k: 41	n:450000
Cons ci ratio: 6.908537e-04	ci left: 9.858729e-01	ci right 9.865564e-01	k: 443798	n:450000
KS ci ratio: 1.959989e+00	ci left: 1.374829e-06	ci right 1.948270e-05	k: 3	n:450000
ZNF814   450000 perm   169 sec   (2657 perm/sec)   p_kst 6.666667e-06   p_cons 9.862178e-01   p_joint 9.111111e-05

Joint ci ratio: 6.625750e-01	ci left: 5.118746e-05	ci right 1.032846e-04	k: 34	n:460000
Cons ci ratio: 6.839125e-04	ci left: 9.858521e-01	ci right 9.865287e-01	k: 453649	n:460000
KS ci ratio: 1.959989e+00	ci left: 1.344941e-06	ci right 1.905917e-05	k: 3	n:460000
ZNF814   460000 perm   175 sec   (2631 perm/sec)   p_kst 6.521739e-06   p_cons 9.861935e-01   p_joint 7.391304e-05

Joint ci ratio: 6.823597e-01	ci left: 4.657061e-05	ci right 9.611451e-05	k: 32	n:470000
Cons ci ratio: 6.753765e-04	ci left: 9.859055e-01	ci right 9.865736e-01	k: 463534	n:470000
KS ci ratio: 1.959990e+00	ci left: 1.316326e-06	ci right 1.865366e-05	k: 3	n:470000
ZNF814   470000 perm   181 sec   (2594 perm/sec)   p_kst 6.382979e-06   p_cons 9.862426e-01   p_joint 6.808511e-05

Joint ci ratio: 6.722499e-01	ci left: 4.732479e-05	ci right 9.654922e-05	k: 33	n:480000
Cons ci ratio: 6.685302e-04	ci left: 9.858997e-01	ci right 9.865611e-01	k: 473392	n:480000
KS ci ratio: 1.959990e+00	ci left: 1.288902e-06	ci right 1.826504e-05	k: 3	n:480000
ZNF814   480000 perm   188 sec   (2555 perm/sec)   p_kst 6.250000e-06   p_cons 9.862333e-01   p_joint 6.875000e-05

Joint ci ratio: 6.722504e-01	ci left: 4.635897e-05	ci right 9.457885e-05	k: 33	n:490000
Cons ci ratio: 6.623350e-04	ci left: 9.858756e-01	ci right 9.865308e-01	k: 483241	n:490000
KS ci ratio: 1.959990e+00	ci left: 1.262598e-06	ci right 1.789229e-05	k: 3	n:490000
ZNF814   490000 perm   194 sec   (2527 perm/sec)   p_kst 6.122449e-06   p_cons 9.862061e-01   p_joint 6.734694e-05

Joint ci ratio: 6.625771e-01	ci left: 4.709242e-05	ci right 9.502190e-05	k: 34	n:500000
Cons ci ratio: 6.556802e-04	ci left: 9.858789e-01	ci right 9.865275e-01	k: 493103	n:500000
KS ci ratio: 1.959990e+00	ci left: 1.237346e-06	ci right 1.753445e-05	k: 3	n:500000
ZNF814   500000 perm   200 sec   (2500 perm/sec)   p_kst 6.000000e-06   p_cons 9.862060e-01   p_joint 6.800000e-05

Joint ci ratio: 6.823617e-01	ci left: 4.291798e-05	ci right 8.857621e-05	k: 32	n:510000
Cons ci ratio: 6.498767e-04	ci left: 9.858543e-01	ci right 9.864971e-01	k: 502951	n:510000
KS ci ratio: 2.771850e+00	ci left: 4.964276e-08	ci right 1.092474e-05	k: 1	n:510000
ZNF814   510000 perm   206 sec   (2477 perm/sec)   p_kst 1.960784e-06   p_cons 9.861784e-01   p_joint 6.274510e-05

Joint ci ratio: 6.722518e-01	ci left: 4.368439e-05	ci right 8.912245e-05	k: 33	n:520000
Cons ci ratio: 6.446303e-04	ci left: 9.858131e-01	ci right 9.864507e-01	k: 512790	n:520000
KS ci ratio: 2.771851e+00	ci left: 4.868809e-08	ci right 1.071465e-05	k: 1	n:520000
ZNF814   520000 perm   212 sec   (2450 perm/sec)   p_kst 1.923077e-06   p_cons 9.861346e-01   p_joint 6.346154e-05

Joint ci ratio: 6.625784e-01	ci left: 4.442679e-05	ci right 8.964337e-05	k: 34	n:530000
Cons ci ratio: 6.382700e-04	ci left: 9.858270e-01	ci right 9.864583e-01	k: 522657	n:530000
KS ci ratio: 2.771851e+00	ci left: 4.776945e-08	ci right 1.051249e-05	k: 1	n:530000
ZNF814   530000 perm   218 sec   (2426 perm/sec)   p_kst 1.886792e-06   p_cons 9.861453e-01   p_joint 6.415094e-05

Joint ci ratio: 7.040319e-01	ci left: 3.748340e-05	ci right 7.930807e-05	k: 30	n:540000
Cons ci ratio: 6.331647e-04	ci left: 9.857936e-01	ci right 9.864197e-01	k: 532499	n:540000
KS ci ratio: 2.771851e+00	ci left: 4.688483e-08	ci right 1.031781e-05	k: 1	n:540000
ZNF814   540000 perm   225 sec   (2399 perm/sec)   p_kst 1.851852e-06   p_cons 9.861093e-01   p_joint 5.555556e-05

Joint ci ratio: 7.040323e-01	ci left: 3.680188e-05	ci right 7.786612e-05	k: 30	n:550000
Cons ci ratio: 6.270523e-04	ci left: 9.858110e-01	ci right 9.864311e-01	k: 542368	n:550000
KS ci ratio: 2.771851e+00	ci left: 4.603238e-08	ci right 1.013022e-05	k: 1	n:550000
ZNF814   550000 perm   231 sec   (2377 perm/sec)   p_kst 1.818182e-06   p_cons 9.861236e-01   p_joint 5.454545e-05

Joint ci ratio: 7.040327e-01	ci left: 3.614470e-05	ci right 7.647567e-05	k: 30	n:560000
Cons ci ratio: 6.205447e-04	ci left: 9.858531e-01	ci right 9.864668e-01	k: 552251	n:560000
KS ci ratio: 2.771851e+00	ci left: 4.521037e-08	ci right 9.949323e-06	k: 1	n:560000
ZNF814   560000 perm   238 sec   (2356 perm/sec)   p_kst 1.785714e-06   p_cons 9.861625e-01   p_joint 5.357143e-05

Joint ci ratio: 7.040330e-01	ci left: 3.551058e-05	ci right 7.513401e-05	k: 30	n:570000
Cons ci ratio: 6.146268e-04	ci left: 9.858761e-01	ci right 9.864839e-01	k: 562124	n:570000
KS ci ratio: 2.771851e+00	ci left: 4.441721e-08	ci right 9.774774e-06	k: 1	n:570000
ZNF814   570000 perm   245 sec   (2327 perm/sec)   p_kst 1.754386e-06   p_cons 9.861825e-01   p_joint 5.263158e-05

Joint ci ratio: 6.929449e-01	ci left: 3.631579e-05	ci right 7.586471e-05	k: 31	n:580000
Cons ci ratio: 6.088737e-04	ci left: 9.858982e-01	ci right 9.865004e-01	k: 571997	n:580000
KS ci ratio: 2.771851e+00	ci left: 4.365139e-08	ci right 9.606244e-06	k: 1	n:580000
ZNF814   580000 perm   252 sec   (2302 perm/sec)   p_kst 1.724138e-06   p_cons 9.862017e-01   p_joint 5.344828e-05

Joint ci ratio: 6.823647e-01	ci left: 3.709855e-05	ci right 7.656601e-05	k: 32	n:590000
Cons ci ratio: 6.038797e-04	ci left: 9.858922e-01	ci right 9.864894e-01	k: 581854	n:590000
KS ci ratio: 2.771852e+00	ci left: 4.291154e-08	ci right 9.443427e-06	k: 1	n:590000
ZNF814   590000 perm   259 sec   (2281 perm/sec)   p_kst 1.694915e-06   p_cons 9.861932e-01   p_joint 5.423729e-05

Joint ci ratio: 6.823651e-01	ci left: 3.648024e-05	ci right 7.528993e-05	k: 32	n:600000
Cons ci ratio: 5.995556e-04	ci left: 9.858612e-01	ci right 9.864541e-01	k: 591696	n:600000
KS ci ratio: 2.771852e+00	ci left: 4.219635e-08	ci right 9.286037e-06	k: 1	n:600000
ZNF814   600000 perm   266 sec   (2254 perm/sec)   p_kst 1.666667e-06   p_cons 9.861600e-01   p_joint 5.333333e-05

Joint ci ratio: 6.823654e-01	ci left: 3.588220e-05	ci right 7.405568e-05	k: 32	n:610000
Cons ci ratio: 5.948917e-04	ci left: 9.858511e-01	ci right 9.864394e-01	k: 601550	n:610000
KS ci ratio: 2.771852e+00	ci left: 4.150460e-08	ci right 9.133807e-06	k: 1	n:610000
ZNF814   610000 perm   273 sec   (2232 perm/sec)   p_kst 1.639344e-06   p_cons 9.861475e-01   p_joint 5.245902e-05

Joint ci ratio: 8.001505e-01	ci left: 2.351631e-05	ci right 5.566286e-05	k: 23	n:620000
Cons ci ratio: 5.899165e-04	ci left: 9.858609e-01	ci right 9.864442e-01	k: 611416	n:620000
KS ci ratio: 2.771852e+00	ci left: 4.083517e-08	ci right 8.986488e-06	k: 1	n:620000
ZNF814   620000 perm   281 sec   (2209 perm/sec)   p_kst 1.612903e-06   p_cons 9.861548e-01   p_joint 3.709677e-05

Joint ci ratio: 7.839838e-01	ci left: 2.440849e-05	ci right 5.668217e-05	k: 24	n:630000
Cons ci ratio: 5.849959e-04	ci left: 9.858736e-01	ci right 9.864521e-01	k: 621284	n:630000
KS ci ratio: 2.771852e+00	ci left: 4.018700e-08	ci right 8.843846e-06	k: 1	n:630000
ZNF814   630000 perm   288 sec   (2188 perm/sec)   p_kst 1.587302e-06   p_cons 9.861651e-01   p_joint 3.809524e-05

Joint ci ratio: 8.357318e-01	ci left: 2.031157e-05	ci right 5.015696e-05	k: 21	n:640000
Cons ci ratio: 5.805617e-04	ci left: 9.858686e-01	ci right 9.864426e-01	k: 631141	n:640000
KS ci ratio: 2.771852e+00	ci left: 3.955907e-08	ci right 8.705662e-06	k: 1	n:640000
ZNF814   640000 perm   295 sec   (2169 perm/sec)   p_kst 1.562500e-06   p_cons 9.861578e-01   p_joint 3.281250e-05

Joint ci ratio: 8.357320e-01	ci left: 1.999908e-05	ci right 4.938532e-05	k: 21	n:650000
Cons ci ratio: 5.761617e-04	ci left: 9.858668e-01	ci right 9.864365e-01	k: 641000	n:650000
KS ci ratio: 2.771852e+00	ci left: 3.895047e-08	ci right 8.571729e-06	k: 1	n:650000
ZNF814   650000 perm   303 sec   (2149 perm/sec)   p_kst 1.538462e-06   p_cons 9.861538e-01   p_joint 3.230769e-05

Joint ci ratio: 8.173616e-01	ci left: 2.088994e-05	ci right 5.046663e-05	k: 22	n:660000
Cons ci ratio: 5.719237e-04	ci left: 9.858621e-01	ci right 9.864276e-01	k: 650857	n:660000
KS ci ratio: 2.263206e+00	ci left: 3.669840e-07	ci right 1.094645e-05	k: 2	n:660000
ZNF814   660000 perm   310 sec   (2126 perm/sec)   p_kst 3.030303e-06   p_cons 9.861470e-01   p_joint 3.333333e-05

Joint ci ratio: 8.173619e-01	ci left: 2.057814e-05	ci right 4.971341e-05	k: 22	n:670000
Cons ci ratio: 5.678397e-04	ci left: 9.858545e-01	ci right 9.864159e-01	k: 660712	n:670000
KS ci ratio: 2.263206e+00	ci left: 3.615066e-07	ci right 1.078307e-05	k: 2	n:670000
ZNF814   670000 perm   318 sec   (2109 perm/sec)   p_kst 2.985075e-06   p_cons 9.861373e-01   p_joint 3.283582e-05

Joint ci ratio: 8.001519e-01	ci left: 2.144133e-05	ci right 5.075147e-05	k: 23	n:680000
Cons ci ratio: 5.635082e-04	ci left: 9.858635e-01	ci right 9.864206e-01	k: 670578	n:680000
KS ci ratio: 2.263206e+00	ci left: 3.561903e-07	ci right 1.062450e-05	k: 2	n:680000
ZNF814   680000 perm   325 sec   (2090 perm/sec)   p_kst 2.941176e-06   p_cons 9.861441e-01   p_joint 3.382353e-05

Joint ci ratio: 8.001522e-01	ci left: 2.113059e-05	ci right 5.001595e-05	k: 23	n:690000
Cons ci ratio: 5.591556e-04	ci left: 9.858781e-01	ci right 9.864309e-01	k: 680448	n:690000
KS ci ratio: 2.263206e+00	ci left: 3.510281e-07	ci right 1.047052e-05	k: 2	n:690000
ZNF814   690000 perm   332 sec   (2075 perm/sec)   p_kst 2.898551e-06   p_cons 9.861565e-01   p_joint 3.333333e-05

Joint ci ratio: 8.001524e-01	ci left: 2.082872e-05	ci right 4.930144e-05	k: 23	n:700000
Cons ci ratio: 5.554827e-04	ci left: 9.858634e-01	ci right 9.864126e-01	k: 690298	n:700000
KS ci ratio: 2.263207e+00	ci left: 3.460134e-07	ci right 1.032094e-05	k: 2	n:700000
ZNF814   700000 perm   340 sec   (2058 perm/sec)   p_kst 2.857143e-06   p_cons 9.861400e-01   p_joint 3.285714e-05

Joint ci ratio: 8.001526e-01	ci left: 2.053536e-05	ci right 4.860706e-05	k: 23	n:710000
Cons ci ratio: 5.519372e-04	ci left: 9.858463e-01	ci right 9.863920e-01	k: 700146	n:710000
KS ci ratio: 2.263207e+00	ci left: 3.411400e-07	ci right 1.017558e-05	k: 2	n:710000
ZNF814   710000 perm   348 sec   (2043 perm/sec)   p_kst 2.816901e-06   p_cons 9.861211e-01   p_joint 3.239437e-05

Joint ci ratio: 7.839858e-01	ci left: 2.135741e-05	ci right 4.959695e-05	k: 24	n:720000
Cons ci ratio: 5.480130e-04	ci left: 9.858522e-01	ci right 9.863939e-01	k: 710010	n:720000
KS ci ratio: 2.263207e+00	ci left: 3.364020e-07	ci right 1.003425e-05	k: 2	n:720000
ZNF814   720000 perm   355 sec   (2028 perm/sec)   p_kst 2.777778e-06   p_cons 9.861250e-01   p_joint 3.333333e-05

Joint ci ratio: 7.839860e-01	ci left: 2.106484e-05	ci right 4.891755e-05	k: 24	n:730000
Cons ci ratio: 5.439260e-04	ci left: 9.858703e-01	ci right 9.864080e-01	k: 719883	n:730000
KS ci ratio: 2.263207e+00	ci left: 3.317937e-07	ci right 9.896797e-06	k: 2	n:730000
ZNF814   730000 perm   364 sec   (2007 perm/sec)   p_kst 2.739726e-06   p_cons 9.861411e-01   p_joint 3.287671e-05

Joint ci ratio: 7.543901e-01	ci left: 2.295156e-05	ci right 5.148069e-05	k: 26	n:740000
Cons ci ratio: 5.411562e-04	ci left: 9.858252e-01	ci right 9.863602e-01	k: 729710	n:740000
KS ci ratio: 2.263207e+00	ci left: 3.273100e-07	ci right 9.763057e-06	k: 2	n:740000
ZNF814   740000 perm   372 sec   (1990 perm/sec)   p_kst 2.702703e-06   p_cons 9.860946e-01   p_joint 3.513514e-05

Joint ci ratio: 7.407960e-01	ci left: 2.372436e-05	ci right 5.237768e-05	k: 27	n:750000
Cons ci ratio: 5.375085e-04	ci left: 9.858284e-01	ci right 9.863598e-01	k: 739572	n:750000
KS ci ratio: 2.263207e+00	ci left: 3.229459e-07	ci right 9.632883e-06	k: 2	n:750000
ZNF814   750000 perm   380 sec   (1975 perm/sec)   p_kst 2.666667e-06   p_cons 9.860960e-01   p_joint 3.600000e-05

Joint ci ratio: 7.279114e-01	ci left: 2.448145e-05	ci right 5.324666e-05	k: 28	n:760000
Cons ci ratio: 5.339336e-04	ci left: 9.858316e-01	ci right 9.863594e-01	k: 749434	n:760000
KS ci ratio: 2.263207e+00	ci left: 3.186966e-07	ci right 9.506135e-06	k: 2	n:760000
ZNF814   760000 perm   388 sec   (1961 perm/sec)   p_kst 2.631579e-06   p_cons 9.860974e-01   p_joint 3.684211e-05

Joint ci ratio: 7.279115e-01	ci left: 2.416350e-05	ci right 5.255515e-05	k: 28	n:770000
Cons ci ratio: 5.304542e-04	ci left: 9.858334e-01	ci right 9.863577e-01	k: 759295	n:770000
KS ci ratio: 2.263207e+00	ci left: 3.145577e-07	ci right 9.382679e-06	k: 2	n:770000
ZNF814   770000 perm   396 sec   (1947 perm/sec)   p_kst 2.597403e-06   p_cons 9.860974e-01   p_joint 3.636364e-05

Joint ci ratio: 7.279117e-01	ci left: 2.385371e-05	ci right 5.188138e-05	k: 28	n:780000
Cons ci ratio: 5.274854e-04	ci left: 9.858119e-01	ci right 9.863332e-01	k: 769138	n:780000
KS ci ratio: 2.263207e+00	ci left: 3.105249e-07	ci right 9.262389e-06	k: 2	n:780000
ZNF814   780000 perm   404 sec   (1931 perm/sec)   p_kst 2.564103e-06   p_cons 9.860744e-01   p_joint 3.589744e-05

Joint ci ratio: 7.156768e-01	ci left: 2.458463e-05	ci right 5.271963e-05	k: 29	n:790000
Cons ci ratio: 5.241056e-04	ci left: 9.858151e-01	ci right 9.863332e-01	k: 779000	n:790000
KS ci ratio: 1.959994e+00	ci left: 7.831300e-07	ci right 1.109777e-05	k: 3	n:790000
ZNF814   790000 perm   412 sec   (1917 perm/sec)   p_kst 3.797468e-06   p_cons 9.860759e-01   p_joint 3.670886e-05

Joint ci ratio: 7.156769e-01	ci left: 2.427732e-05	ci right 5.206064e-05	k: 29	n:800000
Cons ci ratio: 5.209084e-04	ci left: 9.858120e-01	ci right 9.863269e-01	k: 788857	n:800000
KS ci ratio: 1.959994e+00	ci left: 7.733408e-07	ci right 1.095905e-05	k: 3	n:800000
ZNF814   800000 perm   420 sec   (1903 perm/sec)   p_kst 3.750000e-06   p_cons 9.860712e-01   p_joint 3.625000e-05

Joint ci ratio: 8.001543e-01	ci left: 1.800012e-05	ci right 4.260623e-05	k: 23	n:810000
Cons ci ratio: 5.178621e-04	ci left: 9.858041e-01	ci right 9.863159e-01	k: 798710	n:810000
KS ci ratio: 1.959994e+00	ci left: 7.637934e-07	ci right 1.082376e-05	k: 3	n:810000
ZNF814   810000 perm   430 sec   (1885 perm/sec)   p_kst 3.703704e-06   p_cons 9.860617e-01   p_joint 2.839506e-05

Joint ci ratio: 8.001545e-01	ci left: 1.778060e-05	ci right 4.208665e-05	k: 23	n:820000
Cons ci ratio: 5.147085e-04	ci left: 9.858049e-01	ci right 9.863136e-01	k: 808570	n:820000
KS ci ratio: 1.959994e+00	ci left: 7.544788e-07	ci right 1.069176e-05	k: 3	n:820000
ZNF814   820000 perm   438 sec   (1870 perm/sec)   p_kst 3.658537e-06   p_cons 9.860610e-01   p_joint 2.804878e-05

Joint ci ratio: 7.839877e-01	ci left: 1.852690e-05	ci right 4.302391e-05	k: 24	n:830000
Cons ci ratio: 5.114325e-04	ci left: 9.858154e-01	ci right 9.863209e-01	k: 818438	n:830000
KS ci ratio: 1.959994e+00	ci left: 7.453887e-07	ci right 1.056294e-05	k: 3	n:830000
ZNF814   830000 perm   447 sec   (1857 perm/sec)   p_kst 3.614458e-06   p_cons 9.860699e-01   p_joint 2.891566e-05

Joint ci ratio: 7.687629e-01	ci left: 1.926043e-05	ci right 4.393413e-05	k: 25	n:840000
Cons ci ratio: 5.083503e-04	ci left: 9.858185e-01	ci right 9.863210e-01	k: 828300	n:840000
KS ci ratio: 1.959994e+00	ci left: 7.365150e-07	ci right 1.043719e-05	k: 3	n:840000
ZNF814   840000 perm   455 sec   (1845 perm/sec)   p_kst 3.571429e-06   p_cons 9.860714e-01   p_joint 2.976190e-05

Joint ci ratio: 7.687630e-01	ci left: 1.903383e-05	ci right 4.341726e-05	k: 25	n:850000
Cons ci ratio: 5.053230e-04	ci left: 9.858216e-01	ci right 9.863210e-01	k: 838162	n:850000
KS ci ratio: 1.959994e+00	ci left: 7.278501e-07	ci right 1.031440e-05	k: 3	n:850000
ZNF814   850000 perm   465 sec   (1830 perm/sec)   p_kst 3.529412e-06   p_cons 9.860729e-01   p_joint 2.941176e-05

Joint ci ratio: 7.687632e-01	ci left: 1.881251e-05	ci right 4.291241e-05	k: 25	n:860000
Cons ci ratio: 5.023493e-04	ci left: 9.858245e-01	ci right 9.863210e-01	k: 848024	n:860000
KS ci ratio: 1.959994e+00	ci left: 7.193868e-07	ci right 1.019447e-05	k: 3	n:860000
ZNF814   860000 perm   474 sec   (1814 perm/sec)   p_kst 3.488372e-06   p_cons 9.860744e-01   p_joint 2.906977e-05

Joint ci ratio: 7.687633e-01	ci left: 1.859627e-05	ci right 4.241917e-05	k: 25	n:870000
Cons ci ratio: 4.995946e-04	ci left: 9.858182e-01	ci right 9.863119e-01	k: 857878	n:870000
KS ci ratio: 1.959994e+00	ci left: 7.111179e-07	ci right 1.007729e-05	k: 3	n:870000
ZNF814   870000 perm   483 sec   (1801 perm/sec)   p_kst 3.448276e-06   p_cons 9.860667e-01   p_joint 2.873563e-05

Joint ci ratio: 7.687635e-01	ci left: 1.838495e-05	ci right 4.193714e-05	k: 25	n:880000
Cons ci ratio: 4.967819e-04	ci left: 9.858177e-01	ci right 9.863087e-01	k: 867737	n:880000
KS ci ratio: 1.959994e+00	ci left: 7.030371e-07	ci right 9.962778e-06	k: 3	n:880000
ZNF814   880000 perm   493 sec   (1786 perm/sec)   p_kst 3.409091e-06   p_cons 9.860648e-01   p_joint 2.840909e-05

Joint ci ratio: 7.687636e-01	ci left: 1.817837e-05	ci right 4.146594e-05	k: 25	n:890000
Cons ci ratio: 4.937738e-04	ci left: 9.858308e-01	ci right 9.863188e-01	k: 877608	n:890000
KS ci ratio: 1.959994e+00	ci left: 6.951378e-07	ci right 9.850837e-06	k: 3	n:890000
ZNF814   890000 perm   502 sec   (1771 perm/sec)   p_kst 3.370787e-06   p_cons 9.860764e-01   p_joint 2.808989e-05

Joint ci ratio: 7.687637e-01	ci left: 1.797639e-05	ci right 4.100521e-05	k: 25	n:900000
Cons ci ratio: 4.904615e-04	ci left: 9.858638e-01	ci right 9.863486e-01	k: 887497	n:900000
KS ci ratio: 1.959995e+00	ci left: 6.874140e-07	ci right 9.741383e-06	k: 3	n:900000
ZNF814   900000 perm   512 sec   (1759 perm/sec)   p_kst 3.333333e-06   p_cons 9.861078e-01   p_joint 2.777778e-05

Joint ci ratio: 7.687638e-01	ci left: 1.777885e-05	ci right 4.055460e-05	k: 25	n:910000
Cons ci ratio: 4.876627e-04	ci left: 9.858707e-01	ci right 9.863526e-01	k: 897363	n:910000
KS ci ratio: 1.959995e+00	ci left: 6.798600e-07	ci right 9.634335e-06	k: 3	n:910000
ZNF814   910000 perm   520 sec   (1749 perm/sec)   p_kst 3.296703e-06   p_cons 9.861132e-01   p_joint 2.747253e-05

Joint ci ratio: 7.687640e-01	ci left: 1.758560e-05	ci right 4.011380e-05	k: 25	n:920000
Cons ci ratio: 4.850074e-04	ci left: 9.858718e-01	ci right 9.863512e-01	k: 907224	n:920000
KS ci ratio: 1.959995e+00	ci left: 6.724702e-07	ci right 9.529615e-06	k: 3	n:920000
ZNF814   920000 perm   530 sec   (1737 perm/sec)   p_kst 3.260870e-06   p_cons 9.861130e-01   p_joint 2.717391e-05

Joint ci ratio: 7.687641e-01	ci left: 1.739651e-05	ci right 3.968247e-05	k: 25	n:930000
Cons ci ratio: 4.824330e-04	ci left: 9.858708e-01	ci right 9.863476e-01	k: 917083	n:930000
KS ci ratio: 1.959995e+00	ci left: 6.652393e-07	ci right 9.427146e-06	k: 3	n:930000
ZNF814   930000 perm   539 sec   (1725 perm/sec)   p_kst 3.225806e-06   p_cons 9.861108e-01   p_joint 2.688172e-05

Joint ci ratio: 7.687642e-01	ci left: 1.721144e-05	ci right 3.926032e-05	k: 25	n:940000
Cons ci ratio: 4.798432e-04	ci left: 9.858731e-01	ci right 9.863473e-01	k: 926945	n:940000
KS ci ratio: 1.959995e+00	ci left: 6.581623e-07	ci right 9.326858e-06	k: 3	n:940000
ZNF814   940000 perm   550 sec   (1710 perm/sec)   p_kst 3.191489e-06   p_cons 9.861117e-01   p_joint 2.659574e-05

Joint ci ratio: 7.687643e-01	ci left: 1.703026e-05	ci right 3.884705e-05	k: 25	n:950000
Cons ci ratio: 4.775330e-04	ci left: 9.858615e-01	ci right 9.863334e-01	k: 936794	n:950000
KS ci ratio: 1.959995e+00	ci left: 6.512343e-07	ci right 9.228680e-06	k: 3	n:950000
ZNF814   950000 perm   560 sec   (1697 perm/sec)   p_kst 3.157895e-06   p_cons 9.860989e-01   p_joint 2.631579e-05

Joint ci ratio: 7.687644e-01	ci left: 1.685286e-05	ci right 3.844240e-05	k: 25	n:960000
Cons ci ratio: 4.749668e-04	ci left: 9.858670e-01	ci right 9.863363e-01	k: 946659	n:960000
KS ci ratio: 1.959995e+00	ci left: 6.444506e-07	ci right 9.132549e-06	k: 3	n:960000
ZNF814   960000 perm   569 sec   (1686 perm/sec)   p_kst 3.125000e-06   p_cons 9.861031e-01   p_joint 2.604167e-05

Joint ci ratio: 7.687646e-01	ci left: 1.667912e-05	ci right 3.804609e-05	k: 25	n:970000
Cons ci ratio: 4.727080e-04	ci left: 9.858567e-01	ci right 9.863239e-01	k: 956509	n:970000
KS ci ratio: 1.959995e+00	ci left: 6.378068e-07	ci right 9.038399e-06	k: 3	n:970000
ZNF814   970000 perm   579 sec   (1675 perm/sec)   p_kst 3.092784e-06   p_cons 9.860918e-01   p_joint 2.577320e-05

Joint ci ratio: 7.687647e-01	ci left: 1.650892e-05	ci right 3.765786e-05	k: 25	n:980000
Cons ci ratio: 4.701484e-04	ci left: 9.858663e-01	ci right 9.863309e-01	k: 966378	n:980000
KS ci ratio: 1.959995e+00	ci left: 6.312985e-07	ci right 8.946171e-06	k: 3	n:980000
ZNF814   980000 perm   589 sec   (1663 perm/sec)   p_kst 3.061224e-06   p_cons 9.861000e-01   p_joint 2.551020e-05

Joint ci ratio: 7.687648e-01	ci left: 1.634217e-05	ci right 3.727748e-05	k: 25	n:990000
Cons ci ratio: 4.678022e-04	ci left: 9.858654e-01	ci right 9.863277e-01	k: 976237	n:990000
KS ci ratio: 1.959995e+00	ci left: 6.249218e-07	ci right 8.855806e-06	k: 3	n:990000
ZNF814   990000 perm   599 sec   (1652 perm/sec)   p_kst 3.030303e-06   p_cons 9.860980e-01   p_joint 2.525253e-05

Joint ci ratio: 7.687649e-01	ci left: 1.617875e-05	ci right 3.690471e-05	k: 25	n:1000000
Cons ci ratio: 4.655078e-04	ci left: 9.858636e-01	ci right 9.863236e-01	k: 986095	n:1000000
KS ci ratio: 1.959995e+00	ci left: 6.186726e-07	ci right 8.767248e-06	k: 3	n:1000000
ZNF814   1000000 perm   610 sec   (1639 perm/sec)   p_kst 3.000000e-06   p_cons 9.860950e-01   p_joint 2.500000e-05

Joint ci ratio: 7.543939e-01	ci left: 1.681597e-05	ci right 3.771861e-05	k: 26	n:1010000
Cons ci ratio: 4.631631e-04	ci left: 9.858668e-01	ci right 9.863245e-01	k: 995958	n:1010000
KS ci ratio: 1.959995e+00	ci left: 6.125471e-07	ci right 8.680444e-06	k: 3	n:1010000
ZNF814   1010000 perm   621 sec   (1628 perm/sec)   p_kst 2.970297e-06   p_cons 9.860970e-01   p_joint 2.574257e-05

Joint ci ratio: 7.543940e-01	ci left: 1.665111e-05	ci right 3.734882e-05	k: 26	n:1020000
Cons ci ratio: 4.608700e-04	ci left: 9.858689e-01	ci right 9.863244e-01	k: 1005820	n:1020000
KS ci ratio: 1.959995e+00	ci left: 6.065417e-07	ci right 8.595341e-06	k: 3	n:1020000
ZNF814   1020000 perm   631 sec   (1617 perm/sec)   p_kst 2.941176e-06   p_cons 9.860980e-01   p_joint 2.549020e-05

Joint ci ratio: 7.407999e-01	ci left: 1.727499e-05	ci right 3.813917e-05	k: 27	n:1030000
Cons ci ratio: 4.587243e-04	ci left: 9.858642e-01	ci right 9.863175e-01	k: 1015675	n:1030000
KS ci ratio: 1.753072e+00	ci left: 1.058123e-06	ci right 9.943260e-06	k: 4	n:1030000
ZNF814   1030000 perm   641 sec   (1607 perm/sec)   p_kst 3.883495e-06   p_cons 9.860922e-01   p_joint 2.621359e-05

Joint ci ratio: 7.408000e-01	ci left: 1.710888e-05	ci right 3.777245e-05	k: 27	n:1040000
Cons ci ratio: 4.564001e-04	ci left: 9.858722e-01	ci right 9.863232e-01	k: 1025543	n:1040000
KS ci ratio: 1.753072e+00	ci left: 1.047948e-06	ci right 9.847652e-06	k: 4	n:1040000
ZNF814   1040000 perm   651 sec   (1597 perm/sec)   p_kst 3.846154e-06   p_cons 9.860990e-01   p_joint 2.596154e-05

Joint ci ratio: 7.408001e-01	ci left: 1.694594e-05	ci right 3.741272e-05	k: 27	n:1050000
Cons ci ratio: 4.544263e-04	ci left: 9.858608e-01	ci right 9.863098e-01	k: 1035391	n:1050000
KS ci ratio: 1.753072e+00	ci left: 1.037968e-06	ci right 9.753865e-06	k: 4	n:1050000
ZNF814   1050000 perm   661 sec   (1587 perm/sec)   p_kst 3.809524e-06   p_cons 9.860867e-01   p_joint 2.571429e-05

Joint ci ratio: 7.408002e-01	ci left: 1.678607e-05	ci right 3.705977e-05	k: 27	n:1060000
Cons ci ratio: 4.521200e-04	ci left: 9.858715e-01	ci right 9.863183e-01	k: 1045262	n:1060000
KS ci ratio: 1.753072e+00	ci left: 1.028176e-06	ci right 9.661848e-06	k: 4	n:1060000
ZNF814   1060000 perm   672 sec   (1577 perm/sec)   p_kst 3.773585e-06   p_cons 9.860962e-01   p_joint 2.547170e-05

Joint ci ratio: 7.279155e-01	ci left: 1.738866e-05	ci right 3.782015e-05	k: 28	n:1070000
Cons ci ratio: 4.499250e-04	ci left: 9.858773e-01	ci right 9.863219e-01	k: 1055128	n:1070000
KS ci ratio: 1.753072e+00	ci left: 1.018567e-06	ci right 9.571550e-06	k: 4	n:1070000
ZNF814   1070000 perm   682 sec   (1568 perm/sec)   p_kst 3.738318e-06   p_cons 9.861009e-01   p_joint 2.616822e-05

Joint ci ratio: 7.279156e-01	ci left: 1.722766e-05	ci right 3.746997e-05	k: 28	n:1080000
Cons ci ratio: 4.477615e-04	ci left: 9.858830e-01	ci right 9.863255e-01	k: 1064994	n:1080000
KS ci ratio: 1.753072e+00	ci left: 1.009135e-06	ci right 9.482925e-06	k: 4	n:1080000
ZNF814   1080000 perm   693 sec   (1558 perm/sec)   p_kst 3.703704e-06   p_cons 9.861056e-01   p_joint 2.592593e-05

Joint ci ratio: 7.279157e-01	ci left: 1.706960e-05	ci right 3.712621e-05	k: 28	n:1090000
Cons ci ratio: 4.460018e-04	ci left: 9.858655e-01	ci right 9.863062e-01	k: 1074835	n:1090000
KS ci ratio: 1.753072e+00	ci left: 9.998774e-07	ci right 9.395926e-06	k: 4	n:1090000
ZNF814   1090000 perm   704 sec   (1548 perm/sec)   p_kst 3.669725e-06   p_cons 9.860872e-01   p_joint 2.568807e-05

Joint ci ratio: 7.156807e-01	ci left: 1.765621e-05	ci right 3.786236e-05	k: 29	n:1100000
Cons ci ratio: 4.885517e-04	ci left: 9.829599e-01	ci right 9.834412e-01	k: 1081522	n:1100000
KS ci ratio: 1.753073e+00	ci left: 9.907876e-07	ci right 9.310509e-06	k: 4	n:1100000
ZNF814   1100000 perm   714 sec   (1540 perm/sec)   p_kst 3.636364e-06   p_cons 9.832018e-01   p_joint 2.636364e-05

Joint ci ratio: 7.156808e-01	ci left: 1.749714e-05	ci right 3.752126e-05	k: 29	n:1110000
Cons ci ratio: 4.863726e-04	ci left: 9.829592e-01	ci right 9.834383e-01	k: 1091352	n:1110000
KS ci ratio: 1.753073e+00	ci left: 9.818615e-07	ci right 9.226631e-06	k: 4	n:1110000
ZNF814   1110000 perm   725 sec   (1531 perm/sec)   p_kst 3.603604e-06   p_cons 9.832000e-01   p_joint 2.612613e-05

Joint ci ratio: 8.173677e-01	ci left: 1.231011e-05	ci right 2.973937e-05	k: 22	n:1120000
Cons ci ratio: 4.843272e-04	ci left: 9.829513e-01	ci right 9.834284e-01	k: 1101174	n:1120000
KS ci ratio: 1.753073e+00	ci left: 9.730949e-07	ci right 9.144250e-06	k: 4	n:1120000
ZNF814   1120000 perm   737 sec   (1519 perm/sec)   p_kst 3.571429e-06   p_cons 9.831911e-01   p_joint 1.964286e-05

Joint ci ratio: 8.173678e-01	ci left: 1.220117e-05	ci right 2.947619e-05	k: 22	n:1130000
Cons ci ratio: 4.821394e-04	ci left: 9.829551e-01	ci right 9.834300e-01	k: 1111009	n:1130000
KS ci ratio: 1.753073e+00	ci left: 9.644834e-07	ci right 9.063328e-06	k: 4	n:1130000
ZNF814   1130000 perm   748 sec   (1510 perm/sec)   p_kst 3.539823e-06   p_cons 9.831938e-01   p_joint 1.946903e-05

Joint ci ratio: 8.173679e-01	ci left: 1.209415e-05	ci right 2.921763e-05	k: 22	n:1140000
Cons ci ratio: 4.803504e-04	ci left: 9.829333e-01	ci right 9.834064e-01	k: 1120815	n:1140000
KS ci ratio: 1.753073e+00	ci left: 9.560231e-07	ci right 8.983825e-06	k: 4	n:1140000
ZNF814   1140000 perm   760 sec   (1500 perm/sec)   p_kst 3.508772e-06   p_cons 9.831711e-01   p_joint 1.929825e-05

Joint ci ratio: 8.173680e-01	ci left: 1.198898e-05	ci right 2.896357e-05	k: 22	n:1150000
Cons ci ratio: 4.780399e-04	ci left: 9.829494e-01	ci right 9.834203e-01	k: 1130664	n:1150000
KS ci ratio: 1.753073e+00	ci left: 9.477098e-07	ci right 8.905705e-06	k: 4	n:1150000
ZNF814   1150000 perm   771 sec   (1491 perm/sec)   p_kst 3.478261e-06   p_cons 9.831861e-01   p_joint 1.913043e-05

Joint ci ratio: 8.173680e-01	ci left: 1.188563e-05	ci right 2.871388e-05	k: 22	n:1160000
Cons ci ratio: 4.762461e-04	ci left: 9.829315e-01	ci right 9.834006e-01	k: 1140474	n:1160000
KS ci ratio: 1.753073e+00	ci left: 9.395399e-07	ci right 8.828932e-06	k: 4	n:1160000
ZNF814   1160000 perm   783 sec   (1482 perm/sec)   p_kst 3.448276e-06   p_cons 9.831672e-01   p_joint 1.896552e-05

Joint ci ratio: 8.173681e-01	ci left: 1.178404e-05	ci right 2.846846e-05	k: 22	n:1170000
Cons ci ratio: 4.743248e-04	ci left: 9.829242e-01	ci right 9.833914e-01	k: 1150296	n:1170000
KS ci ratio: 1.753073e+00	ci left: 9.315096e-07	ci right 8.753471e-06	k: 4	n:1170000
ZNF814   1170000 perm   796 sec   (1470 perm/sec)   p_kst 3.418803e-06   p_cons 9.831590e-01   p_joint 1.880342e-05

Joint ci ratio: 8.173682e-01	ci left: 1.168417e-05	ci right 2.822721e-05	k: 22	n:1180000
Cons ci ratio: 4.723902e-04	ci left: 9.829196e-01	ci right 9.833848e-01	k: 1160121	n:1180000
KS ci ratio: 1.753073e+00	ci left: 9.236155e-07	ci right 8.679289e-06	k: 4	n:1180000
ZNF814   1180000 perm   807 sec   (1462 perm/sec)   p_kst 3.389831e-06   p_cons 9.831534e-01   p_joint 1.864407e-05

Joint ci ratio: 8.173683e-01	ci left: 1.158599e-05	ci right 2.799001e-05	k: 22	n:1190000
Cons ci ratio: 4.702046e-04	ci left: 9.829345e-01	ci right 9.833976e-01	k: 1169969	n:1190000
KS ci ratio: 1.753073e+00	ci left: 9.158540e-07	ci right 8.606354e-06	k: 4	n:1190000
ZNF814   1190000 perm   819 sec   (1453 perm/sec)   p_kst 3.361345e-06   p_cons 9.831672e-01   p_joint 1.848739e-05

Joint ci ratio: 8.173683e-01	ci left: 1.148944e-05	ci right 2.775676e-05	k: 22	n:1200000
Cons ci ratio: 4.681194e-04	ci left: 9.829441e-01	ci right 9.834052e-01	k: 1179811	n:1200000
KS ci ratio: 1.753073e+00	ci left: 9.082219e-07	ci right 8.534635e-06	k: 4	n:1200000
ZNF814   1200000 perm   831 sec   (1443 perm/sec)   p_kst 3.333333e-06   p_cons 9.831758e-01   p_joint 1.833333e-05

Joint ci ratio: 8.173684e-01	ci left: 1.139448e-05	ci right 2.752736e-05	k: 22	n:1210000
Cons ci ratio: 4.660034e-04	ci left: 9.829578e-01	ci right 9.834168e-01	k: 1189658	n:1210000
KS ci ratio: 1.753073e+00	ci left: 9.007159e-07	ci right 8.464101e-06	k: 4	n:1210000
ZNF814   1210000 perm   843 sec   (1435 perm/sec)   p_kst 3.305785e-06   p_cons 9.831884e-01   p_joint 1.818182e-05

Joint ci ratio: 8.173685e-01	ci left: 1.130108e-05	ci right 2.730173e-05	k: 22	n:1220000
Cons ci ratio: 4.644103e-04	ci left: 9.829357e-01	ci right 9.833931e-01	k: 1199462	n:1220000
KS ci ratio: 1.753073e+00	ci left: 8.933330e-07	ci right 8.394723e-06	k: 4	n:1220000
ZNF814   1220000 perm   856 sec   (1426 perm/sec)   p_kst 3.278689e-06   p_cons 9.831656e-01   p_joint 1.803279e-05

Joint ci ratio: 8.173685e-01	ci left: 1.120921e-05	ci right 2.707977e-05	k: 22	n:1230000
Cons ci ratio: 4.625260e-04	ci left: 9.829361e-01	ci right 9.833917e-01	k: 1209293	n:1230000
KS ci ratio: 1.753073e+00	ci left: 8.860701e-07	ci right 8.326474e-06	k: 4	n:1230000
ZNF814   1230000 perm   868 sec   (1417 perm/sec)   p_kst 3.252033e-06   p_cons 9.831650e-01   p_joint 1.788618e-05

Joint ci ratio: 8.173686e-01	ci left: 1.111881e-05	ci right 2.686138e-05	k: 22	n:1240000
Cons ci ratio: 4.607205e-04	ci left: 9.829325e-01	ci right 9.833862e-01	k: 1219119	n:1240000
KS ci ratio: 1.753073e+00	ci left: 8.789244e-07	ci right 8.259325e-06	k: 4	n:1240000
ZNF814   1240000 perm   880 sec   (1408 perm/sec)   p_kst 3.225806e-06   p_cons 9.831605e-01   p_joint 1.774194e-05

Joint ci ratio: 8.173687e-01	ci left: 1.102986e-05	ci right 2.664649e-05	k: 22	n:1250000
Cons ci ratio: 4.590800e-04	ci left: 9.829184e-01	ci right 9.833705e-01	k: 1228932	n:1250000
KS ci ratio: 1.753073e+00	ci left: 8.718930e-07	ci right 8.193250e-06	k: 4	n:1250000
ZNF814   1250000 perm   893 sec   (1400 perm/sec)   p_kst 3.200000e-06   p_cons 9.831456e-01   p_joint 1.760000e-05

Joint ci ratio: 8.173687e-01	ci left: 1.094232e-05	ci right 2.643501e-05	k: 22	n:1260000
Cons ci ratio: 4.572158e-04	ci left: 9.829222e-01	ci right 9.833724e-01	k: 1238767	n:1260000
KS ci ratio: 1.753073e+00	ci left: 8.649732e-07	ci right 8.128225e-06	k: 4	n:1260000
ZNF814   1260000 perm   905 sec   (1392 perm/sec)   p_kst 3.174603e-06   p_cons 9.831484e-01   p_joint 1.746032e-05

Joint ci ratio: 8.173688e-01	ci left: 1.085616e-05	ci right 2.622686e-05	k: 22	n:1270000
Cons ci ratio: 4.553740e-04	ci left: 9.829258e-01	ci right 9.833743e-01	k: 1248602	n:1270000
KS ci ratio: 1.753073e+00	ci left: 8.581624e-07	ci right 8.064223e-06	k: 4	n:1270000
ZNF814   1270000 perm   918 sec   (1384 perm/sec)   p_kst 3.149606e-06   p_cons 9.831512e-01   p_joint 1.732283e-05

Joint ci ratio: 8.173688e-01	ci left: 1.077135e-05	ci right 2.602197e-05	k: 22	n:1280000
Cons ci ratio: 4.534688e-04	ci left: 9.829358e-01	ci right 9.833824e-01	k: 1258445	n:1280000
KS ci ratio: 1.753073e+00	ci left: 8.514580e-07	ci right 8.001222e-06	k: 4	n:1280000
ZNF814   1280000 perm   930 sec   (1376 perm/sec)   p_kst 3.125000e-06   p_cons 9.831602e-01   p_joint 1.718750e-05

Joint ci ratio: 8.173689e-01	ci left: 1.068785e-05	ci right 2.582025e-05	k: 22	n:1290000
Cons ci ratio: 4.517034e-04	ci left: 9.829369e-01	ci right 9.833818e-01	k: 1268277	n:1290000
KS ci ratio: 1.753073e+00	ci left: 8.448575e-07	ci right 7.939197e-06	k: 4	n:1290000
ZNF814   1290000 perm   943 sec   (1368 perm/sec)   p_kst 3.100775e-06   p_cons 9.831605e-01   p_joint 1.705426e-05

Joint ci ratio: 8.001590e-01	ci left: 1.121544e-05	ci right 2.654703e-05	k: 23	n:1300000
Cons ci ratio: 4.498331e-04	ci left: 9.829474e-01	ci right 9.833904e-01	k: 1278121	n:1300000
KS ci ratio: 1.753073e+00	ci left: 8.383586e-07	ci right 7.878126e-06	k: 4	n:1300000
ZNF814   1300000 perm   956 sec   (1360 perm/sec)   p_kst 3.076923e-06   p_cons 9.831700e-01   p_joint 1.769231e-05

Joint ci ratio: 8.001590e-01	ci left: 1.112982e-05	ci right 2.634438e-05	k: 23	n:1310000
Cons ci ratio: 4.479960e-04	ci left: 9.829570e-01	ci right 9.833982e-01	k: 1287964	n:1310000
KS ci ratio: 1.753073e+00	ci left: 8.319589e-07	ci right 7.817988e-06	k: 4	n:1310000
ZNF814   1310000 perm   969 sec   (1352 perm/sec)   p_kst 3.053435e-06   p_cons 9.831786e-01   p_joint 1.755725e-05

Joint ci ratio: 7.839923e-01	ci left: 1.164947e-05	ci right 2.705298e-05	k: 24	n:1320000
Cons ci ratio: 4.461913e-04	ci left: 9.829656e-01	ci right 9.834050e-01	k: 1297806	n:1320000
KS ci ratio: 1.753073e+00	ci left: 8.256562e-07	ci right 7.758761e-06	k: 4	n:1320000
ZNF814   1320000 perm   982 sec   (1344 perm/sec)   p_kst 3.030303e-06   p_cons 9.831864e-01   p_joint 1.818182e-05

Joint ci ratio: 7.839923e-01	ci left: 1.156188e-05	ci right 2.684958e-05	k: 24	n:1330000
Cons ci ratio: 4.444385e-04	ci left: 9.829718e-01	ci right 9.834095e-01	k: 1307645	n:1330000
KS ci ratio: 1.753073e+00	ci left: 8.194482e-07	ci right 7.700425e-06	k: 4	n:1330000
ZNF814   1330000 perm   995 sec   (1337 perm/sec)   p_kst 3.007519e-06   p_cons 9.831917e-01   p_joint 1.804511e-05

Joint ci ratio: 7.839924e-01	ci left: 1.147559e-05	ci right 2.664921e-05	k: 24	n:1340000
Cons ci ratio: 4.428362e-04	ci left: 9.829682e-01	ci right 9.834043e-01	k: 1317471	n:1340000
KS ci ratio: 1.753073e+00	ci left: 8.133329e-07	ci right 7.642959e-06	k: 4	n:1340000
ZNF814   1340000 perm   1008 sec   (1330 perm/sec)   p_kst 2.985075e-06   p_cons 9.831873e-01   p_joint 1.791045e-05

Joint ci ratio: 7.687676e-01	ci left: 1.198424e-05	ci right 2.733687e-05	k: 25	n:1350000
Cons ci ratio: 4.411323e-04	ci left: 9.829736e-01	ci right 9.834080e-01	k: 1327309	n:1350000
KS ci ratio: 1.753073e+00	ci left: 8.073083e-07	ci right 7.586344e-06	k: 4	n:1350000
ZNF814   1350000 perm   1020 sec   (1323 perm/sec)   p_kst 2.962963e-06   p_cons 9.831919e-01   p_joint 1.851852e-05

Joint ci ratio: 7.687676e-01	ci left: 1.189612e-05	ci right 2.713586e-05	k: 25	n:1360000
Cons ci ratio: 4.394480e-04	ci left: 9.829789e-01	ci right 9.834117e-01	k: 1337147	n:1360000
KS ci ratio: 1.753073e+00	ci left: 8.013722e-07	ci right 7.530563e-06	k: 4	n:1360000
ZNF814   1360000 perm   1033 sec   (1316 perm/sec)   p_kst 2.941176e-06   p_cons 9.831963e-01   p_joint 1.838235e-05

Joint ci ratio: 7.543966e-01	ci left: 1.239716e-05	ci right 2.780719e-05	k: 26	n:1370000
Cons ci ratio: 4.379279e-04	ci left: 9.829731e-01	ci right 9.834044e-01	k: 1346970	n:1370000
KS ci ratio: 1.753073e+00	ci left: 7.955227e-07	ci right 7.475595e-06	k: 4	n:1370000
ZNF814   1370000 perm   1047 sec   (1308 perm/sec)   p_kst 2.919708e-06   p_cons 9.831898e-01   p_joint 1.897810e-05

Joint ci ratio: 7.543967e-01	ci left: 1.230733e-05	ci right 2.760569e-05	k: 26	n:1380000
Cons ci ratio: 4.363946e-04	ci left: 9.829696e-01	ci right 9.833994e-01	k: 1356796	n:1380000
KS ci ratio: 1.753073e+00	ci left: 7.897581e-07	ci right 7.421424e-06	k: 4	n:1380000
ZNF814   1380000 perm   1061 sec   (1301 perm/sec)   p_kst 2.898551e-06   p_cons 9.831855e-01   p_joint 1.884058e-05

Joint ci ratio: 7.543968e-01	ci left: 1.221879e-05	ci right 2.740709e-05	k: 26	n:1390000
Cons ci ratio: 4.348017e-04	ci left: 9.829719e-01	ci right 9.834001e-01	k: 1366630	n:1390000
KS ci ratio: 1.753074e+00	ci left: 7.840763e-07	ci right 7.368033e-06	k: 4	n:1390000
ZNF814   1390000 perm   1074 sec   (1294 perm/sec)   p_kst 2.877698e-06   p_cons 9.831871e-01   p_joint 1.870504e-05

Joint ci ratio: 7.543968e-01	ci left: 1.213151e-05	ci right 2.721133e-05	k: 26	n:1400000
Cons ci ratio: 4.329077e-04	ci left: 9.829987e-01	ci right 9.834250e-01	k: 1376498	n:1400000
KS ci ratio: 1.753074e+00	ci left: 7.784758e-07	ci right 7.315404e-06	k: 4	n:1400000
ZNF814   1400000 perm   1087 sec   (1288 perm/sec)   p_kst 2.857143e-06   p_cons 9.832129e-01   p_joint 1.857143e-05

Joint ci ratio: 7.543969e-01	ci left: 1.204547e-05	ci right 2.701834e-05	k: 26	n:1410000
Cons ci ratio: 4.314543e-04	ci left: 9.829929e-01	ci right 9.834178e-01	k: 1386321	n:1410000
KS ci ratio: 1.753074e+00	ci left: 7.729547e-07	ci right 7.263522e-06	k: 4	n:1410000
ZNF814   1410000 perm   1100 sec   (1282 perm/sec)   p_kst 2.836879e-06   p_cons 9.832064e-01   p_joint 1.843972e-05

Joint ci ratio: 7.408028e-01	ci left: 1.253044e-05	ci right 2.766438e-05	k: 27	n:1420000
Cons ci ratio: 4.300338e-04	ci left: 9.829859e-01	ci right 9.834094e-01	k: 1396142	n:1420000
KS ci ratio: 1.753074e+00	ci left: 7.675113e-07	ci right 7.212371e-06	k: 4	n:1420000
ZNF814   1420000 perm   1113 sec   (1275 perm/sec)   p_kst 2.816901e-06   p_cons 9.831986e-01   p_joint 1.901408e-05

Joint ci ratio: 7.408029e-01	ci left: 1.244281e-05	ci right 2.747092e-05	k: 27	n:1430000
Cons ci ratio: 4.285002e-04	ci left: 9.829887e-01	ci right 9.834107e-01	k: 1405977	n:1430000
KS ci ratio: 1.753074e+00	ci left: 7.621441e-07	ci right 7.161934e-06	k: 4	n:1430000
ZNF814   1430000 perm   1126 sec   (1270 perm/sec)   p_kst 2.797203e-06   p_cons 9.832007e-01   p_joint 1.888112e-05

Joint ci ratio: 7.408029e-01	ci left: 1.235640e-05	ci right 2.728015e-05	k: 27	n:1440000
Cons ci ratio: 4.268122e-04	ci left: 9.830048e-01	ci right 9.834252e-01	k: 1415831	n:1440000
KS ci ratio: 1.753074e+00	ci left: 7.568515e-07	ci right 7.112199e-06	k: 4	n:1440000
ZNF814   1440000 perm   1139 sec   (1264 perm/sec)   p_kst 2.777778e-06   p_cons 9.832160e-01   p_joint 1.875000e-05

Joint ci ratio: 7.408030e-01	ci left: 1.227119e-05	ci right 2.709201e-05	k: 27	n:1450000
Cons ci ratio: 4.252326e-04	ci left: 9.830138e-01	ci right 9.834326e-01	k: 1425675	n:1450000
KS ci ratio: 1.753074e+00	ci left: 7.516318e-07	ci right 7.063149e-06	k: 4	n:1450000
ZNF814   1450000 perm   1152 sec   (1258 perm/sec)   p_kst 2.758621e-06   p_cons 9.832241e-01   p_joint 1.862069e-05

Joint ci ratio: 7.408030e-01	ci left: 1.218714e-05	ci right 2.690645e-05	k: 27	n:1460000
Cons ci ratio: 4.240134e-04	ci left: 9.829957e-01	ci right 9.834133e-01	k: 1435480	n:1460000
KS ci ratio: 1.753074e+00	ci left: 7.464836e-07	ci right 7.014772e-06	k: 4	n:1460000
ZNF814   1460000 perm   1166 sec   (1252 perm/sec)   p_kst 2.739726e-06   p_cons 9.832055e-01   p_joint 1.849315e-05

Joint ci ratio: 7.408031e-01	ci left: 1.210423e-05	ci right 2.672341e-05	k: 27	n:1470000
Cons ci ratio: 4.225604e-04	ci left: 9.829971e-01	ci right 9.834132e-01	k: 1445313	n:1470000
KS ci ratio: 1.753074e+00	ci left: 7.414055e-07	ci right 6.967052e-06	k: 4	n:1470000
ZNF814   1470000 perm   1181 sec   (1245 perm/sec)   p_kst 2.721088e-06   p_cons 9.832061e-01   p_joint 1.836735e-05

Joint ci ratio: 7.839931e-01	ci left: 1.039006e-05	ci right 2.412835e-05	k: 24	n:1480000
Cons ci ratio: 4.211223e-04	ci left: 9.829985e-01	ci right 9.834132e-01	k: 1455146	n:1480000
KS ci ratio: 1.753074e+00	ci left: 7.363960e-07	ci right 6.919978e-06	k: 4	n:1480000
ZNF814   1480000 perm   1195 sec   (1238 perm/sec)   p_kst 2.702703e-06   p_cons 9.832068e-01   p_joint 1.621622e-05

Joint ci ratio: 7.839932e-01	ci left: 1.032033e-05	ci right 2.396641e-05	k: 24	n:1490000
Cons ci ratio: 4.196646e-04	ci left: 9.830025e-01	ci right 9.834158e-01	k: 1464983	n:1490000
KS ci ratio: 1.753074e+00	ci left: 7.314537e-07	ci right 6.873535e-06	k: 4	n:1490000
ZNF814   1490000 perm   1209 sec   (1233 perm/sec)   p_kst 2.684564e-06   p_cons 9.832101e-01   p_joint 1.610738e-05

Joint ci ratio: 7.839932e-01	ci left: 1.025153e-05	ci right 2.380664e-05	k: 24	n:1500000
Cons ci ratio: 4.181459e-04	ci left: 9.830125e-01	ci right 9.834243e-01	k: 1474829	n:1500000
KS ci ratio: 1.753074e+00	ci left: 7.265774e-07	ci right 6.827712e-06	k: 4	n:1500000
ZNF814   1500000 perm   1222 sec   (1227 perm/sec)   p_kst 2.666667e-06   p_cons 9.832193e-01   p_joint 1.600000e-05

Joint ci ratio: 7.839933e-01	ci left: 1.018364e-05	ci right 2.364898e-05	k: 24	n:1510000
Cons ci ratio: 4.167606e-04	ci left: 9.830131e-01	ci right 9.834235e-01	k: 1484661	n:1510000
KS ci ratio: 1.753074e+00	ci left: 7.217656e-07	ci right 6.782495e-06	k: 4	n:1510000
ZNF814   1510000 perm   1236 sec   (1222 perm/sec)   p_kst 2.649007e-06   p_cons 9.832192e-01   p_joint 1.589404e-05

Joint ci ratio: 7.839933e-01	ci left: 1.011664e-05	ci right 2.349339e-05	k: 24	n:1520000
Cons ci ratio: 4.153061e-04	ci left: 9.830202e-01	ci right 9.834292e-01	k: 1494503	n:1520000
KS ci ratio: 1.753074e+00	ci left: 7.170171e-07	ci right 6.737873e-06	k: 4	n:1520000
ZNF814   1520000 perm   1249 sec   (1217 perm/sec)   p_kst 2.631579e-06   p_cons 9.832257e-01   p_joint 1.578947e-05

Joint ci ratio: 7.839933e-01	ci left: 1.005052e-05	ci right 2.333984e-05	k: 24	n:1530000
Cons ci ratio: 4.139816e-04	ci left: 9.830181e-01	ci right 9.834258e-01	k: 1504331	n:1530000
KS ci ratio: 1.753074e+00	ci left: 7.123308e-07	ci right 6.693835e-06	k: 4	n:1530000
ZNF814   1530000 perm   1263 sec   (1212 perm/sec)   p_kst 2.614379e-06   p_cons 9.832229e-01   p_joint 1.568627e-05

Joint ci ratio: 7.839934e-01	ci left: 9.985254e-06	ci right 2.318829e-05	k: 24	n:1540000
Cons ci ratio: 4.126209e-04	ci left: 9.830199e-01	ci right 9.834263e-01	k: 1514165	n:1540000
KS ci ratio: 1.753074e+00	ci left: 7.077052e-07	ci right 6.650369e-06	k: 4	n:1540000
ZNF814   1540000 perm   1277 sec   (1206 perm/sec)   p_kst 2.597403e-06   p_cons 9.832240e-01   p_joint 1.558442e-05

Joint ci ratio: 8.173702e-01	ci left: 8.895042e-06	ci right 2.148912e-05	k: 22	n:1550000
Cons ci ratio: 4.111126e-04	ci left: 9.830347e-01	ci right 9.834396e-01	k: 1524019	n:1550000
KS ci ratio: 1.753074e+00	ci left: 7.031394e-07	ci right 6.607463e-06	k: 4	n:1550000
ZNF814   1550000 perm   1291 sec   (1201 perm/sec)   p_kst 2.580645e-06   p_cons 9.832381e-01   p_joint 1.419355e-05

Joint ci ratio: 8.173702e-01	ci left: 8.838022e-06	ci right 2.135137e-05	k: 22	n:1560000
Cons ci ratio: 4.097958e-04	ci left: 9.830351e-01	ci right 9.834387e-01	k: 1533851	n:1560000
KS ci ratio: 1.753074e+00	ci left: 6.986321e-07	ci right 6.565108e-06	k: 4	n:1560000
ZNF814   1560000 perm   1305 sec   (1196 perm/sec)   p_kst 2.564103e-06   p_cons 9.832378e-01   p_joint 1.410256e-05

Joint ci ratio: 8.173703e-01	ci left: 8.781729e-06	ci right 2.121538e-05	k: 22	n:1570000
Cons ci ratio: 4.084679e-04	ci left: 9.830375e-01	ci right 9.834397e-01	k: 1543686	n:1570000
KS ci ratio: 1.753074e+00	ci left: 6.941822e-07	ci right 6.523292e-06	k: 4	n:1570000
ZNF814   1570000 perm   1319 sec   (1190 perm/sec)   p_kst 2.547771e-06   p_cons 9.832395e-01   p_joint 1.401274e-05

Joint ci ratio: 8.173703e-01	ci left: 8.726148e-06	ci right 2.108110e-05	k: 22	n:1580000
Cons ci ratio: 4.071840e-04	ci left: 9.830372e-01	ci right 9.834382e-01	k: 1553517	n:1580000
KS ci ratio: 1.753074e+00	ci left: 6.897886e-07	ci right 6.482005e-06	k: 4	n:1580000
ZNF814   1580000 perm   1333 sec   (1185 perm/sec)   p_kst 2.531646e-06   p_cons 9.832386e-01   p_joint 1.392405e-05

Joint ci ratio: 9.239473e-01	ci left: 6.228393e-06	ci right 1.711859e-05	k: 17	n:1590000
Cons ci ratio: 4.058348e-04	ci left: 9.830433e-01	ci right 9.834430e-01	k: 1563358	n:1590000
KS ci ratio: 1.753074e+00	ci left: 6.854503e-07	ci right 6.441238e-06	k: 4	n:1590000
ZNF814   1590000 perm   1347 sec   (1180 perm/sec)   p_kst 2.515723e-06   p_cons 9.832440e-01   p_joint 1.069182e-05

Joint ci ratio: 6.929575e-01	ci left: 1.316441e-05	ci right 2.750115e-05	k: 31	n:1600000
Cons ci ratio: 4.045449e-04	ci left: 9.830456e-01	ci right 9.834439e-01	k: 1573193	n:1600000
KS ci ratio: 1.600330e+00	ci left: 1.014680e-06	ci right 7.292692e-06	k: 5	n:1600000
ZNF814   1600000 perm   1362 sec   (1175 perm/sec)   p_kst 3.125000e-06   p_cons 9.832456e-01   p_joint 1.937500e-05

Joint ci ratio: 6.929575e-01	ci left: 1.308264e-05	ci right 2.733034e-05	k: 31	n:1610000
Cons ci ratio: 4.031684e-04	ci left: 9.830559e-01	ci right 9.834529e-01	k: 1583041	n:1610000
KS ci ratio: 1.600330e+00	ci left: 1.008377e-06	ci right 7.247396e-06	k: 5	n:1610000
ZNF814   1610000 perm   1376 sec   (1170 perm/sec)   p_kst 3.105590e-06   p_cons 9.832553e-01   p_joint 1.925466e-05

Joint ci ratio: 6.722672e-01	ci left: 1.402207e-05	ci right 2.860746e-05	k: 33	n:1620000
Cons ci ratio: 4.018358e-04	ci left: 9.830636e-01	ci right 9.834593e-01	k: 1592885	n:1620000
KS ci ratio: 1.481617e+00	ci left: 1.359195e-06	ci right 8.061386e-06	k: 6	n:1620000
ZNF814   1620000 perm   1391 sec   (1165 perm/sec)   p_kst 3.703704e-06   p_cons 9.832623e-01   p_joint 2.037037e-05

Joint ci ratio: 6.722672e-01	ci left: 1.393604e-05	ci right 2.843195e-05	k: 33	n:1630000
Cons ci ratio: 4.005611e-04	ci left: 9.830676e-01	ci right 9.834620e-01	k: 1602723	n:1630000
KS ci ratio: 1.481617e+00	ci left: 1.350857e-06	ci right 8.011930e-06	k: 6	n:1630000
ZNF814   1630000 perm   1406 sec   (1160 perm/sec)   p_kst 3.680982e-06   p_cons 9.832656e-01   p_joint 2.024540e-05

Joint ci ratio: 6.625937e-01	ci left: 1.435735e-05	ci right 2.897036e-05	k: 34	n:1640000
Cons ci ratio: 3.994982e-04	ci left: 9.830549e-01	ci right 9.834483e-01	k: 1612534	n:1640000
KS ci ratio: 1.481617e+00	ci left: 1.342620e-06	ci right 7.963077e-06	k: 6	n:1640000
ZNF814   1640000 perm   1421 sec   (1154 perm/sec)   p_kst 3.658537e-06   p_cons 9.832524e-01   p_joint 2.073171e-05

Joint ci ratio: 6.625937e-01	ci left: 1.427034e-05	ci right 2.879479e-05	k: 34	n:1650000
Cons ci ratio: 3.982455e-04	ci left: 9.830588e-01	ci right 9.834510e-01	k: 1622372	n:1650000
KS ci ratio: 1.481617e+00	ci left: 1.334482e-06	ci right 7.914816e-06	k: 6	n:1650000
ZNF814   1650000 perm   1435 sec   (1149 perm/sec)   p_kst 3.636364e-06   p_cons 9.832558e-01   p_joint 2.060606e-05

Joint ci ratio: 6.625938e-01	ci left: 1.418437e-05	ci right 2.862132e-05	k: 34	n:1660000
Cons ci ratio: 3.969974e-04	ci left: 9.830633e-01	ci right 9.834543e-01	k: 1632211	n:1660000
KS ci ratio: 1.481617e+00	ci left: 1.326443e-06	ci right 7.867136e-06	k: 6	n:1660000
ZNF814   1660000 perm   1450 sec   (1145 perm/sec)   p_kst 3.614458e-06   p_cons 9.832596e-01   p_joint 2.048193e-05

Joint ci ratio: 6.625938e-01	ci left: 1.409943e-05	ci right 2.844994e-05	k: 34	n:1670000
Cons ci ratio: 3.959696e-04	ci left: 9.830503e-01	ci right 9.834402e-01	k: 1642021	n:1670000
KS ci ratio: 1.481617e+00	ci left: 1.318501e-06	ci right 7.820028e-06	k: 6	n:1670000
ZNF814   1670000 perm   1465 sec   (1140 perm/sec)   p_kst 3.592814e-06   p_cons 9.832461e-01   p_joint 2.035928e-05

Joint ci ratio: 6.625938e-01	ci left: 1.401551e-05	ci right 2.828060e-05	k: 34	n:1680000
Cons ci ratio: 3.949708e-04	ci left: 9.830357e-01	ci right 9.834246e-01	k: 1651828	n:1680000
KS ci ratio: 1.481617e+00	ci left: 1.310652e-06	ci right 7.773480e-06	k: 6	n:1680000
ZNF814   1680000 perm   1480 sec   (1135 perm/sec)   p_kst 3.571429e-06   p_cons 9.832310e-01   p_joint 2.023810e-05

Joint ci ratio: 6.625939e-01	ci left: 1.393258e-05	ci right 2.811326e-05	k: 34	n:1690000
Cons ci ratio: 3.938522e-04	ci left: 9.830319e-01	ci right 9.834197e-01	k: 1661653	n:1690000
KS ci ratio: 1.481617e+00	ci left: 1.302897e-06	ci right 7.727483e-06	k: 6	n:1690000
ZNF814   1690000 perm   1496 sec   (1130 perm/sec)   p_kst 3.550296e-06   p_cons 9.832266e-01   p_joint 2.011834e-05

Joint ci ratio: 6.533262e-01	ci left: 1.434050e-05	ci right 2.863314e-05	k: 35	n:1700000
Cons ci ratio: 3.926379e-04	ci left: 9.830370e-01	ci right 9.834237e-01	k: 1671493	n:1700000
KS ci ratio: 1.481617e+00	ci left: 1.295233e-06	ci right 7.682028e-06	k: 6	n:1700000
ZNF814   1700000 perm   1512 sec   (1124 perm/sec)   p_kst 3.529412e-06   p_cons 9.832312e-01   p_joint 2.058824e-05

Joint ci ratio: 6.444369e-01	ci left: 1.474505e-05	ci right 2.914560e-05	k: 36	n:1710000
Cons ci ratio: 3.913930e-04	ci left: 9.830457e-01	ci right 9.834311e-01	k: 1681339	n:1710000
KS ci ratio: 1.481617e+00	ci left: 1.287659e-06	ci right 7.637104e-06	k: 6	n:1710000
ZNF814   1710000 perm   1527 sec   (1120 perm/sec)   p_kst 3.508772e-06   p_cons 9.832392e-01   p_joint 2.105263e-05

Joint ci ratio: 6.444369e-01	ci left: 1.465932e-05	ci right 2.897615e-05	k: 36	n:1720000
Cons ci ratio: 3.901255e-04	ci left: 9.830571e-01	ci right 9.834413e-01	k: 1691190	n:1720000
KS ci ratio: 1.481617e+00	ci left: 1.280172e-06	ci right 7.592702e-06	k: 6	n:1720000
ZNF814   1720000 perm   1543 sec   (1115 perm/sec)   p_kst 3.488372e-06   p_cons 9.832500e-01   p_joint 2.093023e-05

Joint ci ratio: 6.444370e-01	ci left: 1.457458e-05	ci right 2.880866e-05	k: 36	n:1730000
Cons ci ratio: 3.889587e-04	ci left: 9.830609e-01	ci right 9.834439e-01	k: 1701028	n:1730000
KS ci ratio: 1.481617e+00	ci left: 1.272772e-06	ci right 7.548814e-06	k: 6	n:1730000
ZNF814   1730000 perm   1562 sec   (1108 perm/sec)   p_kst 3.468208e-06   p_cons 9.832532e-01   p_joint 2.080925e-05

Joint ci ratio: 6.444370e-01	ci left: 1.449082e-05	ci right 2.864309e-05	k: 36	n:1740000
Cons ci ratio: 3.876534e-04	ci left: 9.830773e-01	ci right 9.834590e-01	k: 1710888	n:1740000
KS ci ratio: 1.481617e+00	ci left: 1.265457e-06	ci right 7.505430e-06	k: 6	n:1740000
ZNF814   1740000 perm   1581 sec   (1100 perm/sec)   p_kst 3.448276e-06   p_cons 9.832690e-01   p_joint 2.068966e-05

Joint ci ratio: 6.444370e-01	ci left: 1.440802e-05	ci right 2.847942e-05	k: 36	n:1750000
Cons ci ratio: 3.866495e-04	ci left: 9.830688e-01	ci right 9.834496e-01	k: 1720705	n:1750000
KS ci ratio: 1.481617e+00	ci left: 1.258226e-06	ci right 7.462542e-06	k: 6	n:1750000
ZNF814   1750000 perm   1602 sec   (1093 perm/sec)   p_kst 3.428571e-06   p_cons 9.832600e-01   p_joint 2.057143e-05

Joint ci ratio: 6.444371e-01	ci left: 1.432615e-05	ci right 2.831760e-05	k: 36	n:1760000
Cons ci ratio: 3.855402e-04	ci left: 9.830702e-01	ci right 9.834498e-01	k: 1730539	n:1760000
KS ci ratio: 1.481617e+00	ci left: 1.251077e-06	ci right 7.420141e-06	k: 6	n:1760000
ZNF814   1760000 perm   1618 sec   (1088 perm/sec)   p_kst 3.409091e-06   p_cons 9.832608e-01   p_joint 2.045455e-05

Joint ci ratio: 6.444371e-01	ci left: 1.424521e-05	ci right 2.815762e-05	k: 36	n:1770000
Cons ci ratio: 3.844073e-04	ci left: 9.830744e-01	ci right 9.834529e-01	k: 1740378	n:1770000
KS ci ratio: 1.481617e+00	ci left: 1.244009e-06	ci right 7.378219e-06	k: 6	n:1770000
ZNF814   1770000 perm   1633 sec   (1084 perm/sec)   p_kst 3.389831e-06   p_cons 9.832644e-01   p_joint 2.033898e-05

Joint ci ratio: 6.444372e-01	ci left: 1.416518e-05	ci right 2.799943e-05	k: 36	n:1780000
Cons ci ratio: 3.833106e-04	ci left: 9.830762e-01	ci right 9.834537e-01	k: 1750213	n:1780000
KS ci ratio: 1.481617e+00	ci left: 1.237020e-06	ci right 7.336769e-06	k: 6	n:1780000
ZNF814   1780000 perm   1649 sec   (1080 perm/sec)   p_kst 3.370787e-06   p_cons 9.832657e-01   p_joint 2.022472e-05

Joint ci ratio: 6.444372e-01	ci left: 1.408605e-05	ci right 2.784301e-05	k: 36	n:1790000
Cons ci ratio: 3.822556e-04	ci left: 9.830753e-01	ci right 9.834517e-01	k: 1760043	n:1790000
KS ci ratio: 1.481617e+00	ci left: 1.230109e-06	ci right 7.295781e-06	k: 6	n:1790000
ZNF814   1790000 perm   1665 sec   (1075 perm/sec)   p_kst 3.351955e-06   p_cons 9.832642e-01   p_joint 2.011173e-05

Joint ci ratio: 6.276954e-01	ci left: 1.493952e-05	ci right 2.897654e-05	k: 38	n:1800000
Cons ci ratio: 3.812414e-04	ci left: 9.830715e-01	ci right 9.834469e-01	k: 1769868	n:1800000
KS ci ratio: 1.481617e+00	ci left: 1.223276e-06	ci right 7.255249e-06	k: 6	n:1800000
ZNF814   1800000 perm   1683 sec   (1069 perm/sec)   p_kst 3.333333e-06   p_cons 9.832600e-01   p_joint 2.111111e-05

Joint ci ratio: 6.276954e-01	ci left: 1.485698e-05	ci right 2.881644e-05	k: 38	n:1810000
Cons ci ratio: 3.802225e-04	ci left: 9.830689e-01	ci right 9.834433e-01	k: 1779695	n:1810000
KS ci ratio: 1.481617e+00	ci left: 1.216517e-06	ci right 7.215165e-06	k: 6	n:1810000
ZNF814   1810000 perm   1706 sec   (1061 perm/sec)   p_kst 3.314917e-06   p_cons 9.832569e-01   p_joint 2.099448e-05

Joint ci ratio: 6.276955e-01	ci left: 1.477535e-05	ci right 2.865811e-05	k: 38	n:1820000
Cons ci ratio: 3.791674e-04	ci left: 9.830702e-01	ci right 9.834436e-01	k: 1789529	n:1820000
KS ci ratio: 1.481617e+00	ci left: 1.209833e-06	ci right 7.175521e-06	k: 6	n:1820000
ZNF814   1820000 perm   1723 sec   (1056 perm/sec)   p_kst 3.296703e-06   p_cons 9.832577e-01   p_joint 2.087912e-05

Joint ci ratio: 6.276955e-01	ci left: 1.469461e-05	ci right 2.850151e-05	k: 38	n:1830000
Cons ci ratio: 3.780708e-04	ci left: 9.830759e-01	ci right 9.834482e-01	k: 1799371	n:1830000
KS ci ratio: 1.481617e+00	ci left: 1.203222e-06	ci right 7.136311e-06	k: 6	n:1830000
ZNF814   1830000 perm   1739 sec   (1052 perm/sec)   p_kst 3.278689e-06   p_cons 9.832628e-01   p_joint 2.076503e-05

Joint ci ratio: 6.276955e-01	ci left: 1.461475e-05	ci right 2.834661e-05	k: 38	n:1840000
Cons ci ratio: 3.770086e-04	ci left: 9.830794e-01	ci right 9.834506e-01	k: 1809209	n:1840000
KS ci ratio: 1.481618e+00	ci left: 1.196683e-06	ci right 7.097527e-06	k: 6	n:1840000
ZNF814   1840000 perm   1755 sec   (1049 perm/sec)   p_kst 3.260870e-06   p_cons 9.832658e-01   p_joint 2.065217e-05

Joint ci ratio: 6.276956e-01	ci left: 1.453575e-05	ci right 2.819339e-05	k: 38	n:1850000
Cons ci ratio: 3.760108e-04	ci left: 9.830779e-01	ci right 9.834482e-01	k: 1819038	n:1850000
KS ci ratio: 1.481618e+00	ci left: 1.190214e-06	ci right 7.059162e-06	k: 6	n:1850000
ZNF814   1850000 perm   1771 sec   (1045 perm/sec)   p_kst 3.243243e-06   p_cons 9.832638e-01   p_joint 2.054054e-05

Joint ci ratio: 6.276956e-01	ci left: 1.445760e-05	ci right 2.804181e-05	k: 38	n:1860000
Cons ci ratio: 3.751128e-04	ci left: 9.830683e-01	ci right 9.834377e-01	k: 1828852	n:1860000
KS ci ratio: 1.481618e+00	ci left: 1.183815e-06	ci right 7.021209e-06	k: 6	n:1860000
ZNF814   1860000 perm   1787 sec   (1041 perm/sec)   p_kst 3.225806e-06   p_cons 9.832538e-01   p_joint 2.043011e-05

Joint ci ratio: 6.121943e-01	ci left: 1.528164e-05	ci right 2.912751e-05	k: 40	n:1870000
Cons ci ratio: 3.740206e-04	ci left: 9.830766e-01	ci right 9.834449e-01	k: 1838699	n:1870000
KS ci ratio: 1.481618e+00	ci left: 1.177484e-06	ci right 6.983663e-06	k: 6	n:1870000
ZNF814   1870000 perm   1803 sec   (1037 perm/sec)   p_kst 3.208556e-06   p_cons 9.832615e-01   p_joint 2.139037e-05

Joint ci ratio: 6.121943e-01	ci left: 1.520035e-05	ci right 2.897257e-05	k: 40	n:1880000
Cons ci ratio: 3.730825e-04	ci left: 9.830720e-01	ci right 9.834393e-01	k: 1848522	n:1880000
KS ci ratio: 1.481618e+00	ci left: 1.171221e-06	ci right 6.946516e-06	k: 6	n:1880000
ZNF814   1880000 perm   1820 sec   (1033 perm/sec)   p_kst 3.191489e-06   p_cons 9.832564e-01   p_joint 2.127660e-05

Joint ci ratio: 6.048623e-01	ci left: 1.556740e-05	ci right 2.942906e-05	k: 41	n:1890000
Cons ci ratio: 3.720497e-04	ci left: 9.830764e-01	ci right 9.834427e-01	k: 1858362	n:1890000
KS ci ratio: 1.481618e+00	ci left: 1.165024e-06	ci right 6.909762e-06	k: 6	n:1890000
ZNF814   1890000 perm   1836 sec   (1030 perm/sec)   p_kst 3.174603e-06   p_cons 9.832603e-01   p_joint 2.169312e-05

Joint ci ratio: 6.048623e-01	ci left: 1.548547e-05	ci right 2.927417e-05	k: 41	n:1900000
Cons ci ratio: 3.709957e-04	ci left: 9.830835e-01	ci right 9.834488e-01	k: 1868207	n:1900000
KS ci ratio: 1.481618e+00	ci left: 1.158893e-06	ci right 6.873395e-06	k: 6	n:1900000
ZNF814   1900000 perm   1852 sec   (1026 perm/sec)   p_kst 3.157895e-06   p_cons 9.832668e-01   p_joint 2.157895e-05

Joint ci ratio: 6.048623e-01	ci left: 1.540439e-05	ci right 2.912090e-05	k: 41	n:1910000
Cons ci ratio: 3.699212e-04	ci left: 9.830931e-01	ci right 9.834573e-01	k: 1878057	n:1910000
KS ci ratio: 1.481618e+00	ci left: 1.152825e-06	ci right 6.837408e-06	k: 6	n:1910000
ZNF814   1910000 perm   1869 sec   (1022 perm/sec)   p_kst 3.141361e-06   p_cons 9.832759e-01   p_joint 2.146597e-05

Joint ci ratio: 6.048624e-01	ci left: 1.532416e-05	ci right 2.896923e-05	k: 41	n:1920000
Cons ci ratio: 3.689785e-04	ci left: 9.830916e-01	ci right 9.834549e-01	k: 1887886	n:1920000
KS ci ratio: 1.481618e+00	ci left: 1.146821e-06	ci right 6.801797e-06	k: 6	n:1920000
ZNF814   1920000 perm   1885 sec   (1019 perm/sec)   p_kst 3.125000e-06   p_cons 9.832740e-01   p_joint 2.135417e-05

Joint ci ratio: 6.048624e-01	ci left: 1.524476e-05	ci right 2.881913e-05	k: 41	n:1930000
Cons ci ratio: 3.679213e-04	ci left: 9.831010e-01	ci right 9.834633e-01	k: 1897736	n:1930000
KS ci ratio: 1.481618e+00	ci left: 1.140879e-06	ci right 6.766554e-06	k: 6	n:1930000
ZNF814   1930000 perm   1902 sec   (1015 perm/sec)   p_kst 3.108808e-06   p_cons 9.832829e-01   p_joint 2.124352e-05

Joint ci ratio: 5.977876e-01	ci left: 1.560309e-05	ci right 2.926370e-05	k: 42	n:1940000
Cons ci ratio: 3.670513e-04	ci left: 9.830943e-01	ci right 9.834558e-01	k: 1907555	n:1940000
KS ci ratio: 1.481618e+00	ci left: 1.134998e-06	ci right 6.731675e-06	k: 6	n:1940000
ZNF814   1940000 perm   1919 sec   (1011 perm/sec)   p_kst 3.092784e-06   p_cons 9.832758e-01   p_joint 2.164948e-05

Joint ci ratio: 5.977877e-01	ci left: 1.552307e-05	ci right 2.911363e-05	k: 42	n:1950000
Cons ci ratio: 3.662731e-04	ci left: 9.830800e-01	ci right 9.834406e-01	k: 1917359	n:1950000
KS ci ratio: 1.481618e+00	ci left: 1.129177e-06	ci right 6.697154e-06	k: 6	n:1950000
ZNF814   1950000 perm   1936 sec   (1007 perm/sec)   p_kst 3.076923e-06   p_cons 9.832610e-01   p_joint 2.153846e-05

Joint ci ratio: 5.909555e-01	ci left: 1.587724e-05	ci right 2.955127e-05	k: 43	n:1960000
Cons ci ratio: 3.652050e-04	ci left: 9.830924e-01	ci right 9.834520e-01	k: 1927215	n:1960000
KS ci ratio: 1.481618e+00	ci left: 1.123416e-06	ci right 6.662985e-06	k: 6	n:1960000
ZNF814   1960000 perm   1953 sec   (1004 perm/sec)   p_kst 3.061224e-06   p_cons 9.832730e-01   p_joint 2.193878e-05

Joint ci ratio: 5.909555e-01	ci left: 1.579665e-05	ci right 2.940127e-05	k: 43	n:1970000
Cons ci ratio: 3.643316e-04	ci left: 9.830879e-01	ci right 9.834467e-01	k: 1937038	n:1970000
KS ci ratio: 1.481618e+00	ci left: 1.117714e-06	ci right 6.629163e-06	k: 6	n:1970000
ZNF814   1970000 perm   1972 sec   (999 perm/sec)   p_kst 3.045685e-06   p_cons 9.832680e-01   p_joint 2.182741e-05

Joint ci ratio: 5.909555e-01	ci left: 1.571687e-05	ci right 2.925278e-05	k: 43	n:1980000
Cons ci ratio: 3.633807e-04	ci left: 9.830911e-01	ci right 9.834489e-01	k: 1946876	n:1980000
KS ci ratio: 1.481618e+00	ci left: 1.112069e-06	ci right 6.595682e-06	k: 6	n:1980000
ZNF814   1980000 perm   1989 sec   (995 perm/sec)   p_kst 3.030303e-06   p_cons 9.832707e-01   p_joint 2.171717e-05

Joint ci ratio: 5.909556e-01	ci left: 1.563789e-05	ci right 2.910578e-05	k: 43	n:1990000
Cons ci ratio: 3.624925e-04	ci left: 9.830892e-01	ci right 9.834461e-01	k: 1956704	n:1990000
KS ci ratio: 1.481618e+00	ci left: 1.106480e-06	ci right 6.562538e-06	k: 6	n:1990000
ZNF814   1990000 perm   2007 sec   (991 perm/sec)   p_kst 3.015075e-06   p_cons 9.832683e-01   p_joint 2.160804e-05

Joint ci ratio: 5.909556e-01	ci left: 1.555970e-05	ci right 2.896025e-05	k: 43	n:2000000
Cons ci ratio: 3.614735e-04	ci left: 9.830998e-01	ci right 9.834558e-01	k: 1966557	n:2000000
KS ci ratio: 1.481618e+00	ci left: 1.100948e-06	ci right 6.529725e-06	k: 6	n:2000000
ZNF814   2000000 perm   2025 sec   (988 perm/sec)   p_kst 3.000000e-06   p_cons 9.832785e-01   p_joint 2.150000e-05

Joint ci ratio: 5.843524e-01	ci left: 1.590575e-05	ci right 2.938693e-05	k: 44	n:2010000
Cons ci ratio: 3.605447e-04	ci left: 9.831029e-01	ci right 9.834579e-01	k: 1976395	n:2010000
KS ci ratio: 1.481618e+00	ci left: 1.095471e-06	ci right 6.497239e-06	k: 6	n:2010000
ZNF814   2010000 perm   2042 sec   (984 perm/sec)   p_kst 2.985075e-06   p_cons 9.832811e-01   p_joint 2.189055e-05

Joint ci ratio: 5.843524e-01	ci left: 1.582701e-05	ci right 2.924145e-05	k: 44	n:2020000
Cons ci ratio: 3.596014e-04	ci left: 9.831079e-01	ci right 9.834620e-01	k: 1986237	n:2020000
KS ci ratio: 1.481618e+00	ci left: 1.090047e-06	ci right 6.465075e-06	k: 6	n:2020000
ZNF814   2020000 perm   2059 sec   (981 perm/sec)   p_kst 2.970297e-06   p_cons 9.832856e-01   p_joint 2.178218e-05

Joint ci ratio: 5.843525e-01	ci left: 1.574904e-05	ci right 2.909740e-05	k: 44	n:2030000
Cons ci ratio: 3.586977e-04	ci left: 9.831099e-01	ci right 9.834631e-01	k: 1996073	n:2030000
KS ci ratio: 1.481618e+00	ci left: 1.084678e-06	ci right 6.433227e-06	k: 6	n:2030000
ZNF814   2030000 perm   2077 sec   (977 perm/sec)   p_kst 2.955665e-06   p_cons 9.832872e-01   p_joint 2.167488e-05

Joint ci ratio: 5.843525e-01	ci left: 1.567184e-05	ci right 2.895477e-05	k: 44	n:2040000
Cons ci ratio: 3.577954e-04	ci left: 9.831124e-01	ci right 9.834647e-01	k: 2005910	n:2040000
KS ci ratio: 1.481618e+00	ci left: 1.079361e-06	ci right 6.401692e-06	k: 6	n:2040000
ZNF814   2040000 perm   2095 sec   (974 perm/sec)   p_kst 2.941176e-06   p_cons 9.832892e-01   p_joint 2.156863e-05

Joint ci ratio: 5.843525e-01	ci left: 1.559539e-05	ci right 2.881353e-05	k: 44	n:2050000
Cons ci ratio: 3.569051e-04	ci left: 9.831143e-01	ci right 9.834658e-01	k: 2015746	n:2050000
KS ci ratio: 1.481618e+00	ci left: 1.074095e-06	ci right 6.370464e-06	k: 6	n:2050000
ZNF814   2050000 perm   2112 sec   (970 perm/sec)   p_kst 2.926829e-06   p_cons 9.832907e-01   p_joint 2.146341e-05

Joint ci ratio: 5.843526e-01	ci left: 1.551969e-05	ci right 2.867366e-05	k: 44	n:2060000
Cons ci ratio: 3.560583e-04	ci left: 9.831129e-01	ci right 9.834634e-01	k: 2025575	n:2060000
KS ci ratio: 1.481618e+00	ci left: 1.068881e-06	ci right 6.339540e-06	k: 6	n:2060000
ZNF814   2060000 perm   2130 sec   (967 perm/sec)   p_kst 2.912621e-06   p_cons 9.832888e-01   p_joint 2.135922e-05

Joint ci ratio: 5.843526e-01	ci left: 1.544471e-05	ci right 2.853514e-05	k: 44	n:2070000
Cons ci ratio: 3.551862e-04	ci left: 9.831143e-01	ci right 9.834640e-01	k: 2035410	n:2070000
KS ci ratio: 1.481618e+00	ci left: 1.063718e-06	ci right 6.308914e-06	k: 6	n:2070000
ZNF814   2070000 perm   2148 sec   (964 perm/sec)   p_kst 2.898551e-06   p_cons 9.832899e-01   p_joint 2.125604e-05

Joint ci ratio: 5.843526e-01	ci left: 1.537046e-05	ci right 2.839795e-05	k: 44	n:2080000
Cons ci ratio: 3.543204e-04	ci left: 9.831158e-01	ci right 9.834646e-01	k: 2045245	n:2080000
KS ci ratio: 1.481618e+00	ci left: 1.058604e-06	ci right 6.278583e-06	k: 6	n:2080000
ZNF814   2080000 perm   2165 sec   (961 perm/sec)   p_kst 2.884615e-06   p_cons 9.832909e-01   p_joint 2.115385e-05

Joint ci ratio: 5.843527e-01	ci left: 1.529691e-05	ci right 2.826207e-05	k: 44	n:2090000
Cons ci ratio: 3.534404e-04	ci left: 9.831191e-01	ci right 9.834671e-01	k: 2055084	n:2090000
KS ci ratio: 1.481618e+00	ci left: 1.053539e-06	ci right 6.248542e-06	k: 6	n:2090000
ZNF814   2090000 perm   2182 sec   (958 perm/sec)   p_kst 2.870813e-06   p_cons 9.832938e-01   p_joint 2.105263e-05

Joint ci ratio: 5.843527e-01	ci left: 1.522407e-05	ci right 2.812749e-05	k: 44	n:2100000
Cons ci ratio: 3.525720e-04	ci left: 9.831219e-01	ci right 9.834691e-01	k: 2064922	n:2100000
KS ci ratio: 1.481618e+00	ci left: 1.048522e-06	ci right 6.218787e-06	k: 6	n:2100000
ZNF814   2100000 perm   2200 sec   (955 perm/sec)   p_kst 2.857143e-06   p_cons 9.832962e-01   p_joint 2.095238e-05

Joint ci ratio: 5.843527e-01	ci left: 1.515192e-05	ci right 2.799419e-05	k: 44	n:2110000
Cons ci ratio: 3.516389e-04	ci left: 9.831314e-01	ci right 9.834777e-01	k: 2074774	n:2110000
KS ci ratio: 1.481618e+00	ci left: 1.043552e-06	ci right 6.189314e-06	k: 6	n:2110000
ZNF814   2110000 perm   2217 sec   (952 perm/sec)   p_kst 2.843602e-06   p_cons 9.833052e-01   p_joint 2.085308e-05

Joint ci ratio: 5.843528e-01	ci left: 1.508045e-05	ci right 2.786214e-05	k: 44	n:2120000
Cons ci ratio: 3.509751e-04	ci left: 9.831162e-01	ci right 9.834617e-01	k: 2084574	n:2120000
KS ci ratio: 1.481618e+00	ci left: 1.038630e-06	ci right 6.160119e-06	k: 6	n:2120000
ZNF814   2120000 perm   2235 sec   (949 perm/sec)   p_kst 2.830189e-06   p_cons 9.832896e-01   p_joint 2.075472e-05

Joint ci ratio: 5.843528e-01	ci left: 1.500965e-05	ci right 2.773133e-05	k: 44	n:2130000
Cons ci ratio: 3.502497e-04	ci left: 9.831072e-01	ci right 9.834521e-01	k: 2094387	n:2130000
KS ci ratio: 1.481618e+00	ci left: 1.033754e-06	ci right 6.131198e-06	k: 6	n:2130000
ZNF814   2130000 perm   2252 sec   (946 perm/sec)   p_kst 2.816901e-06   p_cons 9.832803e-01   p_joint 2.065728e-05

Joint ci ratio: 5.599935e-01	ci left: 1.653809e-05	ci right 2.973869e-05	k: 48	n:2140000
Cons ci ratio: 3.493748e-04	ci left: 9.831129e-01	ci right 9.834569e-01	k: 2104231	n:2140000
KS ci ratio: 1.481618e+00	ci left: 1.028923e-06	ci right 6.102548e-06	k: 6	n:2140000
ZNF814   2140000 perm   2270 sec   (943 perm/sec)   p_kst 2.803738e-06   p_cons 9.832855e-01   p_joint 2.242991e-05

Joint ci ratio: 5.599935e-01	ci left: 1.646117e-05	ci right 2.960037e-05	k: 48	n:2150000
Cons ci ratio: 3.484817e-04	ci left: 9.831208e-01	ci right 9.834639e-01	k: 2114080	n:2150000
KS ci ratio: 1.481618e+00	ci left: 1.024138e-06	ci right 6.074164e-06	k: 6	n:2150000
ZNF814   2150000 perm   2288 sec   (940 perm/sec)   p_kst 2.790698e-06   p_cons 9.832930e-01   p_joint 2.232558e-05

Joint ci ratio: 5.543652e-01	ci left: 1.678267e-05	ci right 2.999091e-05	k: 49	n:2160000
Cons ci ratio: 3.476541e-04	ci left: 9.831231e-01	ci right 9.834654e-01	k: 2123917	n:2160000
KS ci ratio: 1.481618e+00	ci left: 1.019396e-06	ci right 6.046043e-06	k: 6	n:2160000
ZNF814   2160000 perm   2306 sec   (937 perm/sec)   p_kst 2.777778e-06   p_cons 9.832949e-01   p_joint 2.268519e-05

Joint ci ratio: 5.489032e-01	ci left: 1.710187e-05	ci right 3.037720e-05	k: 50	n:2170000
Cons ci ratio: 3.468519e-04	ci left: 9.831235e-01	ci right 9.834650e-01	k: 2133750	n:2170000
KS ci ratio: 1.481618e+00	ci left: 1.014698e-06	ci right 6.018181e-06	k: 6	n:2170000
ZNF814   2170000 perm   2324 sec   (934 perm/sec)   p_kst 2.764977e-06   p_cons 9.832949e-01   p_joint 2.304147e-05

Joint ci ratio: 5.489032e-01	ci left: 1.702342e-05	ci right 3.023786e-05	k: 50	n:2180000
Cons ci ratio: 3.459923e-04	ci left: 9.831299e-01	ci right 9.834706e-01	k: 2143596	n:2180000
KS ci ratio: 1.481618e+00	ci left: 1.010044e-06	ci right 5.990575e-06	k: 6	n:2180000
ZNF814   2180000 perm   2341 sec   (931 perm/sec)   p_kst 2.752294e-06   p_cons 9.833009e-01   p_joint 2.293578e-05

Joint ci ratio: 5.489033e-01	ci left: 1.694569e-05	ci right 3.009978e-05	k: 50	n:2190000
Cons ci ratio: 3.452207e-04	ci left: 9.831285e-01	ci right 9.834684e-01	k: 2153425	n:2190000
KS ci ratio: 1.481618e+00	ci left: 1.005432e-06	ci right 5.963221e-06	k: 6	n:2190000
ZNF814   2190000 perm   2359 sec   (928 perm/sec)   p_kst 2.739726e-06   p_cons 9.832991e-01   p_joint 2.283105e-05

Joint ci ratio: 5.489033e-01	ci left: 1.686867e-05	ci right 2.996297e-05	k: 50	n:2200000
Cons ci ratio: 3.444638e-04	ci left: 9.831261e-01	ci right 9.834653e-01	k: 2163252	n:2200000
KS ci ratio: 1.481618e+00	ci left: 1.000862e-06	ci right 5.936115e-06	k: 6	n:2200000
ZNF814   2200000 perm   2377 sec   (926 perm/sec)   p_kst 2.727273e-06   p_cons 9.832964e-01   p_joint 2.272727e-05

Joint ci ratio: 5.489033e-01	ci left: 1.679234e-05	ci right 2.982739e-05	k: 50	n:2210000
Cons ci ratio: 3.435792e-04	ci left: 9.831366e-01	ci right 9.834748e-01	k: 2173107	n:2210000
KS ci ratio: 1.481618e+00	ci left: 9.963329e-07	ci right 5.909255e-06	k: 6	n:2210000
ZNF814   2210000 perm   2395 sec   (923 perm/sec)   p_kst 2.714932e-06   p_cons 9.833063e-01   p_joint 2.262443e-05

Joint ci ratio: 6.048633e-01	ci left: 1.325332e-05	ci right 2.505448e-05	k: 41	n:2220000
Cons ci ratio: 3.428753e-04	ci left: 9.831301e-01	ci right 9.834677e-01	k: 2182925	n:2220000
KS ci ratio: 1.481618e+00	ci left: 9.918449e-07	ci right 5.882637e-06	k: 6	n:2220000
ZNF814   2220000 perm   2414 sec   (920 perm/sec)   p_kst 2.702703e-06   p_cons 9.832995e-01   p_joint 1.846847e-05

Joint ci ratio: 6.048633e-01	ci left: 1.319389e-05	ci right 2.494213e-05	k: 41	n:2230000
Cons ci ratio: 3.421056e-04	ci left: 9.831305e-01	ci right 9.834673e-01	k: 2192758	n:2230000
KS ci ratio: 1.481618e+00	ci left: 9.873971e-07	ci right 5.856257e-06	k: 6	n:2230000
ZNF814   2230000 perm   2432 sec   (917 perm/sec)   p_kst 2.690583e-06   p_cons 9.832996e-01   p_joint 1.838565e-05

Joint ci ratio: 6.048633e-01	ci left: 1.313499e-05	ci right 2.483078e-05	k: 41	n:2240000
Cons ci ratio: 3.413736e-04	ci left: 9.831277e-01	ci right 9.834639e-01	k: 2202584	n:2240000
KS ci ratio: 1.481618e+00	ci left: 9.829891e-07	ci right 5.830113e-06	k: 6	n:2240000
ZNF814   2240000 perm   2450 sec   (914 perm/sec)   p_kst 2.678571e-06   p_cons 9.832964e-01   p_joint 1.830357e-05

Joint ci ratio: 5.977886e-01	ci left: 1.345332e-05	ci right 2.523183e-05	k: 42	n:2250000
Cons ci ratio: 3.405586e-04	ci left: 9.831335e-01	ci right 9.834688e-01	k: 2212429	n:2250000
KS ci ratio: 1.481618e+00	ci left: 9.786203e-07	ci right 5.804202e-06	k: 6	n:2250000
ZNF814   2250000 perm   2468 sec   (911 perm/sec)   p_kst 2.666667e-06   p_cons 9.833018e-01   p_joint 1.866667e-05

Joint ci ratio: 6.048634e-01	ci left: 1.301875e-05	ci right 2.461104e-05	k: 41	n:2260000
Cons ci ratio: 3.397128e-04	ci left: 9.831428e-01	ci right 9.834772e-01	k: 2222282	n:2260000
KS ci ratio: 1.481618e+00	ci left: 9.742901e-07	ci right 5.778519e-06	k: 6	n:2260000
ZNF814   2260000 perm   2487 sec   (909 perm/sec)   p_kst 2.654867e-06   p_cons 9.833106e-01   p_joint 1.814159e-05

Joint ci ratio: 6.048634e-01	ci left: 1.296140e-05	ci right 2.450262e-05	k: 41	n:2270000
Cons ci ratio: 3.389961e-04	ci left: 9.831400e-01	ci right 9.834738e-01	k: 2232108	n:2270000
KS ci ratio: 1.481618e+00	ci left: 9.699981e-07	ci right 5.753063e-06	k: 6	n:2270000
ZNF814   2270000 perm   2506 sec   (906 perm/sec)   p_kst 2.643172e-06   p_cons 9.833075e-01   p_joint 1.806167e-05

Joint ci ratio: 6.048634e-01	ci left: 1.290455e-05	ci right 2.439515e-05	k: 41	n:2280000
Cons ci ratio: 3.382657e-04	ci left: 9.831390e-01	ci right 9.834720e-01	k: 2241938	n:2280000
KS ci ratio: 1.481618e+00	ci left: 9.657437e-07	ci right 5.727831e-06	k: 6	n:2280000
ZNF814   2280000 perm   2524 sec   (903 perm/sec)   p_kst 2.631579e-06   p_cons 9.833061e-01   p_joint 1.798246e-05

Joint ci ratio: 5.977887e-01	ci left: 1.321833e-05	ci right 2.479110e-05	k: 42	n:2290000
Cons ci ratio: 3.375311e-04	ci left: 9.831389e-01	ci right 9.834712e-01	k: 2251770	n:2290000
KS ci ratio: 1.385927e+00	ci left: 1.228980e-06	ci right 6.298101e-06	k: 7	n:2290000
ZNF814   2290000 perm   2543 sec   (901 perm/sec)   p_kst 3.056769e-06   p_cons 9.833057e-01   p_joint 1.834061e-05

Joint ci ratio: 5.977887e-01	ci left: 1.316086e-05	ci right 2.468331e-05	k: 42	n:2300000
Cons ci ratio: 3.368146e-04	ci left: 9.831375e-01	ci right 9.834691e-01	k: 2261599	n:2300000
KS ci ratio: 1.385927e+00	ci left: 1.223637e-06	ci right 6.270718e-06	k: 7	n:2300000
ZNF814   2300000 perm   2561 sec   (898 perm/sec)   p_kst 3.043478e-06   p_cons 9.833039e-01   p_joint 1.826087e-05

Joint ci ratio: 5.977887e-01	ci left: 1.310389e-05	ci right 2.457646e-05	k: 42	n:2310000
Cons ci ratio: 3.361248e-04	ci left: 9.831339e-01	ci right 9.834649e-01	k: 2271423	n:2310000
KS ci ratio: 1.385927e+00	ci left: 1.218340e-06	ci right 6.243572e-06	k: 7	n:2310000
ZNF814   2310000 perm   2580 sec   (895 perm/sec)   p_kst 3.030303e-06   p_cons 9.833000e-01   p_joint 1.818182e-05

Joint ci ratio: 5.977887e-01	ci left: 1.304740e-05	ci right 2.447053e-05	k: 42	n:2320000
Cons ci ratio: 3.353247e-04	ci left: 9.831416e-01	ci right 9.834718e-01	k: 2281273	n:2320000
KS ci ratio: 1.385927e+00	ci left: 1.213088e-06	ci right 6.216660e-06	k: 7	n:2320000
ZNF814   2320000 perm   2599 sec   (893 perm/sec)   p_kst 3.017241e-06   p_cons 9.833073e-01   p_joint 1.810345e-05

Joint ci ratio: 5.977888e-01	ci left: 1.299141e-05	ci right 2.436550e-05	k: 42	n:2330000
Cons ci ratio: 3.346047e-04	ci left: 9.831420e-01	ci right 9.834714e-01	k: 2291106	n:2330000
KS ci ratio: 1.385927e+00	ci left: 1.207882e-06	ci right 6.189980e-06	k: 7	n:2330000
ZNF814   2330000 perm   2618 sec   (890 perm/sec)   p_kst 3.004292e-06   p_cons 9.833073e-01   p_joint 1.802575e-05

Joint ci ratio: 5.977888e-01	ci left: 1.293589e-05	ci right 2.426138e-05	k: 42	n:2340000
Cons ci ratio: 3.338632e-04	ci left: 9.831449e-01	ci right 9.834736e-01	k: 2300945	n:2340000
KS ci ratio: 1.385927e+00	ci left: 1.202720e-06	ci right 6.163527e-06	k: 7	n:2340000
ZNF814   2340000 perm   2637 sec   (887 perm/sec)   p_kst 2.991453e-06   p_cons 9.833098e-01   p_joint 1.794872e-05

Joint ci ratio: 5.977888e-01	ci left: 1.288084e-05	ci right 2.415814e-05	k: 42	n:2350000
Cons ci ratio: 3.331957e-04	ci left: 9.831409e-01	ci right 9.834690e-01	k: 2310768	n:2350000
KS ci ratio: 1.385927e+00	ci left: 1.197602e-06	ci right 6.137299e-06	k: 7	n:2350000
ZNF814   2350000 perm   2656 sec   (885 perm/sec)   p_kst 2.978723e-06   p_cons 9.833055e-01   p_joint 1.787234e-05

Joint ci ratio: 5.843534e-01	ci left: 1.354684e-05	ci right 2.502871e-05	k: 44	n:2360000
Cons ci ratio: 3.324206e-04	ci left: 9.831481e-01	ci right 9.834753e-01	k: 2320617	n:2360000
KS ci ratio: 1.306664e+00	ci left: 1.463489e-06	ci right 6.679306e-06	k: 8	n:2360000
ZNF814   2360000 perm   2675 sec   (882 perm/sec)   p_kst 3.389831e-06   p_cons 9.833123e-01   p_joint 1.864407e-05

Joint ci ratio: 5.843534e-01	ci left: 1.348968e-05	ci right 2.492310e-05	k: 44	n:2370000
Cons ci ratio: 3.317190e-04	ci left: 9.831483e-01	ci right 9.834749e-01	k: 2330450	n:2370000
KS ci ratio: 1.306664e+00	ci left: 1.457314e-06	ci right 6.651124e-06	k: 8	n:2370000
ZNF814   2370000 perm   2694 sec   (880 perm/sec)   p_kst 3.375527e-06   p_cons 9.833122e-01   p_joint 1.856540e-05

Joint ci ratio: 5.843535e-01	ci left: 1.343300e-05	ci right 2.481839e-05	k: 44	n:2380000
Cons ci ratio: 3.309922e-04	ci left: 9.831516e-01	ci right 9.834775e-01	k: 2340290	n:2380000
KS ci ratio: 1.306664e+00	ci left: 1.451191e-06	ci right 6.623178e-06	k: 8	n:2380000
ZNF814   2380000 perm   2714 sec   (877 perm/sec)   p_kst 3.361345e-06   p_cons 9.833151e-01   p_joint 1.848739e-05

Joint ci ratio: 6.121958e-01	ci left: 1.195676e-05	ci right 2.279016e-05	k: 40	n:2390000
Cons ci ratio: 3.302449e-04	ci left: 9.831573e-01	ci right 9.834825e-01	k: 2350136	n:2390000
KS ci ratio: 1.306664e+00	ci left: 1.445119e-06	ci right 6.595466e-06	k: 8	n:2390000
ZNF814   2390000 perm   2733 sec   (874 perm/sec)   p_kst 3.347280e-06   p_cons 9.833205e-01   p_joint 1.673640e-05

Joint ci ratio: 6.121958e-01	ci left: 1.190694e-05	ci right 2.269520e-05	k: 40	n:2400000
Cons ci ratio: 3.295445e-04	ci left: 9.831589e-01	ci right 9.834833e-01	k: 2359972	n:2400000
KS ci ratio: 1.306664e+00	ci left: 1.439098e-06	ci right 6.567985e-06	k: 8	n:2400000
ZNF814   2400000 perm   2752 sec   (872 perm/sec)   p_kst 3.333333e-06   p_cons 9.833217e-01   p_joint 1.666667e-05

Joint ci ratio: 6.625960e-01	ci left: 9.770139e-06	ci right 1.971430e-05	k: 34	n:2410000
Cons ci ratio: 3.287819e-04	ci left: 9.831670e-01	ci right 9.834907e-01	k: 2369824	n:2410000
KS ci ratio: 1.306664e+00	ci left: 1.433126e-06	ci right 6.540732e-06	k: 8	n:2410000
ZNF814   2410000 perm   2772 sec   (869 perm/sec)   p_kst 3.319502e-06   p_cons 9.833295e-01   p_joint 1.410788e-05

Joint ci ratio: 6.625960e-01	ci left: 9.729766e-06	ci right 1.963283e-05	k: 34	n:2420000
Cons ci ratio: 3.280369e-04	ci left: 9.831739e-01	ci right 9.834969e-01	k: 2379673	n:2420000
KS ci ratio: 1.306664e+00	ci left: 1.427204e-06	ci right 6.513704e-06	k: 8	n:2420000
ZNF814   2420000 perm   2791 sec   (867 perm/sec)   p_kst 3.305785e-06   p_cons 9.833360e-01   p_joint 1.404959e-05

Joint ci ratio: 6.625960e-01	ci left: 9.689726e-06	ci right 1.955204e-05	k: 34	n:2430000
Cons ci ratio: 3.273792e-04	ci left: 9.831724e-01	ci right 9.834947e-01	k: 2389502	n:2430000
KS ci ratio: 1.306664e+00	ci left: 1.421331e-06	ci right 6.486899e-06	k: 8	n:2430000
ZNF814   2430000 perm   2811 sec   (864 perm/sec)   p_kst 3.292181e-06   p_cons 9.833342e-01   p_joint 1.399177e-05

Joint ci ratio: 6.625960e-01	ci left: 9.650014e-06	ci right 1.947191e-05	k: 34	n:2440000
Cons ci ratio: 3.268152e-04	ci left: 9.831619e-01	ci right 9.834837e-01	k: 2399309	n:2440000
KS ci ratio: 1.306664e+00	ci left: 1.415506e-06	ci right 6.460313e-06	k: 8	n:2440000
ZNF814   2440000 perm   2831 sec   (862 perm/sec)   p_kst 3.278689e-06   p_cons 9.833234e-01   p_joint 1.393443e-05

Joint ci ratio: 6.533284e-01	ci left: 9.950543e-06	ci right 1.986791e-05	k: 35	n:2450000
Cons ci ratio: 3.262093e-04	ci left: 9.831560e-01	ci right 9.834772e-01	k: 2409127	n:2450000
KS ci ratio: 1.306664e+00	ci left: 1.409728e-06	ci right 6.433945e-06	k: 8	n:2450000
ZNF814   2450000 perm   2851 sec   (859 perm/sec)   p_kst 3.265306e-06   p_cons 9.833171e-01   p_joint 1.428571e-05

Joint ci ratio: 6.533284e-01	ci left: 9.910094e-06	ci right 1.978715e-05	k: 35	n:2460000
Cons ci ratio: 3.255907e-04	ci left: 9.831518e-01	ci right 9.834723e-01	k: 2418949	n:2460000
KS ci ratio: 1.306664e+00	ci left: 1.403998e-06	ci right 6.407790e-06	k: 8	n:2460000
ZNF814   2460000 perm   2871 sec   (857 perm/sec)   p_kst 3.252033e-06   p_cons 9.833126e-01   p_joint 1.422764e-05

Joint ci ratio: 6.533284e-01	ci left: 9.869972e-06	ci right 1.970704e-05	k: 35	n:2470000
Cons ci ratio: 3.249795e-04	ci left: 9.831471e-01	ci right 9.834671e-01	k: 2428770	n:2470000
KS ci ratio: 1.306664e+00	ci left: 1.398314e-06	ci right 6.381848e-06	k: 8	n:2470000
ZNF814   2470000 perm   2891 sec   (854 perm/sec)   p_kst 3.238866e-06   p_cons 9.833077e-01   p_joint 1.417004e-05

Joint ci ratio: 6.533285e-01	ci left: 9.830173e-06	ci right 1.962758e-05	k: 35	n:2480000
Cons ci ratio: 3.243000e-04	ci left: 9.831499e-01	ci right 9.834692e-01	k: 2438609	n:2480000
KS ci ratio: 1.306664e+00	ci left: 1.392675e-06	ci right 6.356115e-06	k: 8	n:2480000
ZNF814   2480000 perm   2911 sec   (852 perm/sec)   p_kst 3.225806e-06   p_cons 9.833101e-01   p_joint 1.411290e-05

Joint ci ratio: 6.533285e-01	ci left: 9.790695e-06	ci right 1.954875e-05	k: 35	n:2490000
Cons ci ratio: 3.236684e-04	ci left: 9.831481e-01	ci right 9.834668e-01	k: 2448437	n:2490000
KS ci ratio: 1.306664e+00	ci left: 1.387082e-06	ci right 6.330588e-06	k: 8	n:2490000
ZNF814   2490000 perm   2932 sec   (849 perm/sec)   p_kst 3.212851e-06   p_cons 9.833080e-01   p_joint 1.405622e-05

Joint ci ratio: 6.533285e-01	ci left: 9.751532e-06	ci right 1.947056e-05	k: 35	n:2500000
Cons ci ratio: 3.231269e-04	ci left: 9.831376e-01	ci right 9.834557e-01	k: 2458243	n:2500000
KS ci ratio: 1.306664e+00	ci left: 1.381534e-06	ci right 6.305266e-06	k: 8	n:2500000
ZNF814   2500000 perm   2952 sec   (847 perm/sec)   p_kst 3.200000e-06   p_cons 9.832972e-01   p_joint 1.400000e-05

Joint ci ratio: 6.533285e-01	ci left: 9.712681e-06	ci right 1.939299e-05	k: 35	n:2510000
Cons ci ratio: 3.225255e-04	ci left: 9.831335e-01	ci right 9.834510e-01	k: 2468065	n:2510000
KS ci ratio: 1.306664e+00	ci left: 1.376030e-06	ci right 6.280145e-06	k: 8	n:2510000
ZNF814   2510000 perm   2973 sec   (844 perm/sec)   p_kst 3.187251e-06   p_cons 9.832928e-01   p_joint 1.394422e-05

Joint ci ratio: 6.929601e-01	ci left: 8.358347e-06	ci right 1.746108e-05	k: 31	n:2520000
Cons ci ratio: 3.219002e-04	ci left: 9.831323e-01	ci right 9.834492e-01	k: 2477894	n:2520000
KS ci ratio: 1.306664e+00	ci left: 1.370569e-06	ci right 6.255224e-06	k: 8	n:2520000
ZNF814   2520000 perm   2994 sec   (842 perm/sec)   p_kst 3.174603e-06   p_cons 9.832913e-01   p_joint 1.230159e-05

Joint ci ratio: 6.929601e-01	ci left: 8.325310e-06	ci right 1.739206e-05	k: 31	n:2530000
Cons ci ratio: 3.212321e-04	ci left: 9.831358e-01	ci right 9.834520e-01	k: 2487735	n:2530000
KS ci ratio: 1.306664e+00	ci left: 1.365152e-06	ci right 6.230500e-06	k: 8	n:2530000
ZNF814   2530000 perm   3015 sec   (839 perm/sec)   p_kst 3.162055e-06   p_cons 9.832945e-01   p_joint 1.225296e-05

Joint ci ratio: 6.929601e-01	ci left: 8.292533e-06	ci right 1.732359e-05	k: 31	n:2540000
Cons ci ratio: 3.205298e-04	ci left: 9.831432e-01	ci right 9.834588e-01	k: 2497586	n:2540000
KS ci ratio: 1.306664e+00	ci left: 1.359777e-06	ci right 6.205971e-06	k: 8	n:2540000
ZNF814   2540000 perm   3035 sec   (837 perm/sec)   p_kst 3.149606e-06   p_cons 9.833016e-01   p_joint 1.220472e-05

Joint ci ratio: 6.823799e-01	ci left: 8.583535e-06	ci right 1.771543e-05	k: 32	n:2550000
Cons ci ratio: 3.199580e-04	ci left: 9.831376e-01	ci right 9.834526e-01	k: 2507404	n:2550000
KS ci ratio: 1.306664e+00	ci left: 1.354445e-06	ci right 6.181633e-06	k: 8	n:2550000
ZNF814   2550000 perm   3055 sec   (835 perm/sec)   p_kst 3.137255e-06   p_cons 9.832957e-01   p_joint 1.254902e-05

Joint ci ratio: 6.823799e-01	ci left: 8.550006e-06	ci right 1.764622e-05	k: 32	n:2560000
Cons ci ratio: 3.193095e-04	ci left: 9.831403e-01	ci right 9.834547e-01	k: 2517243	n:2560000
KS ci ratio: 1.306664e+00	ci left: 1.349154e-06	ci right 6.157486e-06	k: 8	n:2560000
ZNF814   2560000 perm   3076 sec   (832 perm/sec)   p_kst 3.125000e-06   p_cons 9.832980e-01   p_joint 1.250000e-05

Joint ci ratio: 6.823799e-01	ci left: 8.516737e-06	ci right 1.757756e-05	k: 32	n:2570000
Cons ci ratio: 3.186763e-04	ci left: 9.831418e-01	ci right 9.834555e-01	k: 2527079	n:2570000
KS ci ratio: 1.306664e+00	ci left: 1.343904e-06	ci right 6.133527e-06	k: 8	n:2570000
ZNF814   2570000 perm   3096 sec   (830 perm/sec)   p_kst 3.112840e-06   p_cons 9.832992e-01   p_joint 1.245136e-05

Joint ci ratio: 6.823799e-01	ci left: 8.483727e-06	ci right 1.750943e-05	k: 32	n:2580000
Cons ci ratio: 3.180543e-04	ci left: 9.831425e-01	ci right 9.834556e-01	k: 2536913	n:2580000
KS ci ratio: 1.306664e+00	ci left: 1.338696e-06	ci right 6.109754e-06	k: 8	n:2580000
ZNF814   2580000 perm   3117 sec   (828 perm/sec)   p_kst 3.100775e-06   p_cons 9.832996e-01   p_joint 1.240310e-05

Joint ci ratio: 6.823799e-01	ci left: 8.450971e-06	ci right 1.744183e-05	k: 32	n:2590000
Cons ci ratio: 3.174471e-04	ci left: 9.831420e-01	ci right 9.834546e-01	k: 2546744	n:2590000
KS ci ratio: 1.306664e+00	ci left: 1.333527e-06	ci right 6.086164e-06	k: 8	n:2590000
ZNF814   2590000 perm   3138 sec   (825 perm/sec)   p_kst 3.088803e-06   p_cons 9.832988e-01   p_joint 1.235521e-05

Joint ci ratio: 6.823799e-01	ci left: 8.418467e-06	ci right 1.737475e-05	k: 32	n:2600000
Cons ci ratio: 3.168508e-04	ci left: 9.831408e-01	ci right 9.834527e-01	k: 2556573	n:2600000
KS ci ratio: 1.306664e+00	ci left: 1.328398e-06	ci right 6.062756e-06	k: 8	n:2600000
ZNF814   2600000 perm   3158 sec   (823 perm/sec)   p_kst 3.076923e-06   p_cons 9.832973e-01   p_joint 1.230769e-05

Joint ci ratio: 6.823800e-01	ci left: 8.386212e-06	ci right 1.730818e-05	k: 32	n:2610000
Cons ci ratio: 3.162468e-04	ci left: 9.831407e-01	ci right 9.834521e-01	k: 2566405	n:2610000
KS ci ratio: 1.306664e+00	ci left: 1.323308e-06	ci right 6.039527e-06	k: 8	n:2610000
ZNF814   2610000 perm   3180 sec   (821 perm/sec)   p_kst 3.065134e-06   p_cons 9.832969e-01   p_joint 1.226054e-05

Joint ci ratio: 6.823800e-01	ci left: 8.354204e-06	ci right 1.724211e-05	k: 32	n:2620000
Cons ci ratio: 3.155399e-04	ci left: 9.831518e-01	ci right 9.834624e-01	k: 2576266	n:2620000
KS ci ratio: 1.306664e+00	ci left: 1.318257e-06	ci right 6.016476e-06	k: 8	n:2620000
ZNF814   2620000 perm   3201 sec   (819 perm/sec)   p_kst 3.053435e-06   p_cons 9.833076e-01   p_joint 1.221374e-05

Joint ci ratio: 6.823800e-01	ci left: 8.322439e-06	ci right 1.717655e-05	k: 32	n:2630000
Cons ci ratio: 3.149361e-04	ci left: 9.831524e-01	ci right 9.834625e-01	k: 2586100	n:2630000
KS ci ratio: 1.306664e+00	ci left: 1.313245e-06	ci right 5.993599e-06	k: 8	n:2630000
ZNF814   2630000 perm   3222 sec   (816 perm/sec)   p_kst 3.041825e-06   p_cons 9.833080e-01   p_joint 1.216730e-05

Joint ci ratio: 6.722700e-01	ci left: 8.604440e-06	ci right 1.755460e-05	k: 33	n:2640000
Cons ci ratio: 3.142813e-04	ci left: 9.831588e-01	ci right 9.834682e-01	k: 2595949	n:2640000
KS ci ratio: 1.239610e+00	ci left: 1.558855e-06	ci right 6.471507e-06	k: 9	n:2640000
ZNF814   2640000 perm   3243 sec   (814 perm/sec)   p_kst 3.409091e-06   p_cons 9.833140e-01   p_joint 1.250000e-05

Joint ci ratio: 6.722700e-01	ci left: 8.571970e-06	ci right 1.748836e-05	k: 33	n:2650000
Cons ci ratio: 3.137027e-04	ci left: 9.831575e-01	ci right 9.834663e-01	k: 2605778	n:2650000
KS ci ratio: 1.239610e+00	ci left: 1.552972e-06	ci right 6.447086e-06	k: 9	n:2650000
ZNF814   2650000 perm   3264 sec   (812 perm/sec)   p_kst 3.396226e-06   p_cons 9.833125e-01   p_joint 1.245283e-05

Joint ci ratio: 6.722700e-01	ci left: 8.539745e-06	ci right 1.742261e-05	k: 33	n:2660000
Cons ci ratio: 3.131129e-04	ci left: 9.831578e-01	ci right 9.834660e-01	k: 2615611	n:2660000
KS ci ratio: 1.239610e+00	ci left: 1.547134e-06	ci right 6.422849e-06	k: 9	n:2660000
ZNF814   2660000 perm   3286 sec   (810 perm/sec)   p_kst 3.383459e-06   p_cons 9.833124e-01   p_joint 1.240602e-05

Joint ci ratio: 6.722700e-01	ci left: 8.507761e-06	ci right 1.735736e-05	k: 33	n:2670000
Cons ci ratio: 3.125228e-04	ci left: 9.831584e-01	ci right 9.834660e-01	k: 2625445	n:2670000
KS ci ratio: 1.239610e+00	ci left: 1.541339e-06	ci right 6.398793e-06	k: 9	n:2670000
ZNF814   2670000 perm   3307 sec   (807 perm/sec)   p_kst 3.370787e-06   p_cons 9.833127e-01   p_joint 1.235955e-05

Joint ci ratio: 6.722701e-01	ci left: 8.476015e-06	ci right 1.729259e-05	k: 33	n:2680000
Cons ci ratio: 3.119787e-04	ci left: 9.831545e-01	ci right 9.834616e-01	k: 2635267	n:2680000
KS ci ratio: 1.239610e+00	ci left: 1.535588e-06	ci right 6.374917e-06	k: 9	n:2680000
ZNF814   2680000 perm   3329 sec   (805 perm/sec)   p_kst 3.358209e-06   p_cons 9.833086e-01   p_joint 1.231343e-05

Joint ci ratio: 6.722701e-01	ci left: 8.444506e-06	ci right 1.722831e-05	k: 33	n:2690000
Cons ci ratio: 3.114408e-04	ci left: 9.831503e-01	ci right 9.834569e-01	k: 2645088	n:2690000
KS ci ratio: 1.239610e+00	ci left: 1.529880e-06	ci right 6.351219e-06	k: 9	n:2690000
ZNF814   2690000 perm   3351 sec   (803 perm/sec)   p_kst 3.345725e-06   p_cons 9.833041e-01   p_joint 1.226766e-05

Joint ci ratio: 6.722701e-01	ci left: 8.413230e-06	ci right 1.716450e-05	k: 33	n:2700000
Cons ci ratio: 3.108777e-04	ci left: 9.831490e-01	ci right 9.834551e-01	k: 2654917	n:2700000
KS ci ratio: 1.239610e+00	ci left: 1.524213e-06	ci right 6.327696e-06	k: 9	n:2700000
ZNF814   2700000 perm   3372 sec   (801 perm/sec)   p_kst 3.333333e-06   p_cons 9.833026e-01   p_joint 1.222222e-05

Joint ci ratio: 6.722701e-01	ci left: 8.382185e-06	ci right 1.710116e-05	k: 33	n:2710000
Cons ci ratio: 3.103943e-04	ci left: 9.831397e-01	ci right 9.834453e-01	k: 2664724	n:2710000
KS ci ratio: 1.239610e+00	ci left: 1.518589e-06	ci right 6.304346e-06	k: 9	n:2710000
ZNF814   2710000 perm   3394 sec   (798 perm/sec)   p_kst 3.321033e-06   p_cons 9.832930e-01   p_joint 1.217712e-05

Joint ci ratio: 6.722701e-01	ci left: 8.351368e-06	ci right 1.703829e-05	k: 33	n:2720000
Cons ci ratio: 3.097571e-04	ci left: 9.831470e-01	ci right 9.834520e-01	k: 2674576	n:2720000
KS ci ratio: 1.239610e+00	ci left: 1.513006e-06	ci right 6.281168e-06	k: 9	n:2720000
ZNF814   2720000 perm   3416 sec   (796 perm/sec)   p_kst 3.308824e-06   p_cons 9.833000e-01   p_joint 1.213235e-05

Joint ci ratio: 6.722701e-01	ci left: 8.320777e-06	ci right 1.697588e-05	k: 33	n:2730000
Cons ci ratio: 3.091858e-04	ci left: 9.831477e-01	ci right 9.834520e-01	k: 2684410	n:2730000
KS ci ratio: 1.239610e+00	ci left: 1.507464e-06	ci right 6.258160e-06	k: 9	n:2730000
ZNF814   2730000 perm   3438 sec   (794 perm/sec)   p_kst 3.296703e-06   p_cons 9.833004e-01   p_joint 1.208791e-05

Joint ci ratio: 6.625966e-01	ci left: 8.593441e-06	ci right 1.733995e-05	k: 34	n:2740000
Cons ci ratio: 3.086108e-04	ci left: 9.831490e-01	ci right 9.834529e-01	k: 2694246	n:2740000
KS ci ratio: 1.181922e+00	ci left: 1.750143e-06	ci right 6.711799e-06	k: 10	n:2740000
ZNF814   2740000 perm   3460 sec   (792 perm/sec)   p_kst 3.649635e-06   p_cons 9.833015e-01   p_joint 1.240876e-05

Joint ci ratio: 6.625966e-01	ci left: 8.562192e-06	ci right 1.727690e-05	k: 34	n:2750000
Cons ci ratio: 3.080424e-04	ci left: 9.831500e-01	ci right 9.834533e-01	k: 2704081	n:2750000
KS ci ratio: 1.181922e+00	ci left: 1.743779e-06	ci right 6.687392e-06	k: 10	n:2750000
ZNF814   2750000 perm   3482 sec   (790 perm/sec)   p_kst 3.636364e-06   p_cons 9.833022e-01   p_joint 1.236364e-05

Joint ci ratio: 6.625966e-01	ci left: 8.531170e-06	ci right 1.721430e-05	k: 34	n:2760000
Cons ci ratio: 3.075212e-04	ci left: 9.831463e-01	ci right 9.834491e-01	k: 2713903	n:2760000
KS ci ratio: 1.181922e+00	ci left: 1.737461e-06	ci right 6.663162e-06	k: 10	n:2760000
ZNF814   2760000 perm   3504 sec   (788 perm/sec)   p_kst 3.623188e-06   p_cons 9.832982e-01   p_joint 1.231884e-05

Joint ci ratio: 6.625966e-01	ci left: 8.500371e-06	ci right 1.715216e-05	k: 34	n:2770000
Cons ci ratio: 3.069251e-04	ci left: 9.831509e-01	ci right 9.834531e-01	k: 2723748	n:2770000
KS ci ratio: 1.181922e+00	ci left: 1.731189e-06	ci right 6.639108e-06	k: 10	n:2770000
ZNF814   2770000 perm   3526 sec   (786 perm/sec)   p_kst 3.610108e-06   p_cons 9.833025e-01   p_joint 1.227437e-05

Joint ci ratio: 6.625966e-01	ci left: 8.469794e-06	ci right 1.709046e-05	k: 34	n:2780000
Cons ci ratio: 3.063256e-04	ci left: 9.831563e-01	ci right 9.834578e-01	k: 2733595	n:2780000
KS ci ratio: 1.181922e+00	ci left: 1.724961e-06	ci right 6.615226e-06	k: 10	n:2780000
ZNF814   2780000 perm   3548 sec   (784 perm/sec)   p_kst 3.597122e-06   p_cons 9.833076e-01   p_joint 1.223022e-05

Joint ci ratio: 6.533290e-01	ci left: 8.737930e-06	ci right 1.744674e-05	k: 35	n:2790000
Cons ci ratio: 3.057864e-04	ci left: 9.831554e-01	ci right 9.834565e-01	k: 2743425	n:2790000
KS ci ratio: 1.181922e+00	ci left: 1.718779e-06	ci right 6.591516e-06	k: 10	n:2790000
ZNF814   2790000 perm   3570 sec   (781 perm/sec)   p_kst 3.584229e-06   p_cons 9.833065e-01   p_joint 1.254480e-05

Joint ci ratio: 6.533290e-01	ci left: 8.706723e-06	ci right 1.738443e-05	k: 35	n:2800000
Cons ci ratio: 3.053131e-04	ci left: 9.831478e-01	ci right 9.834484e-01	k: 2753236	n:2800000
KS ci ratio: 1.181922e+00	ci left: 1.712640e-06	ci right 6.567974e-06	k: 10	n:2800000
ZNF814   2800000 perm   3593 sec   (779 perm/sec)   p_kst 3.571429e-06   p_cons 9.832986e-01   p_joint 1.250000e-05

Joint ci ratio: 6.533290e-01	ci left: 8.675738e-06	ci right 1.732257e-05	k: 35	n:2810000
Cons ci ratio: 3.047957e-04	ci left: 9.831452e-01	ci right 9.834453e-01	k: 2763061	n:2810000
KS ci ratio: 1.181922e+00	ci left: 1.706545e-06	ci right 6.544601e-06	k: 10	n:2810000
ZNF814   2810000 perm   3615 sec   (777 perm/sec)   p_kst 3.558719e-06   p_cons 9.832957e-01   p_joint 1.245552e-05

Joint ci ratio: 6.533290e-01	ci left: 8.644973e-06	ci right 1.726114e-05	k: 35	n:2820000
Cons ci ratio: 3.042317e-04	ci left: 9.831480e-01	ci right 9.834475e-01	k: 2772901	n:2820000
KS ci ratio: 1.181922e+00	ci left: 1.700494e-06	ci right 6.521393e-06	k: 10	n:2820000
ZNF814   2820000 perm   3637 sec   (775 perm/sec)   p_kst 3.546099e-06   p_cons 9.832982e-01   p_joint 1.241135e-05

Joint ci ratio: 6.533291e-01	ci left: 8.614425e-06	ci right 1.720014e-05	k: 35	n:2830000
Cons ci ratio: 3.036838e-04	ci left: 9.831493e-01	ci right 9.834483e-01	k: 2782737	n:2830000
KS ci ratio: 1.181922e+00	ci left: 1.694485e-06	ci right 6.498349e-06	k: 10	n:2830000
ZNF814   2830000 perm   3660 sec   (773 perm/sec)   p_kst 3.533569e-06   p_cons 9.832993e-01   p_joint 1.236749e-05

Joint ci ratio: 6.533291e-01	ci left: 8.584093e-06	ci right 1.713958e-05	k: 35	n:2840000
Cons ci ratio: 3.031357e-04	ci left: 9.831510e-01	ci right 9.834494e-01	k: 2792574	n:2840000
KS ci ratio: 1.181922e+00	ci left: 1.688518e-06	ci right 6.475468e-06	k: 10	n:2840000
ZNF814   2840000 perm   3682 sec   (771 perm/sec)   p_kst 3.521127e-06   p_cons 9.833007e-01   p_joint 1.232394e-05

Joint ci ratio: 6.533291e-01	ci left: 8.553973e-06	ci right 1.707944e-05	k: 35	n:2850000
Cons ci ratio: 3.025517e-04	ci left: 9.831569e-01	ci right 9.834547e-01	k: 2802423	n:2850000
KS ci ratio: 1.181922e+00	ci left: 1.682594e-06	ci right 6.452747e-06	k: 10	n:2850000
ZNF814   2850000 perm   3705 sec   (769 perm/sec)   p_kst 3.508772e-06   p_cons 9.833063e-01   p_joint 1.228070e-05

Joint ci ratio: 6.533291e-01	ci left: 8.524064e-06	ci right 1.701972e-05	k: 35	n:2860000
Cons ci ratio: 3.020257e-04	ci left: 9.831568e-01	ci right 9.834541e-01	k: 2812255	n:2860000
KS ci ratio: 1.181922e+00	ci left: 1.676711e-06	ci right 6.430185e-06	k: 10	n:2860000
ZNF814   2860000 perm   3728 sec   (767 perm/sec)   p_kst 3.496503e-06   p_cons 9.833059e-01   p_joint 1.223776e-05

Joint ci ratio: 6.533291e-01	ci left: 8.494364e-06	ci right 1.696042e-05	k: 35	n:2870000
Cons ci ratio: 3.015664e-04	ci left: 9.831497e-01	ci right 9.834466e-01	k: 2822067	n:2870000
KS ci ratio: 1.181922e+00	ci left: 1.670868e-06	ci right 6.407780e-06	k: 10	n:2870000
ZNF814   2870000 perm   3751 sec   (765 perm/sec)   p_kst 3.484321e-06   p_cons 9.832986e-01   p_joint 1.219512e-05

Joint ci ratio: 6.533291e-01	ci left: 8.464869e-06	ci right 1.690153e-05	k: 35	n:2880000
Cons ci ratio: 3.011060e-04	ci left: 9.831430e-01	ci right 9.834394e-01	k: 2831880	n:2880000
KS ci ratio: 1.181922e+00	ci left: 1.665067e-06	ci right 6.385531e-06	k: 10	n:2880000
ZNF814   2880000 perm   3775 sec   (763 perm/sec)   p_kst 3.472222e-06   p_cons 9.832917e-01   p_joint 1.215278e-05

Joint ci ratio: 6.533292e-01	ci left: 8.435579e-06	ci right 1.684305e-05	k: 35	n:2890000
Cons ci ratio: 3.005432e-04	ci left: 9.831478e-01	ci right 9.834436e-01	k: 2841726	n:2890000
KS ci ratio: 1.181922e+00	ci left: 1.659305e-06	ci right 6.363436e-06	k: 10	n:2890000
ZNF814   2890000 perm   3798 sec   (761 perm/sec)   p_kst 3.460208e-06   p_cons 9.832962e-01   p_joint 1.211073e-05

Joint ci ratio: 6.533292e-01	ci left: 8.406491e-06	ci right 1.678497e-05	k: 35	n:2900000
Cons ci ratio: 2.999362e-04	ci left: 9.831577e-01	ci right 9.834530e-01	k: 2851587	n:2900000
KS ci ratio: 1.181922e+00	ci left: 1.653584e-06	ci right 6.341493e-06	k: 10	n:2900000
ZNF814   2900000 perm   3821 sec   (759 perm/sec)   p_kst 3.448276e-06   p_cons 9.833059e-01   p_joint 1.206897e-05

Joint ci ratio: 6.533292e-01	ci left: 8.377602e-06	ci right 1.672729e-05	k: 35	n:2910000
Cons ci ratio: 2.994237e-04	ci left: 9.831576e-01	ci right 9.834524e-01	k: 2861419	n:2910000
KS ci ratio: 1.181922e+00	ci left: 1.647901e-06	ci right 6.319701e-06	k: 10	n:2910000
ZNF814   2910000 perm   3844 sec   (757 perm/sec)   p_kst 3.436426e-06   p_cons 9.833055e-01   p_joint 1.202749e-05

Joint ci ratio: 6.533292e-01	ci left: 8.348912e-06	ci right 1.667000e-05	k: 35	n:2920000
Cons ci ratio: 2.988609e-04	ci left: 9.831634e-01	ci right 9.834576e-01	k: 2871268	n:2920000
KS ci ratio: 1.181922e+00	ci left: 1.642258e-06	ci right 6.298058e-06	k: 10	n:2920000
ZNF814   2920000 perm   3867 sec   (755 perm/sec)   p_kst 3.424658e-06   p_cons 9.833110e-01   p_joint 1.198630e-05

Joint ci ratio: 6.533292e-01	ci left: 8.320417e-06	ci right 1.661311e-05	k: 35	n:2930000
Cons ci ratio: 2.983694e-04	ci left: 9.831615e-01	ci right 9.834553e-01	k: 2881095	n:2930000
KS ci ratio: 1.181922e+00	ci left: 1.636653e-06	ci right 6.276563e-06	k: 10	n:2930000
ZNF814   2930000 perm   3890 sec   (753 perm/sec)   p_kst 3.412969e-06   p_cons 9.833089e-01   p_joint 1.194539e-05

Joint ci ratio: 6.533292e-01	ci left: 8.292116e-06	ci right 1.655660e-05	k: 35	n:2940000
Cons ci ratio: 2.978278e-04	ci left: 9.831655e-01	ci right 9.834587e-01	k: 2890939	n:2940000
KS ci ratio: 1.181922e+00	ci left: 1.631086e-06	ci right 6.255214e-06	k: 10	n:2940000
ZNF814   2940000 perm   3914 sec   (751 perm/sec)   p_kst 3.401361e-06   p_cons 9.833126e-01   p_joint 1.190476e-05

Joint ci ratio: 6.359038e-01	ci left: 8.831003e-06	ci right 1.728797e-05	k: 37	n:2950000
Cons ci ratio: 2.973046e-04	ci left: 9.831678e-01	ci right 9.834604e-01	k: 2900778	n:2950000
KS ci ratio: 1.181922e+00	ci left: 1.625557e-06	ci right 6.234010e-06	k: 10	n:2950000
ZNF814   2950000 perm   3938 sec   (749 perm/sec)   p_kst 3.389831e-06   p_cons 9.833146e-01   p_joint 1.254237e-05

Joint ci ratio: 6.359038e-01	ci left: 8.801168e-06	ci right 1.722956e-05	k: 37	n:2960000
Cons ci ratio: 2.968604e-04	ci left: 9.831615e-01	ci right 9.834538e-01	k: 2910592	n:2960000
KS ci ratio: 1.181922e+00	ci left: 1.620065e-06	ci right 6.212949e-06	k: 10	n:2960000
ZNF814   2960000 perm   3961 sec   (747 perm/sec)   p_kst 3.378378e-06   p_cons 9.833081e-01   p_joint 1.250000e-05

Joint ci ratio: 6.359038e-01	ci left: 8.771535e-06	ci right 1.717155e-05	k: 37	n:2970000
Cons ci ratio: 2.963969e-04	ci left: 9.831577e-01	ci right 9.834495e-01	k: 2920413	n:2970000
KS ci ratio: 1.181922e+00	ci left: 1.614610e-06	ci right 6.192030e-06	k: 10	n:2970000
ZNF814   2970000 perm   3985 sec   (745 perm/sec)   p_kst 3.367003e-06   p_cons 9.833040e-01   p_joint 1.245791e-05

Joint ci ratio: 6.823805e-01	ci left: 7.344970e-06	ci right 1.515918e-05	k: 32	n:2980000
Cons ci ratio: 2.958963e-04	ci left: 9.831583e-01	ci right 9.834495e-01	k: 2930247	n:2980000
KS ci ratio: 1.181922e+00	ci left: 1.609192e-06	ci right 6.171252e-06	k: 10	n:2980000
ZNF814   2980000 perm   4009 sec   (743 perm/sec)   p_kst 3.355705e-06   p_cons 9.833044e-01   p_joint 1.073826e-05

Joint ci ratio: 6.823805e-01	ci left: 7.320405e-06	ci right 1.510848e-05	k: 32	n:2990000
Cons ci ratio: 2.954433e-04	ci left: 9.831538e-01	ci right 9.834446e-01	k: 2940066	n:2990000
KS ci ratio: 1.181922e+00	ci left: 1.603810e-06	ci right 6.150612e-06	k: 10	n:2990000
ZNF814   2990000 perm   4033 sec   (741 perm/sec)   p_kst 3.344482e-06   p_cons 9.832997e-01   p_joint 1.070234e-05

Joint ci ratio: 6.823805e-01	ci left: 7.296003e-06	ci right 1.505812e-05	k: 32	n:3000000
Cons ci ratio: 2.948786e-04	ci left: 9.831621e-01	ci right 9.834523e-01	k: 2949923	n:3000000
KS ci ratio: 1.181922e+00	ci left: 1.598464e-06	ci right 6.130110e-06	k: 10	n:3000000
ZNF814   3000000 perm   4057 sec   (739 perm/sec)   p_kst 3.333333e-06   p_cons 9.833077e-01   p_joint 1.066667e-05

Joint ci ratio: 6.823806e-01	ci left: 7.271764e-06	ci right 1.500809e-05	k: 32	n:3010000
Cons ci ratio: 2.943975e-04	ci left: 9.831613e-01	ci right 9.834511e-01	k: 2959753	n:3010000
KS ci ratio: 1.181922e+00	ci left: 1.593154e-06	ci right 6.109744e-06	k: 10	n:3010000
ZNF814   3010000 perm   4082 sec   (737 perm/sec)   p_kst 3.322259e-06   p_cons 9.833066e-01   p_joint 1.063123e-05

Joint ci ratio: 6.823806e-01	ci left: 7.247685e-06	ci right 1.495840e-05	k: 32	n:3020000
Cons ci ratio: 2.939366e-04	ci left: 9.831585e-01	ci right 9.834479e-01	k: 2969577	n:3020000
KS ci ratio: 1.181922e+00	ci left: 1.587878e-06	ci right 6.089513e-06	k: 10	n:3020000
ZNF814   3020000 perm   4106 sec   (736 perm/sec)   p_kst 3.311258e-06   p_cons 9.833036e-01   p_joint 1.059603e-05

Joint ci ratio: 6.722706e-01	ci left: 7.496936e-06	ci right 1.529510e-05	k: 33	n:3030000
Cons ci ratio: 2.934395e-04	ci left: 9.831601e-01	ci right 9.834489e-01	k: 2979414	n:3030000
KS ci ratio: 1.131604e+00	ci left: 1.812265e-06	ci right 6.495713e-06	k: 11	n:3030000
ZNF814   3030000 perm   4130 sec   (734 perm/sec)   p_kst 3.630363e-06   p_cons 9.833050e-01   p_joint 1.089109e-05

Joint ci ratio: 6.722706e-01	ci left: 7.472275e-06	ci right 1.524479e-05	k: 33	n:3040000
Cons ci ratio: 2.929624e-04	ci left: 9.831596e-01	ci right 9.834480e-01	k: 2989245	n:3040000
KS ci ratio: 1.131604e+00	ci left: 1.806304e-06	ci right 6.474346e-06	k: 11	n:3040000
ZNF814   3040000 perm   4154 sec   (732 perm/sec)   p_kst 3.618421e-06   p_cons 9.833043e-01   p_joint 1.085526e-05

Joint ci ratio: 6.722706e-01	ci left: 7.447776e-06	ci right 1.519481e-05	k: 33	n:3050000
Cons ci ratio: 2.925520e-04	ci left: 9.831519e-01	ci right 9.834399e-01	k: 2999054	n:3050000
KS ci ratio: 1.131604e+00	ci left: 1.800382e-06	ci right 6.453118e-06	k: 11	n:3050000
ZNF814   3050000 perm   4178 sec   (730 perm/sec)   p_kst 3.606557e-06   p_cons 9.832964e-01   p_joint 1.081967e-05

Joint ci ratio: 6.722706e-01	ci left: 7.423437e-06	ci right 1.514515e-05	k: 33	n:3060000
Cons ci ratio: 2.921257e-04	ci left: 9.831463e-01	ci right 9.834338e-01	k: 3008869	n:3060000
KS ci ratio: 1.131604e+00	ci left: 1.794498e-06	ci right 6.432030e-06	k: 11	n:3060000
ZNF814   3060000 perm   4203 sec   (728 perm/sec)   p_kst 3.594771e-06   p_cons 9.832905e-01   p_joint 1.078431e-05

Joint ci ratio: 6.722706e-01	ci left: 7.399256e-06	ci right 1.509582e-05	k: 33	n:3070000
Cons ci ratio: 2.915799e-04	ci left: 9.831544e-01	ci right 9.834414e-01	k: 3018726	n:3070000
KS ci ratio: 1.131604e+00	ci left: 1.788653e-06	ci right 6.411078e-06	k: 11	n:3070000
ZNF814   3070000 perm   4227 sec   (726 perm/sec)   p_kst 3.583062e-06   p_cons 9.832984e-01   p_joint 1.074919e-05

Joint ci ratio: 6.722706e-01	ci left: 7.375232e-06	ci right 1.504681e-05	k: 33	n:3080000
Cons ci ratio: 2.910716e-04	ci left: 9.831586e-01	ci right 9.834451e-01	k: 3028571	n:3080000
KS ci ratio: 1.131604e+00	ci left: 1.782846e-06	ci right 6.390263e-06	k: 11	n:3080000
ZNF814   3080000 perm   4252 sec   (724 perm/sec)   p_kst 3.571429e-06   p_cons 9.833023e-01   p_joint 1.071429e-05

Joint ci ratio: 6.722706e-01	ci left: 7.351364e-06	ci right 1.499811e-05	k: 33	n:3090000
Cons ci ratio: 2.905430e-04	ci left: 9.831653e-01	ci right 9.834513e-01	k: 3038424	n:3090000
KS ci ratio: 1.131604e+00	ci left: 1.777076e-06	ci right 6.369583e-06	k: 11	n:3090000
ZNF814   3090000 perm   4277 sec   (722 perm/sec)   p_kst 3.559871e-06   p_cons 9.833087e-01   p_joint 1.067961e-05

Joint ci ratio: 6.722707e-01	ci left: 7.327650e-06	ci right 1.494973e-05	k: 33	n:3100000
Cons ci ratio: 2.900856e-04	ci left: 9.831642e-01	ci right 9.834497e-01	k: 3048253	n:3100000
KS ci ratio: 1.131604e+00	ci left: 1.771343e-06	ci right 6.349036e-06	k: 11	n:3100000
ZNF814   3100000 perm   4301 sec   (721 perm/sec)   p_kst 3.548387e-06   p_cons 9.833074e-01   p_joint 1.064516e-05

Joint ci ratio: 6.722707e-01	ci left: 7.304089e-06	ci right 1.490166e-05	k: 33	n:3110000
Cons ci ratio: 2.895198e-04	ci left: 9.831757e-01	ci right 9.834607e-01	k: 3058121	n:3110000
KS ci ratio: 1.131604e+00	ci left: 1.765648e-06	ci right 6.328621e-06	k: 11	n:3110000
ZNF814   3110000 perm   4326 sec   (719 perm/sec)   p_kst 3.536977e-06   p_cons 9.833186e-01   p_joint 1.061093e-05

Joint ci ratio: 6.722707e-01	ci left: 7.280678e-06	ci right 1.485390e-05	k: 33	n:3120000
Cons ci ratio: 2.890221e-04	ci left: 9.831797e-01	ci right 9.834642e-01	k: 3067966	n:3120000
KS ci ratio: 1.131604e+00	ci left: 1.759989e-06	ci right 6.308337e-06	k: 11	n:3120000
ZNF814   3120000 perm   4351 sec   (717 perm/sec)   p_kst 3.525641e-06   p_cons 9.833224e-01   p_joint 1.057692e-05

Joint ci ratio: 6.722707e-01	ci left: 7.257417e-06	ci right 1.480644e-05	k: 33	n:3130000
Cons ci ratio: 2.885128e-04	ci left: 9.831853e-01	ci right 9.834694e-01	k: 3077816	n:3130000
KS ci ratio: 1.131604e+00	ci left: 1.754366e-06	ci right 6.288182e-06	k: 11	n:3130000
ZNF814   3130000 perm   4375 sec   (715 perm/sec)   p_kst 3.514377e-06   p_cons 9.833278e-01   p_joint 1.054313e-05

Joint ci ratio: 5.489052e-01	ci left: 1.181880e-05	ci right 2.099318e-05	k: 50	n:3140000
Cons ci ratio: 2.880454e-04	ci left: 9.831864e-01	ci right 9.834700e-01	k: 3087652	n:3140000
KS ci ratio: 1.087210e+00	ci left: 1.974707e-06	ci right 6.675654e-06	k: 12	n:3140000
ZNF814   3140000 perm   4400 sec   (714 perm/sec)   p_kst 3.821656e-06   p_cons 9.833287e-01   p_joint 1.592357e-05

Joint ci ratio: 5.489053e-01	ci left: 1.178128e-05	ci right 2.092654e-05	k: 50	n:3150000
Cons ci ratio: 2.875747e-04	ci left: 9.831882e-01	ci right 9.834713e-01	k: 3097490	n:3150000
KS ci ratio: 1.087210e+00	ci left: 1.968438e-06	ci right 6.654462e-06	k: 12	n:3150000
ZNF814   3150000 perm   4425 sec   (712 perm/sec)   p_kst 3.809524e-06   p_cons 9.833302e-01   p_joint 1.587302e-05

Joint ci ratio: 5.489053e-01	ci left: 1.174400e-05	ci right 2.086032e-05	k: 50	n:3160000
Cons ci ratio: 2.871146e-04	ci left: 9.831889e-01	ci right 9.834716e-01	k: 3107325	n:3160000
KS ci ratio: 1.087210e+00	ci left: 1.962209e-06	ci right 6.633404e-06	k: 12	n:3160000
ZNF814   3160000 perm   4450 sec   (710 perm/sec)   p_kst 3.797468e-06   p_cons 9.833307e-01   p_joint 1.582278e-05

Joint ci ratio: 5.489053e-01	ci left: 1.170695e-05	ci right 2.079451e-05	k: 50	n:3170000
Cons ci ratio: 2.866484e-04	ci left: 9.831906e-01	ci right 9.834728e-01	k: 3117163	n:3170000
KS ci ratio: 1.087210e+00	ci left: 1.956019e-06	ci right 6.612478e-06	k: 12	n:3170000
ZNF814   3170000 perm   4475 sec   (708 perm/sec)   p_kst 3.785489e-06   p_cons 9.833322e-01   p_joint 1.577287e-05

Joint ci ratio: 4.496494e-01	ci left: 1.855107e-05	ci right 2.956380e-05	k: 75	n:3180000
Cons ci ratio: 2.861653e-04	ci left: 9.831946e-01	ci right 9.834763e-01	k: 3127008	n:3180000
KS ci ratio: 1.047662e+00	ci left: 2.176716e-06	ci right 6.990680e-06	k: 13	n:3180000
ZNF814   3180000 perm   4500 sec   (707 perm/sec)   p_kst 4.088050e-06   p_cons 9.833358e-01   p_joint 2.358491e-05

Joint ci ratio: 4.467200e-01	ci left: 1.877100e-05	ci right 2.981976e-05	k: 76	n:3190000
Cons ci ratio: 2.857420e-04	ci left: 9.831918e-01	ci right 9.834731e-01	k: 3136832	n:3190000
KS ci ratio: 1.047662e+00	ci left: 2.169893e-06	ci right 6.968766e-06	k: 13	n:3190000
ZNF814   3190000 perm   4525 sec   (705 perm/sec)   p_kst 4.075235e-06   p_cons 9.833329e-01   p_joint 2.382445e-05

Joint ci ratio: 4.788991e-01	ci left: 1.595141e-05	ci right 2.623998e-05	k: 66	n:3200000
Cons ci ratio: 2.853042e-04	ci left: 9.831910e-01	ci right 9.834719e-01	k: 3146662	n:3200000
KS ci ratio: 1.047662e+00	ci left: 2.163112e-06	ci right 6.946989e-06	k: 13	n:3200000
ZNF814   3200000 perm   4550 sec   (703 perm/sec)   p_kst 4.062500e-06   p_cons 9.833319e-01   p_joint 2.062500e-05

Joint ci ratio: 4.788991e-01	ci left: 1.590172e-05	ci right 2.615824e-05	k: 66	n:3210000
Cons ci ratio: 2.848522e-04	ci left: 9.831921e-01	ci right 9.834725e-01	k: 3156498	n:3210000
KS ci ratio: 1.047662e+00	ci left: 2.156373e-06	ci right 6.925347e-06	k: 13	n:3210000
ZNF814   3210000 perm   4576 sec   (701 perm/sec)   p_kst 4.049844e-06   p_cons 9.833327e-01   p_joint 2.056075e-05

Joint ci ratio: 4.788992e-01	ci left: 1.585233e-05	ci right 2.607700e-05	k: 66	n:3220000
Cons ci ratio: 2.844185e-04	ci left: 9.831913e-01	ci right 9.834712e-01	k: 3166328	n:3220000
KS ci ratio: 1.047662e+00	ci left: 2.149676e-06	ci right 6.903840e-06	k: 13	n:3220000
ZNF814   3220000 perm   4602 sec   (700 perm/sec)   p_kst 4.037267e-06   p_cons 9.833317e-01   p_joint 2.049689e-05

Joint ci ratio: 4.788992e-01	ci left: 1.580325e-05	ci right 2.599627e-05	k: 66	n:3230000
Cons ci ratio: 2.840163e-04	ci left: 9.831870e-01	ci right 9.834666e-01	k: 3176147	n:3230000
KS ci ratio: 1.047662e+00	ci left: 2.143021e-06	ci right 6.882466e-06	k: 13	n:3230000
ZNF814   3230000 perm   4627 sec   (698 perm/sec)   p_kst 4.024768e-06   p_cons 9.833272e-01   p_joint 2.043344e-05

Joint ci ratio: 4.788992e-01	ci left: 1.575448e-05	ci right 2.591603e-05	k: 66	n:3240000
Cons ci ratio: 2.835703e-04	ci left: 9.831881e-01	ci right 9.834672e-01	k: 3185983	n:3240000
KS ci ratio: 1.047662e+00	ci left: 2.136407e-06	ci right 6.861224e-06	k: 13	n:3240000
ZNF814   3240000 perm   4653 sec   (696 perm/sec)   p_kst 4.012346e-06   p_cons 9.833281e-01   p_joint 2.037037e-05

Joint ci ratio: 4.788992e-01	ci left: 1.570600e-05	ci right 2.583629e-05	k: 66	n:3250000
Cons ci ratio: 2.830734e-04	ci left: 9.831953e-01	ci right 9.834740e-01	k: 3195839	n:3250000
KS ci ratio: 1.047662e+00	ci left: 2.129833e-06	ci right 6.840112e-06	k: 13	n:3250000
ZNF814   3250000 perm   4679 sec   (695 perm/sec)   p_kst 4.000000e-06   p_cons 9.833351e-01   p_joint 2.030769e-05

Joint ci ratio: 4.788992e-01	ci left: 1.565782e-05	ci right 2.575704e-05	k: 66	n:3260000
Cons ci ratio: 2.826424e-04	ci left: 9.831951e-01	ci right 9.834733e-01	k: 3205671	n:3260000
KS ci ratio: 1.047662e+00	ci left: 2.123300e-06	ci right 6.819130e-06	k: 13	n:3260000
ZNF814   3260000 perm   4705 sec   (693 perm/sec)   p_kst 3.987730e-06   p_cons 9.833347e-01   p_joint 2.024540e-05

Joint ci ratio: 4.788992e-01	ci left: 1.560994e-05	ci right 2.567827e-05	k: 66	n:3270000
Cons ci ratio: 2.821950e-04	ci left: 9.831971e-01	ci right 9.834749e-01	k: 3215510	n:3270000
KS ci ratio: 1.047662e+00	ci left: 2.116807e-06	ci right 6.798277e-06	k: 13	n:3270000
ZNF814   3270000 perm   4731 sec   (691 perm/sec)   p_kst 3.975535e-06   p_cons 9.833364e-01   p_joint 2.018349e-05

Joint ci ratio: 4.753648e-01	ci left: 1.583055e-05	ci right 2.594128e-05	k: 67	n:3280000
Cons ci ratio: 2.817812e-04	ci left: 9.831953e-01	ci right 9.834727e-01	k: 3225337	n:3280000
KS ci ratio: 1.047662e+00	ci left: 2.110353e-06	ci right 6.777550e-06	k: 13	n:3280000
ZNF814   3280000 perm   4757 sec   (690 perm/sec)   p_kst 3.963415e-06   p_cons 9.833345e-01   p_joint 2.042683e-05

Joint ci ratio: 4.685246e-01	ci left: 1.631800e-05	ci right 2.654215e-05	k: 69	n:3290000
Cons ci ratio: 2.813509e-04	ci left: 9.831957e-01	ci right 9.834727e-01	k: 3235171	n:3290000
KS ci ratio: 1.047662e+00	ci left: 2.103939e-06	ci right 6.756950e-06	k: 13	n:3290000
ZNF814   3290000 perm   4783 sec   (688 perm/sec)   p_kst 3.951368e-06   p_cons 9.833347e-01   p_joint 2.097264e-05

Joint ci ratio: 4.685246e-01	ci left: 1.626856e-05	ci right 2.646172e-05	k: 69	n:3300000
Cons ci ratio: 2.809070e-04	ci left: 9.831980e-01	ci right 9.834745e-01	k: 3245011	n:3300000
KS ci ratio: 1.047662e+00	ci left: 2.097563e-06	ci right 6.736474e-06	k: 13	n:3300000
ZNF814   3300000 perm   4809 sec   (686 perm/sec)   p_kst 3.939394e-06   p_cons 9.833367e-01   p_joint 2.090909e-05

Joint ci ratio: 4.685246e-01	ci left: 1.621941e-05	ci right 2.638177e-05	k: 69	n:3310000
Cons ci ratio: 2.805014e-04	ci left: 9.831960e-01	ci right 9.834721e-01	k: 3254837	n:3310000
KS ci ratio: 1.047662e+00	ci left: 2.091226e-06	ci right 6.716122e-06	k: 13	n:3310000
ZNF814   3310000 perm   4835 sec   (685 perm/sec)   p_kst 3.927492e-06   p_cons 9.833344e-01   p_joint 2.084592e-05

Joint ci ratio: 4.685246e-01	ci left: 1.617055e-05	ci right 2.630231e-05	k: 69	n:3320000
Cons ci ratio: 2.800821e-04	ci left: 9.831958e-01	ci right 9.834715e-01	k: 3264669	n:3320000
KS ci ratio: 1.047662e+00	ci left: 2.084927e-06	ci right 6.695893e-06	k: 13	n:3320000
ZNF814   3320000 perm   4862 sec   (683 perm/sec)   p_kst 3.915663e-06   p_cons 9.833340e-01   p_joint 2.078313e-05

Joint ci ratio: 4.685246e-01	ci left: 1.612199e-05	ci right 2.622333e-05	k: 69	n:3330000
Cons ci ratio: 2.796647e-04	ci left: 9.831956e-01	ci right 9.834709e-01	k: 3274501	n:3330000
KS ci ratio: 1.047662e+00	ci left: 2.078666e-06	ci right 6.675785e-06	k: 13	n:3330000
ZNF814   3330000 perm   4888 sec   (681 perm/sec)   p_kst 3.903904e-06   p_cons 9.833336e-01   p_joint 2.072072e-05

Joint ci ratio: 4.685246e-01	ci left: 1.607372e-05	ci right 2.614481e-05	k: 69	n:3340000
Cons ci ratio: 2.792542e-04	ci left: 9.831948e-01	ci right 9.834697e-01	k: 3284331	n:3340000
KS ci ratio: 1.047662e+00	ci left: 2.072442e-06	ci right 6.655798e-06	k: 13	n:3340000
ZNF814   3340000 perm   4914 sec   (680 perm/sec)   p_kst 3.892216e-06   p_cons 9.833326e-01   p_joint 2.065868e-05

Joint ci ratio: 4.685246e-01	ci left: 1.602574e-05	ci right 2.606677e-05	k: 69	n:3350000
Cons ci ratio: 2.788024e-04	ci left: 9.831991e-01	ci right 9.834735e-01	k: 3294178	n:3350000
KS ci ratio: 1.047662e+00	ci left: 2.066256e-06	ci right 6.635930e-06	k: 13	n:3350000
ZNF814   3350000 perm   4940 sec   (678 perm/sec)   p_kst 3.880597e-06   p_cons 9.833367e-01   p_joint 2.059701e-05

Joint ci ratio: 4.685247e-01	ci left: 1.597805e-05	ci right 2.598919e-05	k: 69	n:3360000
Cons ci ratio: 2.784159e-04	ci left: 9.831959e-01	ci right 9.834699e-01	k: 3304000	n:3360000
KS ci ratio: 1.047662e+00	ci left: 2.060106e-06	ci right 6.616180e-06	k: 13	n:3360000
ZNF814   3360000 perm   4966 sec   (677 perm/sec)   p_kst 3.869048e-06   p_cons 9.833333e-01   p_joint 2.053571e-05

Joint ci ratio: 4.652134e-01	ci left: 1.619245e-05	ci right 2.624349e-05	k: 70	n:3370000
Cons ci ratio: 2.780059e-04	ci left: 9.831957e-01	ci right 9.834694e-01	k: 3313832	n:3370000
KS ci ratio: 1.047662e+00	ci left: 2.053993e-06	ci right 6.596548e-06	k: 13	n:3370000
ZNF814   3370000 perm   4993 sec   (675 perm/sec)   p_kst 3.857567e-06   p_cons 9.833329e-01   p_joint 2.077151e-05

Joint ci ratio: 4.619714e-01	ci left: 1.640583e-05	ci right 2.649603e-05	k: 71	n:3380000
Cons ci ratio: 2.776052e-04	ci left: 9.831946e-01	ci right 9.834679e-01	k: 3323661	n:3380000
KS ci ratio: 1.047662e+00	ci left: 2.047916e-06	ci right 6.577031e-06	k: 13	n:3380000
ZNF814   3380000 perm   5019 sec   (673 perm/sec)   p_kst 3.846154e-06   p_cons 9.833317e-01   p_joint 2.100592e-05

Joint ci ratio: 4.619715e-01	ci left: 1.635744e-05	ci right 2.641787e-05	k: 71	n:3390000
Cons ci ratio: 2.772585e-04	ci left: 9.831873e-01	ci right 9.834602e-01	k: 3333469	n:3390000
KS ci ratio: 1.047662e+00	ci left: 2.041875e-06	ci right 6.557630e-06	k: 13	n:3390000
ZNF814   3390000 perm   5046 sec   (672 perm/sec)   p_kst 3.834808e-06   p_cons 9.833242e-01   p_joint 2.094395e-05

Joint ci ratio: 4.619715e-01	ci left: 1.630933e-05	ci right 2.634017e-05	k: 71	n:3400000
Cons ci ratio: 2.768089e-04	ci left: 9.831925e-01	ci right 9.834649e-01	k: 3343319	n:3400000
KS ci ratio: 1.047662e+00	ci left: 2.035870e-06	ci right 6.538343e-06	k: 13	n:3400000
ZNF814   3400000 perm   5073 sec   (670 perm/sec)   p_kst 3.823529e-06   p_cons 9.833291e-01   p_joint 2.088235e-05

Joint ci ratio: 4.619715e-01	ci left: 1.626150e-05	ci right 2.626293e-05	k: 71	n:3410000
Cons ci ratio: 2.764010e-04	ci left: 9.831929e-01	ci right 9.834650e-01	k: 3353153	n:3410000
KS ci ratio: 1.047662e+00	ci left: 2.029900e-06	ci right 6.519169e-06	k: 13	n:3410000
ZNF814   3410000 perm   5100 sec   (669 perm/sec)   p_kst 3.812317e-06   p_cons 9.833293e-01   p_joint 2.082111e-05

Joint ci ratio: 4.619715e-01	ci left: 1.621395e-05	ci right 2.618614e-05	k: 71	n:3420000
Cons ci ratio: 2.760760e-04	ci left: 9.831836e-01	ci right 9.834554e-01	k: 3362954	n:3420000
KS ci ratio: 1.047662e+00	ci left: 2.023964e-06	ci right 6.500107e-06	k: 13	n:3420000
ZNF814   3420000 perm   5127 sec   (667 perm/sec)   p_kst 3.801170e-06   p_cons 9.833199e-01   p_joint 2.076023e-05

Joint ci ratio: 4.619715e-01	ci left: 1.616668e-05	ci right 2.610980e-05	k: 71	n:3430000
Cons ci ratio: 2.756738e-04	ci left: 9.831837e-01	ci right 9.834551e-01	k: 3372787	n:3430000
KS ci ratio: 1.047662e+00	ci left: 2.018063e-06	ci right 6.481156e-06	k: 13	n:3430000
ZNF814   3430000 perm   5153 sec   (666 perm/sec)   p_kst 3.790087e-06   p_cons 9.833198e-01   p_joint 2.069971e-05

Joint ci ratio: 4.619715e-01	ci left: 1.611968e-05	ci right 2.603389e-05	k: 71	n:3440000
Cons ci ratio: 2.752903e-04	ci left: 9.831818e-01	ci right 9.834528e-01	k: 3382613	n:3440000
KS ci ratio: 1.047662e+00	ci left: 2.012197e-06	ci right 6.462316e-06	k: 13	n:3440000
ZNF814   3440000 perm   5180 sec   (664 perm/sec)   p_kst 3.779070e-06   p_cons 9.833177e-01   p_joint 2.063953e-05

Joint ci ratio: 4.619715e-01	ci left: 1.607296e-05	ci right 2.595843e-05	k: 71	n:3450000
Cons ci ratio: 2.748964e-04	ci left: 9.831814e-01	ci right 9.834520e-01	k: 3392444	n:3450000
KS ci ratio: 1.047662e+00	ci left: 2.006365e-06	ci right 6.443584e-06	k: 13	n:3450000
ZNF814   3450000 perm   5207 sec   (663 perm/sec)   p_kst 3.768116e-06   p_cons 9.833171e-01   p_joint 2.057971e-05

Joint ci ratio: 4.587964e-01	ci left: 1.628199e-05	ci right 2.620573e-05	k: 72	n:3460000
Cons ci ratio: 2.745017e-04	ci left: 9.831813e-01	ci right 9.834515e-01	k: 3402276	n:3460000
KS ci ratio: 1.012137e+00	ci left: 2.212120e-06	ci right 6.788899e-06	k: 14	n:3460000
ZNF814   3460000 perm   5234 sec   (661 perm/sec)   p_kst 4.046243e-06   p_cons 9.833168e-01   p_joint 2.080925e-05

Joint ci ratio: 4.587964e-01	ci left: 1.623507e-05	ci right 2.613021e-05	k: 72	n:3470000
Cons ci ratio: 2.741183e-04	ci left: 9.831800e-01	ci right 9.834498e-01	k: 3412104	n:3470000
KS ci ratio: 1.012137e+00	ci left: 2.205745e-06	ci right 6.769334e-06	k: 14	n:3470000
ZNF814   3470000 perm   5261 sec   (660 perm/sec)   p_kst 4.034582e-06   p_cons 9.833153e-01   p_joint 2.074928e-05

Joint ci ratio: 4.587964e-01	ci left: 1.618842e-05	ci right 2.605513e-05	k: 72	n:3480000
Cons ci ratio: 2.737533e-04	ci left: 9.831766e-01	ci right 9.834461e-01	k: 3421925	n:3480000
KS ci ratio: 1.012137e+00	ci left: 2.199407e-06	ci right 6.749882e-06	k: 14	n:3480000
ZNF814   3480000 perm   5288 sec   (658 perm/sec)   p_kst 4.022989e-06   p_cons 9.833118e-01   p_joint 2.068966e-05

Joint ci ratio: 4.587964e-01	ci left: 1.614203e-05	ci right 2.598047e-05	k: 72	n:3490000
Cons ci ratio: 2.733587e-04	ci left: 9.831771e-01	ci right 9.834462e-01	k: 3431759	n:3490000
KS ci ratio: 1.012137e+00	ci left: 2.193105e-06	ci right 6.730541e-06	k: 14	n:3490000
ZNF814   3490000 perm   5316 sec   (657 perm/sec)   p_kst 4.011461e-06   p_cons 9.833120e-01   p_joint 2.063037e-05

Joint ci ratio: 4.587964e-01	ci left: 1.609591e-05	ci right 2.590624e-05	k: 72	n:3500000
Cons ci ratio: 2.730157e-04	ci left: 9.831715e-01	ci right 9.834403e-01	k: 3441572	n:3500000
KS ci ratio: 1.012137e+00	ci left: 2.186839e-06	ci right 6.711311e-06	k: 14	n:3500000
ZNF814   3500000 perm   5343 sec   (655 perm/sec)   p_kst 4.000000e-06   p_cons 9.833063e-01   p_joint 2.057143e-05

Joint ci ratio: 4.587965e-01	ci left: 1.605005e-05	ci right 2.583243e-05	k: 72	n:3510000
Cons ci ratio: 2.725722e-04	ci left: 9.831783e-01	ci right 9.834466e-01	k: 3451428	n:3510000
KS ci ratio: 1.012137e+00	ci left: 2.180609e-06	ci right 6.692191e-06	k: 14	n:3510000
ZNF814   3510000 perm   5371 sec   (654 perm/sec)   p_kst 3.988604e-06   p_cons 9.833128e-01   p_joint 2.051282e-05

Joint ci ratio: 4.587965e-01	ci left: 1.600446e-05	ci right 2.575905e-05	k: 72	n:3520000
Cons ci ratio: 2.721756e-04	ci left: 9.831796e-01	ci right 9.834475e-01	k: 3461265	n:3520000
KS ci ratio: 1.012137e+00	ci left: 2.174414e-06	ci right 6.673179e-06	k: 14	n:3520000
ZNF814   3520000 perm   5398 sec   (652 perm/sec)   p_kst 3.977273e-06   p_cons 9.833139e-01   p_joint 2.045455e-05

Joint ci ratio: 4.556859e-01	ci left: 1.620976e-05	ci right 2.600178e-05	k: 73	n:3530000
Cons ci ratio: 2.718324e-04	ci left: 9.831746e-01	ci right 9.834422e-01	k: 3471080	n:3530000
KS ci ratio: 1.012137e+00	ci left: 2.168254e-06	ci right 6.654275e-06	k: 14	n:3530000
ZNF814   3530000 perm   5426 sec   (651 perm/sec)   p_kst 3.966006e-06   p_cons 9.833088e-01   p_joint 2.067989e-05

Joint ci ratio: 4.556859e-01	ci left: 1.616397e-05	ci right 2.592833e-05	k: 73	n:3540000
Cons ci ratio: 2.714694e-04	ci left: 9.831722e-01	ci right 9.834394e-01	k: 3480904	n:3540000
KS ci ratio: 1.012137e+00	ci left: 2.162129e-06	ci right 6.635477e-06	k: 14	n:3540000
ZNF814   3540000 perm   5453 sec   (649 perm/sec)   p_kst 3.954802e-06   p_cons 9.833062e-01   p_joint 2.062147e-05

Joint ci ratio: 4.556859e-01	ci left: 1.611844e-05	ci right 2.585530e-05	k: 73	n:3550000
Cons ci ratio: 2.711102e-04	ci left: 9.831696e-01	ci right 9.834364e-01	k: 3490727	n:3550000
KS ci ratio: 1.012137e+00	ci left: 2.156038e-06	ci right 6.616786e-06	k: 14	n:3550000
ZNF814   3550000 perm   5481 sec   (648 perm/sec)   p_kst 3.943662e-06   p_cons 9.833034e-01   p_joint 2.056338e-05

Joint ci ratio: 4.556859e-01	ci left: 1.607316e-05	ci right 2.578267e-05	k: 73	n:3560000
Cons ci ratio: 2.707663e-04	ci left: 9.831652e-01	ci right 9.834317e-01	k: 3500544	n:3560000
KS ci ratio: 1.012137e+00	ci left: 2.149982e-06	ci right 6.598199e-06	k: 14	n:3560000
ZNF814   3560000 perm   5509 sec   (646 perm/sec)   p_kst 3.932584e-06   p_cons 9.832989e-01   p_joint 2.050562e-05

Joint ci ratio: 4.556860e-01	ci left: 1.602814e-05	ci right 2.571045e-05	k: 73	n:3570000
Cons ci ratio: 2.704905e-04	ci left: 9.831528e-01	ci right 9.834190e-01	k: 3510332	n:3570000
KS ci ratio: 1.012137e+00	ci left: 2.143960e-06	ci right 6.579717e-06	k: 14	n:3570000
ZNF814   3570000 perm   5537 sec   (645 perm/sec)   p_kst 3.921569e-06   p_cons 9.832863e-01   p_joint 2.044818e-05

Joint ci ratio: 4.556860e-01	ci left: 1.598337e-05	ci right 2.563863e-05	k: 73	n:3580000
Cons ci ratio: 2.701190e-04	ci left: 9.831521e-01	ci right 9.834180e-01	k: 3520162	n:3580000
KS ci ratio: 1.012137e+00	ci left: 2.137971e-06	ci right 6.561338e-06	k: 14	n:3580000
ZNF814   3580000 perm   5565 sec   (643 perm/sec)   p_kst 3.910615e-06   p_cons 9.832855e-01   p_joint 2.039106e-05

Joint ci ratio: 4.556860e-01	ci left: 1.593885e-05	ci right 2.556721e-05	k: 73	n:3590000
Cons ci ratio: 2.697628e-04	ci left: 9.831499e-01	ci right 9.834154e-01	k: 3529986	n:3590000
KS ci ratio: 1.012137e+00	ci left: 2.132016e-06	ci right 6.543061e-06	k: 14	n:3590000
ZNF814   3590000 perm   5594 sec   (642 perm/sec)   p_kst 3.899721e-06   p_cons 9.832830e-01   p_joint 2.033426e-05

Joint ci ratio: 4.556860e-01	ci left: 1.589457e-05	ci right 2.549619e-05	k: 73	n:3600000
Cons ci ratio: 2.693738e-04	ci left: 9.831518e-01	ci right 9.834169e-01	k: 3539825	n:3600000
KS ci ratio: 1.012137e+00	ci left: 2.126093e-06	ci right 6.524886e-06	k: 14	n:3600000
ZNF814   3600000 perm   5623 sec   (640 perm/sec)   p_kst 3.888889e-06   p_cons 9.832847e-01   p_joint 2.027778e-05

Joint ci ratio: 4.556860e-01	ci left: 1.585054e-05	ci right 2.542557e-05	k: 73	n:3610000
Cons ci ratio: 2.689638e-04	ci left: 9.831564e-01	ci right 9.834212e-01	k: 3549674	n:3610000
KS ci ratio: 1.012137e+00	ci left: 2.120204e-06	ci right 6.506812e-06	k: 14	n:3610000
ZNF814   3610000 perm   5652 sec   (639 perm/sec)   p_kst 3.878116e-06   p_cons 9.832892e-01   p_joint 2.022161e-05

Joint ci ratio: 4.556860e-01	ci left: 1.580676e-05	ci right 2.535533e-05	k: 73	n:3620000
Cons ci ratio: 2.685963e-04	ci left: 9.831561e-01	ci right 9.834205e-01	k: 3559505	n:3620000
KS ci ratio: 1.012137e+00	ci left: 2.114347e-06	ci right 6.488837e-06	k: 14	n:3620000
ZNF814   3620000 perm   5680 sec   (637 perm/sec)   p_kst 3.867403e-06   p_cons 9.832887e-01   p_joint 2.016575e-05

Joint ci ratio: 4.556860e-01	ci left: 1.576321e-05	ci right 2.528548e-05	k: 73	n:3630000
Cons ci ratio: 2.681831e-04	ci left: 9.831616e-01	ci right 9.834255e-01	k: 3569357	n:3630000
KS ci ratio: 1.012137e+00	ci left: 2.108522e-06	ci right 6.470962e-06	k: 14	n:3630000
ZNF814   3630000 perm   5709 sec   (636 perm/sec)   p_kst 3.856749e-06   p_cons 9.832939e-01   p_joint 2.011019e-05

Joint ci ratio: 4.556860e-01	ci left: 1.571991e-05	ci right 2.521602e-05	k: 73	n:3640000
Cons ci ratio: 2.678009e-04	ci left: 9.831634e-01	ci right 9.834270e-01	k: 3579196	n:3640000
KS ci ratio: 1.012137e+00	ci left: 2.102730e-06	ci right 6.453184e-06	k: 14	n:3640000
ZNF814   3640000 perm   5737 sec   (634 perm/sec)   p_kst 3.846154e-06   p_cons 9.832956e-01   p_joint 2.005495e-05

Joint ci ratio: 4.556861e-01	ci left: 1.567684e-05	ci right 2.514693e-05	k: 73	n:3650000
Cons ci ratio: 2.674783e-04	ci left: 9.831581e-01	ci right 9.834214e-01	k: 3589009	n:3650000
KS ci ratio: 1.012137e+00	ci left: 2.096969e-06	ci right 6.435504e-06	k: 14	n:3650000
ZNF814   3650000 perm   5766 sec   (633 perm/sec)   p_kst 3.835616e-06   p_cons 9.832901e-01   p_joint 2.000000e-05

Joint ci ratio: 4.556861e-01	ci left: 1.563401e-05	ci right 2.507823e-05	k: 73	n:3660000
Cons ci ratio: 2.670813e-04	ci left: 9.831622e-01	ci right 9.834250e-01	k: 3598856	n:3660000
KS ci ratio: 1.012137e+00	ci left: 2.091239e-06	ci right 6.417921e-06	k: 14	n:3660000
ZNF814   3660000 perm   5796 sec   (632 perm/sec)   p_kst 3.825137e-06   p_cons 9.832940e-01   p_joint 1.994536e-05

Joint ci ratio: 4.556861e-01	ci left: 1.559141e-05	ci right 2.500989e-05	k: 73	n:3670000
Cons ci ratio: 2.667436e-04	ci left: 9.831591e-01	ci right 9.834216e-01	k: 3608677	n:3670000
KS ci ratio: 1.012137e+00	ci left: 2.085541e-06	ci right 6.400433e-06	k: 14	n:3670000
ZNF814   3670000 perm   5825 sec   (630 perm/sec)   p_kst 3.814714e-06   p_cons 9.832907e-01   p_joint 1.989101e-05

Joint ci ratio: 4.526379e-01	ci left: 1.578968e-05	ci right 2.524456e-05	k: 74	n:3680000
Cons ci ratio: 2.663939e-04	ci left: 9.831576e-01	ci right 9.834199e-01	k: 3618504	n:3680000
KS ci ratio: 1.012137e+00	ci left: 2.079874e-06	ci right 6.383041e-06	k: 14	n:3680000
ZNF814   3680000 perm   5855 sec   (629 perm/sec)   p_kst 3.804348e-06   p_cons 9.832891e-01   p_joint 2.010870e-05

Joint ci ratio: 4.526379e-01	ci left: 1.574689e-05	ci right 2.517615e-05	k: 74	n:3690000
Cons ci ratio: 2.660281e-04	ci left: 9.831584e-01	ci right 9.834202e-01	k: 3628339	n:3690000
KS ci ratio: 1.012137e+00	ci left: 2.074237e-06	ci right 6.365743e-06	k: 14	n:3690000
ZNF814   3690000 perm   5884 sec   (627 perm/sec)   p_kst 3.794038e-06   p_cons 9.832897e-01   p_joint 2.005420e-05

Joint ci ratio: 4.526380e-01	ci left: 1.570433e-05	ci right 2.510810e-05	k: 74	n:3700000
Cons ci ratio: 2.656550e-04	ci left: 9.831602e-01	ci right 9.834217e-01	k: 3638178	n:3700000
KS ci ratio: 1.012137e+00	ci left: 2.068631e-06	ci right 6.348538e-06	k: 14	n:3700000
ZNF814   3700000 perm   5912 sec   (626 perm/sec)   p_kst 3.783784e-06   p_cons 9.832914e-01   p_joint 2.000000e-05

Joint ci ratio: 4.526380e-01	ci left: 1.566200e-05	ci right 2.504043e-05	k: 74	n:3710000
Cons ci ratio: 2.653009e-04	ci left: 9.831599e-01	ci right 9.834210e-01	k: 3648009	n:3710000
KS ci ratio: 1.012137e+00	ci left: 2.063055e-06	ci right 6.331426e-06	k: 14	n:3710000
ZNF814   3710000 perm   5941 sec   (624 perm/sec)   p_kst 3.773585e-06   p_cons 9.832908e-01   p_joint 1.994609e-05

Joint ci ratio: 4.526380e-01	ci left: 1.561990e-05	ci right 2.497311e-05	k: 74	n:3720000
Cons ci ratio: 2.649547e-04	ci left: 9.831587e-01	ci right 9.834195e-01	k: 3657837	n:3720000
KS ci ratio: 1.012137e+00	ci left: 2.057510e-06	ci right 6.314406e-06	k: 14	n:3720000
ZNF814   3720000 perm   5971 sec   (623 perm/sec)   p_kst 3.763441e-06   p_cons 9.832895e-01   p_joint 1.989247e-05

Joint ci ratio: 4.526380e-01	ci left: 1.557802e-05	ci right 2.490616e-05	k: 74	n:3730000
Cons ci ratio: 2.646077e-04	ci left: 9.831579e-01	ci right 9.834183e-01	k: 3667666	n:3730000
KS ci ratio: 1.012137e+00	ci left: 2.051994e-06	ci right 6.297478e-06	k: 14	n:3730000
ZNF814   3730000 perm   6000 sec   (622 perm/sec)   p_kst 3.753351e-06   p_cons 9.832885e-01   p_joint 1.983914e-05

Joint ci ratio: 4.467208e-01	ci left: 1.601056e-05	ci right 2.543452e-05	k: 76	n:3740000
Cons ci ratio: 2.642255e-04	ci left: 9.831616e-01	ci right 9.834216e-01	k: 3677512	n:3740000
KS ci ratio: 1.012137e+00	ci left: 2.046507e-06	ci right 6.280639e-06	k: 14	n:3740000
ZNF814   3740000 perm   6029 sec   (620 perm/sec)   p_kst 3.743316e-06   p_cons 9.832920e-01   p_joint 2.032086e-05

Joint ci ratio: 4.467208e-01	ci left: 1.596786e-05	ci right 2.536669e-05	k: 76	n:3750000
Cons ci ratio: 2.638899e-04	ci left: 9.831596e-01	ci right 9.834194e-01	k: 3687337	n:3750000
KS ci ratio: 1.012137e+00	ci left: 2.041050e-06	ci right 6.263891e-06	k: 14	n:3750000
ZNF814   3750000 perm   6059 sec   (619 perm/sec)   p_kst 3.733333e-06   p_cons 9.832899e-01   p_joint 2.026667e-05

Joint ci ratio: 4.467208e-01	ci left: 1.592539e-05	ci right 2.529923e-05	k: 76	n:3760000
Cons ci ratio: 2.635386e-04	ci left: 9.831598e-01	ci right 9.834192e-01	k: 3697170	n:3760000
KS ci ratio: 1.012137e+00	ci left: 2.035621e-06	ci right 6.247232e-06	k: 14	n:3760000
ZNF814   3760000 perm   6089 sec   (618 perm/sec)   p_kst 3.723404e-06   p_cons 9.832899e-01   p_joint 2.021277e-05

Joint ci ratio: 4.467208e-01	ci left: 1.588315e-05	ci right 2.523212e-05	k: 76	n:3770000
Cons ci ratio: 2.631865e-04	ci left: 9.831603e-01	ci right 9.834193e-01	k: 3707004	n:3770000
KS ci ratio: 1.012138e+00	ci left: 2.030222e-06	ci right 6.230661e-06	k: 14	n:3770000
ZNF814   3770000 perm   6118 sec   (616 perm/sec)   p_kst 3.713528e-06   p_cons 9.832902e-01   p_joint 2.015915e-05

Joint ci ratio: 4.438480e-01	ci left: 1.607601e-05	ci right 2.545940e-05	k: 77	n:3780000
Cons ci ratio: 2.628506e-04	ci left: 9.831589e-01	ci right 9.834176e-01	k: 3716831	n:3780000
KS ci ratio: 1.012138e+00	ci left: 2.024851e-06	ci right 6.214178e-06	k: 14	n:3780000
ZNF814   3780000 perm   6148 sec   (615 perm/sec)   p_kst 3.703704e-06   p_cons 9.832886e-01   p_joint 2.037037e-05

Joint ci ratio: 4.438480e-01	ci left: 1.603359e-05	ci right 2.539223e-05	k: 77	n:3790000
Cons ci ratio: 2.624970e-04	ci left: 9.831599e-01	ci right 9.834183e-01	k: 3726667	n:3790000
KS ci ratio: 1.012138e+00	ci left: 2.019508e-06	ci right 6.197781e-06	k: 14	n:3790000
ZNF814   3790000 perm   6178 sec   (614 perm/sec)   p_kst 3.693931e-06   p_cons 9.832894e-01   p_joint 2.031662e-05

Joint ci ratio: 4.410298e-01	ci left: 1.622523e-05	ci right 2.561771e-05	k: 78	n:3800000
Cons ci ratio: 2.621806e-04	ci left: 9.831564e-01	ci right 9.834144e-01	k: 3736486	n:3800000
KS ci ratio: 1.012138e+00	ci left: 2.014194e-06	ci right 6.181472e-06	k: 14	n:3800000
ZNF814   3800000 perm   6207 sec   (612 perm/sec)   p_kst 3.684211e-06   p_cons 9.832858e-01   p_joint 2.052632e-05

Joint ci ratio: 4.410298e-01	ci left: 1.618265e-05	ci right 2.555047e-05	k: 78	n:3810000
Cons ci ratio: 2.618360e-04	ci left: 9.831566e-01	ci right 9.834143e-01	k: 3746319	n:3810000
KS ci ratio: 1.012138e+00	ci left: 2.008907e-06	ci right 6.165247e-06	k: 14	n:3810000
ZNF814   3810000 perm   6237 sec   (611 perm/sec)   p_kst 3.674541e-06   p_cons 9.832858e-01   p_joint 2.047244e-05

Joint ci ratio: 4.382647e-01	ci left: 1.637308e-05	ci right 2.577417e-05	k: 79	n:3820000
Cons ci ratio: 2.614677e-04	ci left: 9.831600e-01	ci right 9.834173e-01	k: 3756164	n:3820000
KS ci ratio: 1.012138e+00	ci left: 2.003648e-06	ci right 6.149108e-06	k: 14	n:3820000
ZNF814   3820000 perm   6267 sec   (610 perm/sec)   p_kst 3.664921e-06   p_cons 9.832890e-01   p_joint 2.068063e-05

Joint ci ratio: 4.382647e-01	ci left: 1.633033e-05	ci right 2.570687e-05	k: 79	n:3830000
Cons ci ratio: 2.611176e-04	ci left: 9.831612e-01	ci right 9.834182e-01	k: 3766001	n:3830000
KS ci ratio: 1.012138e+00	ci left: 1.998417e-06	ci right 6.133053e-06	k: 14	n:3830000
ZNF814   3830000 perm   6297 sec   (608 perm/sec)   p_kst 3.655352e-06   p_cons 9.832901e-01   p_joint 2.062663e-05

Joint ci ratio: 4.382647e-01	ci left: 1.628780e-05	ci right 2.563993e-05	k: 79	n:3840000
Cons ci ratio: 2.608041e-04	ci left: 9.831580e-01	ci right 9.834147e-01	k: 3775821	n:3840000
KS ci ratio: 1.012138e+00	ci left: 1.993212e-06	ci right 6.117081e-06	k: 14	n:3840000
ZNF814   3840000 perm   6327 sec   (607 perm/sec)   p_kst 3.645833e-06   p_cons 9.832867e-01   p_joint 2.057292e-05

Joint ci ratio: 4.382647e-01	ci left: 1.624550e-05	ci right 2.557333e-05	k: 79	n:3850000
Cons ci ratio: 2.604999e-04	ci left: 9.831538e-01	ci right 9.834102e-01	k: 3785637	n:3850000
KS ci ratio: 1.012138e+00	ci left: 1.988035e-06	ci right 6.101193e-06	k: 14	n:3850000
ZNF814   3850000 perm   6357 sec   (606 perm/sec)   p_kst 3.636364e-06   p_cons 9.832823e-01   p_joint 2.051948e-05

Joint ci ratio: 4.382647e-01	ci left: 1.620341e-05	ci right 2.550708e-05	k: 79	n:3860000
Cons ci ratio: 2.601536e-04	ci left: 9.831550e-01	ci right 9.834111e-01	k: 3795474	n:3860000
KS ci ratio: 1.012138e+00	ci left: 1.982885e-06	ci right 6.085387e-06	k: 14	n:3860000
ZNF814   3860000 perm   6387 sec   (604 perm/sec)   p_kst 3.626943e-06   p_cons 9.832834e-01   p_joint 2.046632e-05

Joint ci ratio: 4.355509e-01	ci left: 1.639151e-05	ci right 2.572782e-05	k: 80	n:3870000
Cons ci ratio: 2.598415e-04	ci left: 9.831521e-01	ci right 9.834079e-01	k: 3805295	n:3870000
KS ci ratio: 1.012138e+00	ci left: 1.977761e-06	ci right 6.069662e-06	k: 14	n:3870000
ZNF814   3870000 perm   6417 sec   (603 perm/sec)   p_kst 3.617571e-06   p_cons 9.832804e-01   p_joint 2.067183e-05

Joint ci ratio: 4.789000e-01	ci left: 1.315580e-05	ci right 2.164123e-05	k: 66	n:3880000
Cons ci ratio: 2.594796e-04	ci left: 9.831557e-01	ci right 9.834111e-01	k: 3815141	n:3880000
KS ci ratio: 1.012138e+00	ci left: 1.972664e-06	ci right 6.054019e-06	k: 14	n:3880000
ZNF814   3880000 perm   6447 sec   (602 perm/sec)   p_kst 3.608247e-06   p_cons 9.832838e-01   p_joint 1.701031e-05

Joint ci ratio: 4.789000e-01	ci left: 1.312198e-05	ci right 2.158560e-05	k: 66	n:3890000
Cons ci ratio: 2.591799e-04	ci left: 9.831515e-01	ci right 9.834066e-01	k: 3824957	n:3890000
KS ci ratio: 1.012138e+00	ci left: 1.967593e-06	ci right 6.038456e-06	k: 14	n:3890000
ZNF814   3890000 perm   6478 sec   (601 perm/sec)   p_kst 3.598972e-06   p_cons 9.832794e-01   p_joint 1.696658e-05

Joint ci ratio: 4.789000e-01	ci left: 1.308833e-05	ci right 2.153025e-05	k: 66	n:3900000
Cons ci ratio: 2.588410e-04	ci left: 9.831525e-01	ci right 9.834073e-01	k: 3834793	n:3900000
KS ci ratio: 1.012138e+00	ci left: 1.962548e-06	ci right 6.022972e-06	k: 14	n:3900000
ZNF814   3900000 perm   6508 sec   (599 perm/sec)   p_kst 3.589744e-06   p_cons 9.832803e-01   p_joint 1.692308e-05

Joint ci ratio: 4.789001e-01	ci left: 1.305486e-05	ci right 2.147519e-05	k: 66	n:3910000
Cons ci ratio: 2.585797e-04	ci left: 9.831437e-01	ci right 9.833982e-01	k: 3844591	n:3910000
KS ci ratio: 1.012138e+00	ci left: 1.957528e-06	ci right 6.007568e-06	k: 14	n:3910000
ZNF814   3910000 perm   6538 sec   (598 perm/sec)   p_kst 3.580563e-06   p_cons 9.832714e-01   p_joint 1.687980e-05

Joint ci ratio: 4.789001e-01	ci left: 1.302155e-05	ci right 2.142041e-05	k: 66	n:3920000
Cons ci ratio: 2.582591e-04	ci left: 9.831427e-01	ci right 9.833969e-01	k: 3854419	n:3920000
KS ci ratio: 1.012138e+00	ci left: 1.952535e-06	ci right 5.992243e-06	k: 14	n:3920000
ZNF814   3920000 perm   6569 sec   (597 perm/sec)   p_kst 3.571429e-06   p_cons 9.832702e-01   p_joint 1.683673e-05

Joint ci ratio: 4.789001e-01	ci left: 1.298842e-05	ci right 2.136590e-05	k: 66	n:3930000
Cons ci ratio: 2.579477e-04	ci left: 9.831406e-01	ci right 9.833945e-01	k: 3864243	n:3930000
KS ci ratio: 1.012138e+00	ci left: 1.947566e-06	ci right 5.976996e-06	k: 14	n:3930000
ZNF814   3930000 perm   6599 sec   (596 perm/sec)   p_kst 3.562341e-06   p_cons 9.832679e-01   p_joint 1.679389e-05

Joint ci ratio: 4.789001e-01	ci left: 1.295545e-05	ci right 2.131167e-05	k: 66	n:3940000
Cons ci ratio: 2.576573e-04	ci left: 9.831360e-01	ci right 9.833896e-01	k: 3874057	n:3940000
KS ci ratio: 1.012138e+00	ci left: 1.942623e-06	ci right 5.961826e-06	k: 14	n:3940000
ZNF814   3940000 perm   6630 sec   (594 perm/sec)   p_kst 3.553299e-06   p_cons 9.832632e-01   p_joint 1.675127e-05

Joint ci ratio: 4.789001e-01	ci left: 1.292265e-05	ci right 2.125772e-05	k: 66	n:3950000
Cons ci ratio: 2.573203e-04	ci left: 9.831376e-01	ci right 9.833908e-01	k: 3883895	n:3950000
KS ci ratio: 1.012138e+00	ci left: 1.937705e-06	ci right 5.946732e-06	k: 14	n:3950000
ZNF814   3950000 perm   6661 sec   (593 perm/sec)   p_kst 3.544304e-06   p_cons 9.832646e-01   p_joint 1.670886e-05

Joint ci ratio: 4.789001e-01	ci left: 1.289002e-05	ci right 2.120404e-05	k: 66	n:3960000
Cons ci ratio: 2.570457e-04	ci left: 9.831312e-01	ci right 9.833842e-01	k: 3893702	n:3960000
KS ci ratio: 1.012138e+00	ci left: 1.932812e-06	ci right 5.931715e-06	k: 14	n:3960000
ZNF814   3960000 perm   6693 sec   (592 perm/sec)   p_kst 3.535354e-06   p_cons 9.832581e-01   p_joint 1.666667e-05

Joint ci ratio: 4.753657e-01	ci left: 1.307914e-05	ci right 2.143260e-05	k: 67	n:3970000
Cons ci ratio: 2.567210e-04	ci left: 9.831315e-01	ci right 9.833842e-01	k: 3903535	n:3970000
KS ci ratio: 1.012138e+00	ci left: 1.927943e-06	ci right 5.916774e-06	k: 14	n:3970000
ZNF814   3970000 perm   6723 sec   (590 perm/sec)   p_kst 3.526448e-06   p_cons 9.832582e-01   p_joint 1.687657e-05

Joint ci ratio: 4.753657e-01	ci left: 1.304627e-05	ci right 2.137875e-05	k: 67	n:3980000
Cons ci ratio: 2.563700e-04	ci left: 9.831353e-01	ci right 9.833876e-01	k: 3913382	n:3980000
KS ci ratio: 1.012138e+00	ci left: 1.923099e-06	ci right 5.901908e-06	k: 14	n:3980000
ZNF814   3980000 perm   6754 sec   (589 perm/sec)   p_kst 3.517588e-06   p_cons 9.832618e-01   p_joint 1.683417e-05

Joint ci ratio: 4.753657e-01	ci left: 1.301358e-05	ci right 2.132517e-05	k: 67	n:3990000
Cons ci ratio: 2.560283e-04	ci left: 9.831381e-01	ci right 9.833901e-01	k: 3923225	n:3990000
KS ci ratio: 1.012138e+00	ci left: 1.918280e-06	ci right 5.887116e-06	k: 14	n:3990000
ZNF814   3990000 perm   6785 sec   (588 perm/sec)   p_kst 3.508772e-06   p_cons 9.832644e-01   p_joint 1.679198e-05

Joint ci ratio: 4.753657e-01	ci left: 1.298104e-05	ci right 2.127186e-05	k: 67	n:4000000
Cons ci ratio: 2.557462e-04	ci left: 9.831333e-01	ci right 9.833850e-01	k: 3933038	n:4000000
KS ci ratio: 1.012138e+00	ci left: 1.913484e-06	ci right 5.872398e-06	k: 14	n:4000000
ZNF814   4000000 perm   6816 sec   (587 perm/sec)   p_kst 3.500000e-06   p_cons 9.832595e-01   p_joint 1.675000e-05

Joint ci ratio: 4.719084e-01	ci left: 1.316827e-05	ci right 2.149776e-05	k: 68	n:4010000
Cons ci ratio: 2.554476e-04	ci left: 9.831308e-01	ci right 9.833822e-01	k: 3942860	n:4010000
KS ci ratio: 1.012138e+00	ci left: 1.908712e-06	ci right 5.857754e-06	k: 14	n:4010000
ZNF814   4010000 perm   6847 sec   (586 perm/sec)   p_kst 3.491272e-06   p_cons 9.832569e-01   p_joint 1.695761e-05

Joint ci ratio: 4.719084e-01	ci left: 1.313551e-05	ci right 2.144428e-05	k: 68	n:4020000
Cons ci ratio: 2.551424e-04	ci left: 9.831293e-01	ci right 9.833804e-01	k: 3952686	n:4020000
KS ci ratio: 1.012138e+00	ci left: 1.903964e-06	ci right 5.843182e-06	k: 14	n:4020000
ZNF814   4020000 perm   6880 sec   (584 perm/sec)   p_kst 3.482587e-06   p_cons 9.832552e-01   p_joint 1.691542e-05

Joint ci ratio: 4.719084e-01	ci left: 1.310292e-05	ci right 2.139107e-05	k: 68	n:4030000
Cons ci ratio: 2.547960e-04	ci left: 9.831333e-01	ci right 9.833841e-01	k: 3962534	n:4030000
KS ci ratio: 1.012138e+00	ci left: 1.899240e-06	ci right 5.828683e-06	k: 14	n:4030000
ZNF814   4030000 perm   6911 sec   (583 perm/sec)   p_kst 3.473945e-06   p_cons 9.832591e-01   p_joint 1.687345e-05

Joint ci ratio: 4.719085e-01	ci left: 1.307048e-05	ci right 2.133812e-05	k: 68	n:4040000
Cons ci ratio: 2.544930e-04	ci left: 9.831318e-01	ci right 9.833823e-01	k: 3972360	n:4040000
KS ci ratio: 1.012138e+00	ci left: 1.894538e-06	ci right 5.814256e-06	k: 14	n:4040000
ZNF814   4040000 perm   6942 sec   (582 perm/sec)   p_kst 3.465347e-06   p_cons 9.832574e-01   p_joint 1.683168e-05

Joint ci ratio: 4.719085e-01	ci left: 1.303821e-05	ci right 2.128543e-05	k: 68	n:4050000
Cons ci ratio: 2.541607e-04	ci left: 9.831343e-01	ci right 9.833845e-01	k: 3982202	n:4050000
KS ci ratio: 1.012138e+00	ci left: 1.889861e-06	ci right 5.799900e-06	k: 14	n:4050000
ZNF814   4050000 perm   6974 sec   (581 perm/sec)   p_kst 3.456790e-06   p_cons 9.832598e-01   p_joint 1.679012e-05

Joint ci ratio: 4.719085e-01	ci left: 1.300610e-05	ci right 2.123301e-05	k: 68	n:4060000
Cons ci ratio: 2.538144e-04	ci left: 9.831388e-01	ci right 9.833886e-01	k: 3992052	n:4060000
KS ci ratio: 1.012138e+00	ci left: 1.885206e-06	ci right 5.785614e-06	k: 14	n:4060000
ZNF814   4060000 perm   7006 sec   (580 perm/sec)   p_kst 3.448276e-06   p_cons 9.832640e-01   p_joint 1.674877e-05

Joint ci ratio: 4.719085e-01	ci left: 1.297414e-05	ci right 2.118084e-05	k: 68	n:4070000
Cons ci ratio: 2.535150e-04	ci left: 9.831373e-01	ci right 9.833868e-01	k: 4001878	n:4070000
KS ci ratio: 1.012138e+00	ci left: 1.880574e-06	ci right 5.771399e-06	k: 14	n:4070000
ZNF814   4070000 perm   7038 sec   (578 perm/sec)   p_kst 3.439803e-06   p_cons 9.832624e-01   p_joint 1.670762e-05

Joint ci ratio: 4.719085e-01	ci left: 1.294234e-05	ci right 2.112892e-05	k: 68	n:4080000
Cons ci ratio: 2.532204e-04	ci left: 9.831353e-01	ci right 9.833846e-01	k: 4011702	n:4080000
KS ci ratio: 1.012138e+00	ci left: 1.875965e-06	ci right 5.757253e-06	k: 14	n:4080000
ZNF814   4080000 perm   7070 sec   (577 perm/sec)   p_kst 3.431373e-06   p_cons 9.832603e-01   p_joint 1.666667e-05

Joint ci ratio: 4.719085e-01	ci left: 1.291070e-05	ci right 2.107726e-05	k: 68	n:4090000
Cons ci ratio: 2.529080e-04	ci left: 9.831358e-01	ci right 9.833847e-01	k: 4021536	n:4090000
KS ci ratio: 1.012138e+00	ci left: 1.871378e-06	ci right 5.743177e-06	k: 14	n:4090000
ZNF814   4090000 perm   7101 sec   (576 perm/sec)   p_kst 3.422983e-06   p_cons 9.832606e-01   p_joint 1.662592e-05

Joint ci ratio: 4.719085e-01	ci left: 1.287921e-05	ci right 2.102586e-05	k: 68	n:4100000
Cons ci ratio: 2.526024e-04	ci left: 9.831356e-01	ci right 9.833842e-01	k: 4031367	n:4100000
KS ci ratio: 1.012138e+00	ci left: 1.866813e-06	ci right 5.729169e-06	k: 14	n:4100000
ZNF814   4100000 perm   7133 sec   (575 perm/sec)   p_kst 3.414634e-06   p_cons 9.832602e-01   p_joint 1.658537e-05

Joint ci ratio: 4.719085e-01	ci left: 1.284787e-05	ci right 2.097470e-05	k: 68	n:4110000
Cons ci ratio: 2.522979e-04	ci left: 9.831354e-01	ci right 9.833837e-01	k: 4041198	n:4110000
KS ci ratio: 1.012138e+00	ci left: 1.862271e-06	ci right 5.715230e-06	k: 14	n:4110000
ZNF814   4110000 perm   7165 sec   (574 perm/sec)   p_kst 3.406326e-06   p_cons 9.832599e-01   p_joint 1.654501e-05

Joint ci ratio: 4.719085e-01	ci left: 1.281669e-05	ci right 2.092379e-05	k: 68	n:4120000
Cons ci ratio: 2.520075e-04	ci left: 9.831334e-01	ci right 9.833814e-01	k: 4051022	n:4120000
KS ci ratio: 1.012138e+00	ci left: 1.857751e-06	ci right 5.701358e-06	k: 14	n:4120000
ZNF814   4120000 perm   7197 sec   (572 perm/sec)   p_kst 3.398058e-06   p_cons 9.832578e-01   p_joint 1.650485e-05

Joint ci ratio: 4.719085e-01	ci left: 1.278565e-05	ci right 2.087313e-05	k: 68	n:4130000
Cons ci ratio: 2.516662e-04	ci left: 9.831383e-01	ci right 9.833860e-01	k: 4060874	n:4130000
KS ci ratio: 1.012138e+00	ci left: 1.853253e-06	ci right 5.687553e-06	k: 14	n:4130000
ZNF814   4130000 perm   7230 sec   (571 perm/sec)   p_kst 3.389831e-06   p_cons 9.832625e-01   p_joint 1.646489e-05

Joint ci ratio: 4.719086e-01	ci left: 1.275477e-05	ci right 2.082271e-05	k: 68	n:4140000
Cons ci ratio: 2.513577e-04	ci left: 9.831390e-01	ci right 9.833864e-01	k: 4070709	n:4140000
KS ci ratio: 1.012138e+00	ci left: 1.848777e-06	ci right 5.673815e-06	k: 14	n:4140000
ZNF814   4140000 perm   7263 sec   (570 perm/sec)   p_kst 3.381643e-06   p_cons 9.832630e-01   p_joint 1.642512e-05

Joint ci ratio: 4.719086e-01	ci left: 1.272404e-05	ci right 2.077253e-05	k: 68	n:4150000
Cons ci ratio: 2.510154e-04	ci left: 9.831443e-01	ci right 9.833914e-01	k: 4080563	n:4150000
KS ci ratio: 1.012138e+00	ci left: 1.844322e-06	ci right 5.660143e-06	k: 14	n:4150000
ZNF814   4150000 perm   7295 sec   (569 perm/sec)   p_kst 3.373494e-06   p_cons 9.832682e-01   p_joint 1.638554e-05

Joint ci ratio: 4.719086e-01	ci left: 1.269345e-05	ci right 2.072260e-05	k: 68	n:4160000
Cons ci ratio: 2.507294e-04	ci left: 9.831424e-01	ci right 9.833892e-01	k: 4090387	n:4160000
KS ci ratio: 1.012138e+00	ci left: 1.839888e-06	ci right 5.646537e-06	k: 14	n:4160000
ZNF814   4160000 perm   7328 sec   (568 perm/sec)   p_kst 3.365385e-06   p_cons 9.832661e-01   p_joint 1.634615e-05

Joint ci ratio: 4.719086e-01	ci left: 1.266301e-05	ci right 2.067291e-05	k: 68	n:4170000
Cons ci ratio: 2.504353e-04	ci left: 9.831417e-01	ci right 9.833881e-01	k: 4100216	n:4170000
KS ci ratio: 1.012138e+00	ci left: 1.835476e-06	ci right 5.632996e-06	k: 14	n:4170000
ZNF814   4170000 perm   7361 sec   (567 perm/sec)   p_kst 3.357314e-06   p_cons 9.832652e-01   p_joint 1.630695e-05

Joint ci ratio: 4.719086e-01	ci left: 1.263272e-05	ci right 2.062345e-05	k: 68	n:4180000
Cons ci ratio: 2.501222e-04	ci left: 9.831436e-01	ci right 9.833897e-01	k: 4110056	n:4180000
KS ci ratio: 1.012138e+00	ci left: 1.831085e-06	ci right 5.619520e-06	k: 14	n:4180000
ZNF814   4180000 perm   7393 sec   (565 perm/sec)   p_kst 3.349282e-06   p_cons 9.832670e-01   p_joint 1.626794e-05

Joint ci ratio: 4.719086e-01	ci left: 1.260257e-05	ci right 2.057423e-05	k: 68	n:4190000
Cons ci ratio: 2.498012e-04	ci left: 9.831467e-01	ci right 9.833925e-01	k: 4119901	n:4190000
KS ci ratio: 1.012138e+00	ci left: 1.826715e-06	ci right 5.606108e-06	k: 14	n:4190000
ZNF814   4190000 perm   7425 sec   (564 perm/sec)   p_kst 3.341289e-06   p_cons 9.832699e-01   p_joint 1.622912e-05

Joint ci ratio: 4.719086e-01	ci left: 1.257256e-05	ci right 2.052524e-05	k: 68	n:4200000
Cons ci ratio: 2.495013e-04	ci left: 9.831471e-01	ci right 9.833927e-01	k: 4129735	n:4200000
KS ci ratio: 1.012138e+00	ci left: 1.822366e-06	ci right 5.592761e-06	k: 14	n:4200000
ZNF814   4200000 perm   7458 sec   (563 perm/sec)   p_kst 3.333333e-06   p_cons 9.832702e-01   p_joint 1.619048e-05

Joint ci ratio: 4.719086e-01	ci left: 1.254270e-05	ci right 2.047649e-05	k: 68	n:4210000
Cons ci ratio: 2.492312e-04	ci left: 9.831438e-01	ci right 9.833891e-01	k: 4139553	n:4210000
KS ci ratio: 1.012138e+00	ci left: 1.818037e-06	ci right 5.579476e-06	k: 14	n:4210000
ZNF814   4210000 perm   7492 sec   (562 perm/sec)   p_kst 3.325416e-06   p_cons 9.832667e-01   p_joint 1.615202e-05

Joint ci ratio: 4.719086e-01	ci left: 1.251297e-05	ci right 2.042797e-05	k: 68	n:4220000
Cons ci ratio: 2.489387e-04	ci left: 9.831435e-01	ci right 9.833885e-01	k: 4149384	n:4220000
KS ci ratio: 1.012138e+00	ci left: 1.813729e-06	ci right 5.566255e-06	k: 14	n:4220000
ZNF814   4220000 perm   7525 sec   (561 perm/sec)   p_kst 3.317536e-06   p_cons 9.832664e-01   p_joint 1.611374e-05

Joint ci ratio: 4.719086e-01	ci left: 1.248339e-05	ci right 2.037967e-05	k: 68	n:4230000
Cons ci ratio: 2.486419e-04	ci left: 9.831440e-01	ci right 9.833887e-01	k: 4159218	n:4230000
KS ci ratio: 1.012138e+00	ci left: 1.809441e-06	ci right 5.553096e-06	k: 14	n:4230000
ZNF814   4230000 perm   7558 sec   (560 perm/sec)   p_kst 3.309693e-06   p_cons 9.832667e-01   p_joint 1.607565e-05

Joint ci ratio: 4.719086e-01	ci left: 1.245395e-05	ci right 2.033161e-05	k: 68	n:4240000
Cons ci ratio: 2.483319e-04	ci left: 9.831463e-01	ci right 9.833907e-01	k: 4169060	n:4240000
KS ci ratio: 1.012138e+00	ci left: 1.805173e-06	ci right 5.539999e-06	k: 14	n:4240000
ZNF814   4240000 perm   7592 sec   (558 perm/sec)   p_kst 3.301887e-06   p_cons 9.832689e-01   p_joint 1.603774e-05

Joint ci ratio: 4.719087e-01	ci left: 1.242465e-05	ci right 2.028377e-05	k: 68	n:4250000
Cons ci ratio: 2.479982e-04	ci left: 9.831520e-01	ci right 9.833961e-01	k: 4178916	n:4250000
KS ci ratio: 1.012138e+00	ci left: 1.800926e-06	ci right 5.526964e-06	k: 14	n:4250000
ZNF814   4250000 perm   7626 sec   (557 perm/sec)   p_kst 3.294118e-06   p_cons 9.832744e-01   p_joint 1.600000e-05

Joint ci ratio: 4.719087e-01	ci left: 1.239548e-05	ci right 2.023615e-05	k: 68	n:4260000
Cons ci ratio: 2.477118e-04	ci left: 9.831515e-01	ci right 9.833953e-01	k: 4188746	n:4260000
KS ci ratio: 1.012138e+00	ci left: 1.796698e-06	ci right 5.513989e-06	k: 14	n:4260000
ZNF814   4260000 perm   7660 sec   (556 perm/sec)   p_kst 3.286385e-06   p_cons 9.832737e-01   p_joint 1.596244e-05

Joint ci ratio: 4.719087e-01	ci left: 1.236645e-05	ci right 2.018876e-05	k: 68	n:4270000
Cons ci ratio: 2.474035e-04	ci left: 9.831540e-01	ci right 9.833975e-01	k: 4198589	n:4270000
KS ci ratio: 1.012138e+00	ci left: 1.792491e-06	ci right 5.501076e-06	k: 14	n:4270000
ZNF814   4270000 perm   7693 sec   (555 perm/sec)   p_kst 3.278689e-06   p_cons 9.832761e-01   p_joint 1.592506e-05

Joint ci ratio: 4.719087e-01	ci left: 1.233756e-05	ci right 2.014159e-05	k: 68	n:4280000
Cons ci ratio: 2.471437e-04	ci left: 9.831503e-01	ci right 9.833935e-01	k: 4208405	n:4280000
KS ci ratio: 1.012138e+00	ci left: 1.788303e-06	ci right 5.488223e-06	k: 14	n:4280000
ZNF814   4280000 perm   7727 sec   (554 perm/sec)   p_kst 3.271028e-06   p_cons 9.832722e-01   p_joint 1.588785e-05

Joint ci ratio: 4.719087e-01	ci left: 1.230880e-05	ci right 2.009464e-05	k: 68	n:4290000
Cons ci ratio: 2.467973e-04	ci left: 9.831582e-01	ci right 9.834011e-01	k: 4218271	n:4290000
KS ci ratio: 1.012138e+00	ci left: 1.784134e-06	ci right 5.475430e-06	k: 14	n:4290000
ZNF814   4290000 perm   7761 sec   (553 perm/sec)   p_kst 3.263403e-06   p_cons 9.832800e-01   p_joint 1.585082e-05

Joint ci ratio: 4.719087e-01	ci left: 1.228017e-05	ci right 2.004791e-05	k: 68	n:4300000
Cons ci ratio: 2.465743e-04	ci left: 9.831497e-01	ci right 9.833924e-01	k: 4228067	n:4300000
KS ci ratio: 1.012138e+00	ci left: 1.779985e-06	ci right 5.462697e-06	k: 14	n:4300000
ZNF814   4300000 perm   7795 sec   (552 perm/sec)   p_kst 3.255814e-06   p_cons 9.832714e-01   p_joint 1.581395e-05

Joint ci ratio: 4.719087e-01	ci left: 1.225168e-05	ci right 2.000140e-05	k: 68	n:4310000
Cons ci ratio: 2.462858e-04	ci left: 9.831502e-01	ci right 9.833926e-01	k: 4237901	n:4310000
KS ci ratio: 1.012138e+00	ci left: 1.775855e-06	ci right 5.450022e-06	k: 14	n:4310000
ZNF814   4310000 perm   7828 sec   (551 perm/sec)   p_kst 3.248260e-06   p_cons 9.832717e-01   p_joint 1.577726e-05

Joint ci ratio: 4.719087e-01	ci left: 1.222332e-05	ci right 1.995510e-05	k: 68	n:4320000
Cons ci ratio: 2.459898e-04	ci left: 9.831518e-01	ci right 9.833939e-01	k: 4247740	n:4320000
KS ci ratio: 1.012138e+00	ci left: 1.771744e-06	ci right 5.437406e-06	k: 14	n:4320000
ZNF814   4320000 perm   7862 sec   (549 perm/sec)   p_kst 3.240741e-06   p_cons 9.832731e-01   p_joint 1.574074e-05

Joint ci ratio: 4.719087e-01	ci left: 1.219509e-05	ci right 1.990901e-05	k: 68	n:4330000
Cons ci ratio: 2.457068e-04	ci left: 9.831517e-01	ci right 9.833936e-01	k: 4257572	n:4330000
KS ci ratio: 1.012138e+00	ci left: 1.767652e-06	ci right 5.424849e-06	k: 14	n:4330000
ZNF814   4330000 perm   7897 sec   (548 perm/sec)   p_kst 3.233256e-06   p_cons 9.832730e-01   p_joint 1.570439e-05

Joint ci ratio: 4.719087e-01	ci left: 1.216699e-05	ci right 1.986314e-05	k: 68	n:4340000
Cons ci ratio: 2.454214e-04	ci left: 9.831522e-01	ci right 9.833937e-01	k: 4267406	n:4340000
KS ci ratio: 1.012138e+00	ci left: 1.763579e-06	ci right 5.412349e-06	k: 14	n:4340000
ZNF814   4340000 perm   7931 sec   (547 perm/sec)   p_kst 3.225806e-06   p_cons 9.832733e-01   p_joint 1.566820e-05

Joint ci ratio: 4.685258e-01	ci left: 1.234166e-05	ci right 2.007442e-05	k: 69	n:4350000
Cons ci ratio: 2.451301e-04	ci left: 9.831535e-01	ci right 9.833948e-01	k: 4277244	n:4350000
KS ci ratio: 9.799981e-01	ci left: 1.929975e-06	ci right 5.687400e-06	k: 15	n:4350000
ZNF814   4350000 perm   7965 sec   (546 perm/sec)   p_kst 3.448276e-06   p_cons 9.832745e-01   p_joint 1.586207e-05

Joint ci ratio: 4.685258e-01	ci left: 1.231335e-05	ci right 2.002838e-05	k: 69	n:4360000
Cons ci ratio: 2.448313e-04	ci left: 9.831560e-01	ci right 9.833970e-01	k: 4287087	n:4360000
KS ci ratio: 9.799981e-01	ci left: 1.925549e-06	ci right 5.674356e-06	k: 15	n:4360000
ZNF814   4360000 perm   8001 sec   (545 perm/sec)   p_kst 3.440367e-06   p_cons 9.832768e-01   p_joint 1.582569e-05

Joint ci ratio: 4.685258e-01	ci left: 1.228517e-05	ci right 1.998255e-05	k: 69	n:4370000
Cons ci ratio: 2.445081e-04	ci left: 9.831620e-01	ci right 9.834026e-01	k: 4296945	n:4370000
KS ci ratio: 9.799981e-01	ci left: 1.921142e-06	ci right 5.661371e-06	k: 15	n:4370000
ZNF814   4370000 perm   8036 sec   (544 perm/sec)   p_kst 3.432494e-06   p_cons 9.832826e-01   p_joint 1.578947e-05

Joint ci ratio: 4.685258e-01	ci left: 1.225712e-05	ci right 1.993693e-05	k: 69	n:4380000
Cons ci ratio: 2.441946e-04	ci left: 9.831667e-01	ci right 9.834071e-01	k: 4306798	n:4380000
KS ci ratio: 9.799981e-01	ci left: 1.916756e-06	ci right 5.648446e-06	k: 15	n:4380000
ZNF814   4380000 perm   8072 sec   (543 perm/sec)   p_kst 3.424658e-06   p_cons 9.832872e-01   p_joint 1.575342e-05

Joint ci ratio: 4.685258e-01	ci left: 1.222920e-05	ci right 1.989151e-05	k: 69	n:4390000
Cons ci ratio: 2.439465e-04	ci left: 9.831628e-01	ci right 9.834029e-01	k: 4316613	n:4390000
KS ci ratio: 9.799981e-01	ci left: 1.912390e-06	ci right 5.635579e-06	k: 15	n:4390000
ZNF814   4390000 perm   8106 sec   (542 perm/sec)   p_kst 3.416856e-06   p_cons 9.832831e-01   p_joint 1.571754e-05

Joint ci ratio: 4.685258e-01	ci left: 1.220141e-05	ci right 1.984630e-05	k: 69	n:4400000
Cons ci ratio: 2.436503e-04	ci left: 9.831655e-01	ci right 9.834053e-01	k: 4326457	n:4400000
KS ci ratio: 9.799981e-01	ci left: 1.908044e-06	ci right 5.622771e-06	k: 15	n:4400000
ZNF814   4400000 perm   8140 sec   (541 perm/sec)   p_kst 3.409091e-06   p_cons 9.832857e-01   p_joint 1.568182e-05

Joint ci ratio: 4.685258e-01	ci left: 1.217374e-05	ci right 1.980130e-05	k: 69	n:4410000
Cons ci ratio: 2.433552e-04	ci left: 9.831681e-01	ci right 9.834076e-01	k: 4336301	n:4410000
KS ci ratio: 9.799981e-01	ci left: 1.903717e-06	ci right 5.610021e-06	k: 15	n:4410000
ZNF814   4410000 perm   8176 sec   (539 perm/sec)   p_kst 3.401361e-06   p_cons 9.832882e-01   p_joint 1.564626e-05

Joint ci ratio: 4.685259e-01	ci left: 1.214620e-05	ci right 1.975650e-05	k: 69	n:4420000
Cons ci ratio: 2.430779e-04	ci left: 9.831685e-01	ci right 9.834078e-01	k: 4346135	n:4420000
KS ci ratio: 9.799981e-01	ci left: 1.899410e-06	ci right 5.597328e-06	k: 15	n:4420000
ZNF814   4420000 perm   8211 sec   (538 perm/sec)   p_kst 3.393665e-06   p_cons 9.832885e-01   p_joint 1.561086e-05

Joint ci ratio: 4.685259e-01	ci left: 1.211878e-05	ci right 1.971190e-05	k: 69	n:4430000
Cons ci ratio: 2.427998e-04	ci left: 9.831691e-01	ci right 9.834081e-01	k: 4355970	n:4430000
KS ci ratio: 9.799981e-01	ci left: 1.895122e-06	ci right 5.584693e-06	k: 15	n:4430000
ZNF814   4430000 perm   8247 sec   (537 perm/sec)   p_kst 3.386005e-06   p_cons 9.832889e-01   p_joint 1.557562e-05

Joint ci ratio: 4.685259e-01	ci left: 1.209149e-05	ci right 1.966751e-05	k: 69	n:4440000
Cons ci ratio: 2.425028e-04	ci left: 9.831725e-01	ci right 9.834111e-01	k: 4365817	n:4440000
KS ci ratio: 9.799981e-01	ci left: 1.890854e-06	ci right 5.572115e-06	k: 15	n:4440000
ZNF814   4440000 perm   8282 sec   (536 perm/sec)   p_kst 3.378378e-06   p_cons 9.832921e-01   p_joint 1.554054e-05

Joint ci ratio: 4.685259e-01	ci left: 1.206432e-05	ci right 1.962331e-05	k: 69	n:4450000
Cons ci ratio: 2.422234e-04	ci left: 9.831735e-01	ci right 9.834119e-01	k: 4375654	n:4450000
KS ci ratio: 9.799981e-01	ci left: 1.886605e-06	ci right 5.559594e-06	k: 15	n:4450000
ZNF814   4450000 perm   8318 sec   (535 perm/sec)   p_kst 3.370787e-06   p_cons 9.832930e-01   p_joint 1.550562e-05

Joint ci ratio: 4.685259e-01	ci left: 1.203727e-05	ci right 1.957931e-05	k: 69	n:4460000
Cons ci ratio: 2.420011e-04	ci left: 9.831669e-01	ci right 9.834051e-01	k: 4385457	n:4460000
KS ci ratio: 9.799981e-01	ci left: 1.882375e-06	ci right 5.547128e-06	k: 15	n:4460000
ZNF814   4460000 perm   8353 sec   (534 perm/sec)   p_kst 3.363229e-06   p_cons 9.832863e-01   p_joint 1.547085e-05

Joint ci ratio: 4.685259e-01	ci left: 1.201034e-05	ci right 1.953551e-05	k: 69	n:4470000
Cons ci ratio: 2.417679e-04	ci left: 9.831619e-01	ci right 9.833999e-01	k: 4395267	n:4470000
KS ci ratio: 9.799981e-01	ci left: 1.878164e-06	ci right 5.534719e-06	k: 15	n:4470000
ZNF814   4470000 perm   8387 sec   (533 perm/sec)   p_kst 3.355705e-06   p_cons 9.832812e-01   p_joint 1.543624e-05

Joint ci ratio: 4.685259e-01	ci left: 1.198353e-05	ci right 1.949191e-05	k: 69	n:4480000
Cons ci ratio: 2.415009e-04	ci left: 9.831617e-01	ci right 9.833993e-01	k: 4405098	n:4480000
KS ci ratio: 9.799981e-01	ci left: 1.873971e-06	ci right 5.522364e-06	k: 15	n:4480000
ZNF814   4480000 perm   8422 sec   (532 perm/sec)   p_kst 3.348214e-06   p_cons 9.832808e-01   p_joint 1.540179e-05

Joint ci ratio: 4.685259e-01	ci left: 1.195684e-05	ci right 1.944849e-05	k: 69	n:4490000
Cons ci ratio: 2.412690e-04	ci left: 9.831567e-01	ci right 9.833941e-01	k: 4414908	n:4490000
KS ci ratio: 9.799981e-01	ci left: 1.869798e-06	ci right 5.510065e-06	k: 15	n:4490000
ZNF814   4490000 perm   8458 sec   (531 perm/sec)   p_kst 3.340757e-06   p_cons 9.832757e-01   p_joint 1.536748e-05

Joint ci ratio: 4.685259e-01	ci left: 1.193027e-05	ci right 1.940528e-05	k: 69	n:4500000
Cons ci ratio: 2.410102e-04	ci left: 9.831555e-01	ci right 9.833927e-01	k: 4424735	n:4500000
KS ci ratio: 9.799981e-01	ci left: 1.865643e-06	ci right 5.497820e-06	k: 15	n:4500000
ZNF814   4500000 perm   8494 sec   (530 perm/sec)   p_kst 3.333333e-06   p_cons 9.832744e-01   p_joint 1.533333e-05

Joint ci ratio: 4.685259e-01	ci left: 1.190381e-05	ci right 1.936225e-05	k: 69	n:4510000
Cons ci ratio: 2.407440e-04	ci left: 9.831555e-01	ci right 9.833924e-01	k: 4434567	n:4510000
KS ci ratio: 9.799982e-01	ci left: 1.861506e-06	ci right 5.485630e-06	k: 15	n:4510000
ZNF814   4510000 perm   8530 sec   (529 perm/sec)   p_kst 3.325942e-06   p_cons 9.832743e-01   p_joint 1.529933e-05

Joint ci ratio: 4.685259e-01	ci left: 1.187748e-05	ci right 1.931941e-05	k: 69	n:4520000
Cons ci ratio: 2.404917e-04	ci left: 9.831537e-01	ci right 9.833904e-01	k: 4444391	n:4520000
KS ci ratio: 9.799982e-01	ci left: 1.857387e-06	ci right 5.473494e-06	k: 15	n:4520000
ZNF814   4520000 perm   8566 sec   (528 perm/sec)   p_kst 3.318584e-06   p_cons 9.832723e-01   p_joint 1.526549e-05

Joint ci ratio: 4.685259e-01	ci left: 1.185126e-05	ci right 1.927676e-05	k: 69	n:4530000
Cons ci ratio: 2.402289e-04	ci left: 9.831534e-01	ci right 9.833899e-01	k: 4454222	n:4530000
KS ci ratio: 9.799982e-01	ci left: 1.853287e-06	ci right 5.461411e-06	k: 15	n:4530000
ZNF814   4530000 perm   8602 sec   (527 perm/sec)   p_kst 3.311258e-06   p_cons 9.832720e-01   p_joint 1.523179e-05

Joint ci ratio: 4.685260e-01	ci left: 1.182515e-05	ci right 1.923430e-05	k: 69	n:4540000
Cons ci ratio: 2.399509e-04	ci left: 9.831554e-01	ci right 9.833916e-01	k: 4464063	n:4540000
KS ci ratio: 9.799982e-01	ci left: 1.849205e-06	ci right 5.449382e-06	k: 15	n:4540000
ZNF814   4540000 perm   8639 sec   (526 perm/sec)   p_kst 3.303965e-06   p_cons 9.832738e-01   p_joint 1.519824e-05

Joint ci ratio: 4.685260e-01	ci left: 1.179917e-05	ci right 1.919203e-05	k: 69	n:4550000
Cons ci ratio: 2.397011e-04	ci left: 9.831536e-01	ci right 9.833895e-01	k: 4473887	n:4550000
KS ci ratio: 9.799982e-01	ci left: 1.845141e-06	ci right 5.437405e-06	k: 15	n:4550000
ZNF814   4550000 perm   8675 sec   (524 perm/sec)   p_kst 3.296703e-06   p_cons 9.832719e-01   p_joint 1.516484e-05

Joint ci ratio: 4.685260e-01	ci left: 1.177329e-05	ci right 1.914994e-05	k: 69	n:4560000
Cons ci ratio: 2.394839e-04	ci left: 9.831474e-01	ci right 9.833831e-01	k: 4483691	n:4560000
KS ci ratio: 9.799982e-01	ci left: 1.841095e-06	ci right 5.425481e-06	k: 15	n:4560000
ZNF814   4560000 perm   8712 sec   (523 perm/sec)   p_kst 3.289474e-06   p_cons 9.832656e-01   p_joint 1.513158e-05

Joint ci ratio: 4.652147e-01	ci left: 1.194060e-05	ci right 1.935243e-05	k: 70	n:4570000
Cons ci ratio: 2.392164e-04	ci left: 9.831483e-01	ci right 9.833837e-01	k: 4493527	n:4570000
KS ci ratio: 9.799982e-01	ci left: 1.837066e-06	ci right 5.413609e-06	k: 15	n:4570000
ZNF814   4570000 perm   8748 sec   (522 perm/sec)   p_kst 3.282276e-06   p_cons 9.832663e-01   p_joint 1.531729e-05

Joint ci ratio: 4.652148e-01	ci left: 1.191452e-05	ci right 1.931018e-05	k: 70	n:4580000
Cons ci ratio: 2.389498e-04	ci left: 9.831491e-01	ci right 9.833843e-01	k: 4503363	n:4580000
KS ci ratio: 9.799982e-01	ci left: 1.833055e-06	ci right 5.401789e-06	k: 15	n:4580000
ZNF814   4580000 perm   8785 sec   (521 perm/sec)   p_kst 3.275109e-06   p_cons 9.832670e-01   p_joint 1.528384e-05

Joint ci ratio: 4.652148e-01	ci left: 1.188857e-05	ci right 1.926811e-05	k: 70	n:4590000
Cons ci ratio: 2.386810e-04	ci left: 9.831504e-01	ci right 9.833853e-01	k: 4513201	n:4590000
KS ci ratio: 9.799982e-01	ci left: 1.829061e-06	ci right 5.390020e-06	k: 15	n:4590000
ZNF814   4590000 perm   8821 sec   (520 perm/sec)   p_kst 3.267974e-06   p_cons 9.832682e-01   p_joint 1.525054e-05

Joint ci ratio: 4.652148e-01	ci left: 1.186272e-05	ci right 1.922622e-05	k: 70	n:4600000
Cons ci ratio: 2.384240e-04	ci left: 9.831502e-01	ci right 9.833848e-01	k: 4523032	n:4600000
KS ci ratio: 9.799982e-01	ci left: 1.825085e-06	ci right 5.378303e-06	k: 15	n:4600000
ZNF814   4600000 perm   8858 sec   (519 perm/sec)   p_kst 3.260870e-06   p_cons 9.832678e-01   p_joint 1.521739e-05

Joint ci ratio: 4.652148e-01	ci left: 1.183699e-05	ci right 1.918451e-05	k: 70	n:4610000
Cons ci ratio: 2.381334e-04	ci left: 9.831547e-01	ci right 9.833891e-01	k: 4532885	n:4610000
KS ci ratio: 9.799982e-01	ci left: 1.821126e-06	ci right 5.366636e-06	k: 15	n:4610000
ZNF814   4610000 perm   8895 sec   (518 perm/sec)   p_kst 3.253796e-06   p_cons 9.832722e-01   p_joint 1.518438e-05

Joint ci ratio: 4.652148e-01	ci left: 1.181137e-05	ci right 1.914299e-05	k: 70	n:4620000
Cons ci ratio: 2.378986e-04	ci left: 9.831517e-01	ci right 9.833858e-01	k: 4542703	n:4620000
KS ci ratio: 9.799982e-01	ci left: 1.817184e-06	ci right 5.355020e-06	k: 15	n:4620000
ZNF814   4620000 perm   8931 sec   (517 perm/sec)   p_kst 3.246753e-06   p_cons 9.832690e-01   p_joint 1.515152e-05

Joint ci ratio: 4.652148e-01	ci left: 1.178586e-05	ci right 1.910164e-05	k: 70	n:4630000
Cons ci ratio: 2.376379e-04	ci left: 9.831523e-01	ci right 9.833862e-01	k: 4552538	n:4630000
KS ci ratio: 9.799982e-01	ci left: 1.813259e-06	ci right 5.343454e-06	k: 15	n:4630000
ZNF814   4630000 perm   8968 sec   (516 perm/sec)   p_kst 3.239741e-06   p_cons 9.832695e-01   p_joint 1.511879e-05

Joint ci ratio: 4.652148e-01	ci left: 1.176046e-05	ci right 1.906048e-05	k: 70	n:4640000
Cons ci ratio: 2.373921e-04	ci left: 9.831510e-01	ci right 9.833846e-01	k: 4562364	n:4640000
KS ci ratio: 9.799982e-01	ci left: 1.809352e-06	ci right 5.331938e-06	k: 15	n:4640000
ZNF814   4640000 perm   9005 sec   (515 perm/sec)   p_kst 3.232759e-06   p_cons 9.832681e-01   p_joint 1.508621e-05

Joint ci ratio: 4.652148e-01	ci left: 1.173517e-05	ci right 1.901949e-05	k: 70	n:4650000
Cons ci ratio: 2.371378e-04	ci left: 9.831510e-01	ci right 9.833843e-01	k: 4572196	n:4650000
KS ci ratio: 9.799982e-01	ci left: 1.805460e-06	ci right 5.320472e-06	k: 15	n:4650000
ZNF814   4650000 perm   9042 sec   (514 perm/sec)   p_kst 3.225806e-06   p_cons 9.832680e-01   p_joint 1.505376e-05

Joint ci ratio: 4.652148e-01	ci left: 1.170998e-05	ci right 1.897867e-05	k: 70	n:4660000
Cons ci ratio: 2.368951e-04	ci left: 9.831494e-01	ci right 9.833826e-01	k: 4582021	n:4660000
KS ci ratio: 9.799982e-01	ci left: 1.801586e-06	ci right 5.309054e-06	k: 15	n:4660000
ZNF814   4660000 perm   9079 sec   (513 perm/sec)   p_kst 3.218884e-06   p_cons 9.832663e-01   p_joint 1.502146e-05

Joint ci ratio: 4.619728e-01	ci left: 1.187402e-05	ci right 1.917702e-05	k: 71	n:4670000
Cons ci ratio: 2.366485e-04	ci left: 9.831486e-01	ci right 9.833815e-01	k: 4591849	n:4670000
KS ci ratio: 9.799982e-01	ci left: 1.797728e-06	ci right 5.297686e-06	k: 15	n:4670000
ZNF814   4670000 perm   9117 sec   (512 perm/sec)   p_kst 3.211991e-06   p_cons 9.832653e-01   p_joint 1.520343e-05

Joint ci ratio: 4.619728e-01	ci left: 1.184865e-05	ci right 1.913604e-05	k: 71	n:4680000
Cons ci ratio: 2.364088e-04	ci left: 9.831468e-01	ci right 9.833795e-01	k: 4601673	n:4680000
KS ci ratio: 9.799982e-01	ci left: 1.793887e-06	ci right 5.286366e-06	k: 15	n:4680000
ZNF814   4680000 perm   9154 sec   (511 perm/sec)   p_kst 3.205128e-06   p_cons 9.832635e-01   p_joint 1.517094e-05

Joint ci ratio: 4.587977e-01	ci left: 1.201187e-05	ci right 1.933303e-05	k: 72	n:4690000
Cons ci ratio: 2.361377e-04	ci left: 9.831496e-01	ci right 9.833820e-01	k: 4611518	n:4690000
KS ci ratio: 9.799982e-01	ci left: 1.790062e-06	ci right 5.275094e-06	k: 15	n:4690000
ZNF814   4690000 perm   9192 sec   (510 perm/sec)   p_kst 3.198294e-06   p_cons 9.832661e-01   p_joint 1.535181e-05

Joint ci ratio: 4.587977e-01	ci left: 1.198631e-05	ci right 1.929189e-05	k: 72	n:4700000
Cons ci ratio: 2.358843e-04	ci left: 9.831500e-01	ci right 9.833822e-01	k: 4621352	n:4700000
KS ci ratio: 9.799982e-01	ci left: 1.786253e-06	ci right 5.263871e-06	k: 15	n:4700000
ZNF814   4700000 perm   9229 sec   (509 perm/sec)   p_kst 3.191489e-06   p_cons 9.832664e-01   p_joint 1.531915e-05

Joint ci ratio: 4.587977e-01	ci left: 1.196086e-05	ci right 1.925094e-05	k: 72	n:4710000
Cons ci ratio: 2.356211e-04	ci left: 9.831519e-01	ci right 9.833838e-01	k: 4631193	n:4710000
KS ci ratio: 9.799982e-01	ci left: 1.782461e-06	ci right 5.252695e-06	k: 15	n:4710000
ZNF814   4710000 perm   9266 sec   (508 perm/sec)   p_kst 3.184713e-06   p_cons 9.832682e-01   p_joint 1.528662e-05

Joint ci ratio: 4.587977e-01	ci left: 1.193552e-05	ci right 1.921015e-05	k: 72	n:4720000
Cons ci ratio: 2.353572e-04	ci left: 9.831540e-01	ci right 9.833856e-01	k: 4641035	n:4720000
KS ci ratio: 9.799982e-01	ci left: 1.778685e-06	ci right 5.241566e-06	k: 15	n:4720000
ZNF814   4720000 perm   9304 sec   (507 perm/sec)   p_kst 3.177966e-06   p_cons 9.832701e-01   p_joint 1.525424e-05

Joint ci ratio: 4.587977e-01	ci left: 1.191029e-05	ci right 1.916954e-05	k: 72	n:4730000
Cons ci ratio: 2.351094e-04	ci left: 9.831540e-01	ci right 9.833854e-01	k: 4650867	n:4730000
KS ci ratio: 9.799982e-01	ci left: 1.774924e-06	ci right 5.230485e-06	k: 15	n:4730000
ZNF814   4730000 perm   9342 sec   (506 perm/sec)   p_kst 3.171247e-06   p_cons 9.832700e-01   p_joint 1.522199e-05

Joint ci ratio: 4.587977e-01	ci left: 1.188516e-05	ci right 1.912909e-05	k: 72	n:4740000
Cons ci ratio: 2.348894e-04	ci left: 9.831502e-01	ci right 9.833813e-01	k: 4660681	n:4740000
KS ci ratio: 9.799982e-01	ci left: 1.771180e-06	ci right 5.219450e-06	k: 15	n:4740000
ZNF814   4740000 perm   9379 sec   (505 perm/sec)   p_kst 3.164557e-06   p_cons 9.832660e-01   p_joint 1.518987e-05

Joint ci ratio: 4.587977e-01	ci left: 1.186014e-05	ci right 1.908882e-05	k: 72	n:4750000
Cons ci ratio: 2.346505e-04	ci left: 9.831491e-01	ci right 9.833800e-01	k: 4670508	n:4750000
KS ci ratio: 9.799982e-01	ci left: 1.767451e-06	ci right 5.208462e-06	k: 15	n:4750000
ZNF814   4750000 perm   9418 sec   (504 perm/sec)   p_kst 3.157895e-06   p_cons 9.832648e-01   p_joint 1.515789e-05

Joint ci ratio: 4.587977e-01	ci left: 1.183522e-05	ci right 1.904872e-05	k: 72	n:4760000
Cons ci ratio: 2.344108e-04	ci left: 9.831482e-01	ci right 9.833789e-01	k: 4680336	n:4760000
KS ci ratio: 9.799982e-01	ci left: 1.763738e-06	ci right 5.197520e-06	k: 15	n:4760000
ZNF814   4760000 perm   9456 sec   (503 perm/sec)   p_kst 3.151261e-06   p_cons 9.832639e-01   p_joint 1.512605e-05

Joint ci ratio: 4.556872e-01	ci left: 1.199590e-05	ci right 1.924242e-05	k: 73	n:4770000
Cons ci ratio: 2.341615e-04	ci left: 9.831488e-01	ci right 9.833793e-01	k: 4690171	n:4770000
KS ci ratio: 9.507379e-01	ci left: 1.917272e-06	ci right 5.447164e-06	k: 16	n:4770000
ZNF814   4770000 perm   9494 sec   (502 perm/sec)   p_kst 3.354298e-06   p_cons 9.832644e-01   p_joint 1.530398e-05

Joint ci ratio: 4.556872e-01	ci left: 1.197080e-05	ci right 1.920217e-05	k: 73	n:4780000
Cons ci ratio: 2.338891e-04	ci left: 9.831528e-01	ci right 9.833830e-01	k: 4700022	n:4780000
KS ci ratio: 9.507379e-01	ci left: 1.913261e-06	ci right 5.435768e-06	k: 16	n:4780000
ZNF814   4780000 perm   9533 sec   (501 perm/sec)   p_kst 3.347280e-06   p_cons 9.832682e-01   p_joint 1.527197e-05

Joint ci ratio: 4.556872e-01	ci left: 1.194581e-05	ci right 1.916208e-05	k: 73	n:4790000
Cons ci ratio: 2.336355e-04	ci left: 9.831543e-01	ci right 9.833842e-01	k: 4709861	n:4790000
KS ci ratio: 9.507379e-01	ci left: 1.909267e-06	ci right 5.424420e-06	k: 16	n:4790000
ZNF814   4790000 perm   9572 sec   (500 perm/sec)   p_kst 3.340292e-06   p_cons 9.832695e-01   p_joint 1.524008e-05

Joint ci ratio: 4.556872e-01	ci left: 1.192092e-05	ci right 1.912216e-05	k: 73	n:4800000
Cons ci ratio: 2.333782e-04	ci left: 9.831563e-01	ci right 9.833860e-01	k: 4719703	n:4800000
KS ci ratio: 9.507379e-01	ci left: 1.905289e-06	ci right 5.413119e-06	k: 16	n:4800000
ZNF814   4800000 perm   9611 sec   (499 perm/sec)   p_kst 3.333333e-06   p_cons 9.832715e-01   p_joint 1.520833e-05

Joint ci ratio: 4.556872e-01	ci left: 1.189614e-05	ci right 1.908240e-05	k: 73	n:4810000
Cons ci ratio: 2.331557e-04	ci left: 9.831536e-01	ci right 9.833830e-01	k: 4729522	n:4810000
KS ci ratio: 9.507379e-01	ci left: 1.901328e-06	ci right 5.401865e-06	k: 16	n:4810000
ZNF814   4810000 perm   9650 sec   (498 perm/sec)   p_kst 3.326403e-06   p_cons 9.832686e-01   p_joint 1.517672e-05

Joint ci ratio: 4.556872e-01	ci left: 1.187146e-05	ci right 1.904281e-05	k: 73	n:4820000
Cons ci ratio: 2.329323e-04	ci left: 9.831511e-01	ci right 9.833803e-01	k: 4739342	n:4820000
KS ci ratio: 9.507379e-01	ci left: 1.897383e-06	ci right 5.390658e-06	k: 16	n:4820000
ZNF814   4820000 perm   9689 sec   (497 perm/sec)   p_kst 3.319502e-06   p_cons 9.832660e-01   p_joint 1.514523e-05

Joint ci ratio: 4.556872e-01	ci left: 1.184688e-05	ci right 1.900339e-05	k: 73	n:4830000
Cons ci ratio: 2.326774e-04	ci left: 9.831531e-01	ci right 9.833821e-01	k: 4749184	n:4830000
KS ci ratio: 9.507379e-01	ci left: 1.893455e-06	ci right 5.379497e-06	k: 16	n:4830000
ZNF814   4830000 perm   9728 sec   (496 perm/sec)   p_kst 3.312629e-06   p_cons 9.832679e-01   p_joint 1.511387e-05

Joint ci ratio: 4.556872e-01	ci left: 1.182240e-05	ci right 1.896412e-05	k: 73	n:4840000
Cons ci ratio: 2.323985e-04	ci left: 9.831587e-01	ci right 9.833874e-01	k: 4759043	n:4840000
KS ci ratio: 9.507379e-01	ci left: 1.889543e-06	ci right 5.368382e-06	k: 16	n:4840000
ZNF814   4840000 perm   9767 sec   (496 perm/sec)   p_kst 3.305785e-06   p_cons 9.832733e-01   p_joint 1.508264e-05

Joint ci ratio: 4.556872e-01	ci left: 1.179803e-05	ci right 1.892502e-05	k: 73	n:4850000
Cons ci ratio: 2.321729e-04	ci left: 9.831568e-01	ci right 9.833853e-01	k: 4768866	n:4850000
KS ci ratio: 9.507379e-01	ci left: 1.885647e-06	ci right 5.357314e-06	k: 16	n:4850000
ZNF814   4850000 perm   9807 sec   (495 perm/sec)   p_kst 3.298969e-06   p_cons 9.832713e-01   p_joint 1.505155e-05

Joint ci ratio: 4.556872e-01	ci left: 1.177375e-05	ci right 1.888608e-05	k: 73	n:4860000
Cons ci ratio: 2.319466e-04	ci left: 9.831551e-01	ci right 9.833834e-01	k: 4778690	n:4860000
KS ci ratio: 9.507379e-01	ci left: 1.881767e-06	ci right 5.346290e-06	k: 16	n:4860000
ZNF814   4860000 perm   9846 sec   (494 perm/sec)   p_kst 3.292181e-06   p_cons 9.832695e-01   p_joint 1.502058e-05

Joint ci ratio: 4.556872e-01	ci left: 1.174958e-05	ci right 1.884730e-05	k: 73	n:4870000
Cons ci ratio: 2.317050e-04	ci left: 9.831557e-01	ci right 9.833837e-01	k: 4788525	n:4870000
KS ci ratio: 9.507379e-01	ci left: 1.877903e-06	ci right 5.335312e-06	k: 16	n:4870000
ZNF814   4870000 perm   9885 sec   (493 perm/sec)   p_kst 3.285421e-06   p_cons 9.832700e-01   p_joint 1.498973e-05

Joint ci ratio: 4.556872e-01	ci left: 1.172550e-05	ci right 1.880868e-05	k: 73	n:4880000
Cons ci ratio: 2.314757e-04	ci left: 9.831547e-01	ci right 9.833825e-01	k: 4798352	n:4880000
KS ci ratio: 9.507379e-01	ci left: 1.874055e-06	ci right 5.324379e-06	k: 16	n:4880000
ZNF814   4880000 perm   9924 sec   (492 perm/sec)   p_kst 3.278689e-06   p_cons 9.832689e-01   p_joint 1.495902e-05

Joint ci ratio: 4.556872e-01	ci left: 1.170152e-05	ci right 1.877022e-05	k: 73	n:4890000
Cons ci ratio: 2.312255e-04	ci left: 9.831567e-01	ci right 9.833842e-01	k: 4808194	n:4890000
KS ci ratio: 9.507379e-01	ci left: 1.870222e-06	ci right 5.313491e-06	k: 16	n:4890000
ZNF814   4890000 perm   9963 sec   (491 perm/sec)   p_kst 3.271984e-06   p_cons 9.832708e-01   p_joint 1.492843e-05

Joint ci ratio: 4.556873e-01	ci left: 1.167764e-05	ci right 1.873191e-05	k: 73	n:4900000
Cons ci ratio: 2.309532e-04	ci left: 9.831620e-01	ci right 9.833893e-01	k: 4818052	n:4900000
KS ci ratio: 9.507379e-01	ci left: 1.866406e-06	ci right 5.302647e-06	k: 16	n:4900000
ZNF814   4900000 perm   10003 sec   (490 perm/sec)   p_kst 3.265306e-06   p_cons 9.832759e-01   p_joint 1.489796e-05

Joint ci ratio: 4.556873e-01	ci left: 1.165386e-05	ci right 1.869376e-05	k: 73	n:4910000
Cons ci ratio: 2.306918e-04	ci left: 9.831658e-01	ci right 9.833929e-01	k: 4827903	n:4910000
KS ci ratio: 9.507379e-01	ci left: 1.862604e-06	ci right 5.291847e-06	k: 16	n:4910000
ZNF814   4910000 perm   10043 sec   (489 perm/sec)   p_kst 3.258656e-06   p_cons 9.832796e-01   p_joint 1.486762e-05

Joint ci ratio: 4.556873e-01	ci left: 1.163017e-05	ci right 1.865577e-05	k: 73	n:4920000
Cons ci ratio: 2.304513e-04	ci left: 9.831668e-01	ci right 9.833936e-01	k: 4837740	n:4920000
KS ci ratio: 9.507379e-01	ci left: 1.858819e-06	ci right 5.281092e-06	k: 16	n:4920000
ZNF814   4920000 perm   10082 sec   (488 perm/sec)   p_kst 3.252033e-06   p_cons 9.832805e-01   p_joint 1.483740e-05

Joint ci ratio: 4.556873e-01	ci left: 1.160658e-05	ci right 1.861792e-05	k: 73	n:4930000
Cons ci ratio: 2.302214e-04	ci left: 9.831663e-01	ci right 9.833929e-01	k: 4847570	n:4930000
KS ci ratio: 9.507379e-01	ci left: 1.855048e-06	ci right 5.270380e-06	k: 16	n:4930000
ZNF814   4930000 perm   10122 sec   (487 perm/sec)   p_kst 3.245436e-06   p_cons 9.832799e-01   p_joint 1.480730e-05

Joint ci ratio: 4.556873e-01	ci left: 1.158308e-05	ci right 1.858024e-05	k: 73	n:4940000
Cons ci ratio: 2.299696e-04	ci left: 9.831691e-01	ci right 9.833955e-01	k: 4857416	n:4940000
KS ci ratio: 9.507379e-01	ci left: 1.851293e-06	ci right 5.259711e-06	k: 16	n:4940000
ZNF814   4940000 perm   10161 sec   (486 perm/sec)   p_kst 3.238866e-06   p_cons 9.832826e-01   p_joint 1.477733e-05

Joint ci ratio: 4.556873e-01	ci left: 1.155968e-05	ci right 1.854270e-05	k: 73	n:4950000
Cons ci ratio: 2.297157e-04	ci left: 9.831723e-01	ci right 9.833984e-01	k: 4867264	n:4950000
KS ci ratio: 9.507379e-01	ci left: 1.847553e-06	ci right 5.249085e-06	k: 16	n:4950000
ZNF814   4950000 perm   10201 sec   (485 perm/sec)   p_kst 3.232323e-06   p_cons 9.832857e-01   p_joint 1.474747e-05

Joint ci ratio: 4.556873e-01	ci left: 1.153638e-05	ci right 1.850532e-05	k: 73	n:4960000
Cons ci ratio: 2.295120e-04	ci left: 9.831684e-01	ci right 9.833943e-01	k: 4877077	n:4960000
KS ci ratio: 9.507379e-01	ci left: 1.843828e-06	ci right 5.238502e-06	k: 16	n:4960000
ZNF814   4960000 perm   10240 sec   (484 perm/sec)   p_kst 3.225806e-06   p_cons 9.832817e-01   p_joint 1.471774e-05

Joint ci ratio: 4.556873e-01	ci left: 1.151317e-05	ci right 1.846808e-05	k: 73	n:4970000
Cons ci ratio: 2.292947e-04	ci left: 9.831666e-01	ci right 9.833922e-01	k: 4886900	n:4970000
KS ci ratio: 9.507379e-01	ci left: 1.840118e-06	ci right 5.227962e-06	k: 16	n:4970000
ZNF814   4970000 perm   10280 sec   (483 perm/sec)   p_kst 3.219316e-06   p_cons 9.832797e-01   p_joint 1.468813e-05

Joint ci ratio: 4.556873e-01	ci left: 1.149005e-05	ci right 1.843100e-05	k: 73	n:4980000
Cons ci ratio: 2.290627e-04	ci left: 9.831669e-01	ci right 9.833924e-01	k: 4896734	n:4980000
KS ci ratio: 9.507379e-01	ci left: 1.836423e-06	ci right 5.217464e-06	k: 16	n:4980000
ZNF814   4980000 perm   10320 sec   (483 perm/sec)   p_kst 3.212851e-06   p_cons 9.832799e-01   p_joint 1.465863e-05

Joint ci ratio: 4.556873e-01	ci left: 1.146702e-05	ci right 1.839406e-05	k: 73	n:4990000
Cons ci ratio: 2.288523e-04	ci left: 9.831643e-01	ci right 9.833895e-01	k: 4906553	n:4990000
KS ci ratio: 9.507379e-01	ci left: 1.832743e-06	ci right 5.207008e-06	k: 16	n:4990000
ZNF814   4990000 perm   10359 sec   (482 perm/sec)   p_kst 3.206413e-06   p_cons 9.832772e-01   p_joint 1.462926e-05

Joint ci ratio: 4.556873e-01	ci left: 1.144409e-05	ci right 1.835727e-05	k: 73	n:5000000
Cons ci ratio: 2.286217e-04	ci left: 9.831646e-01	ci right 9.833896e-01	k: 4916387	n:5000000
KS ci ratio: 9.507379e-01	ci left: 1.829078e-06	ci right 5.196594e-06	k: 16	n:5000000
ZNF814   5000000 perm   10399 sec   (481 perm/sec)   p_kst 3.200000e-06   p_cons 9.832774e-01   p_joint 1.460000e-05

Outputting figure to mutsig2_images.part000000000200/ZNF814.3_2580_5000000_3.2e-06_0.98328_1.46e-05.png
                gene_name: ZNF814
               theta_stop: 0.95 
                    nperm: 5000000 
                     p_ks: 3.20e-06 
        ci_ks_bounds_left: 1.83e-06 
       ci_ks_bounds_right: 5.20e-06 
                   p_cons: 0.98 
      ci_cons_bounds_left: 0.98 
     ci_cons_bounds_right: 0.98 
                  p_joint: 1.46e-05 
     ci_joint_bounds_left: 1.14e-05 
    ci_joint_bounds_right: 1.84e-05 

Current progress: 10 percent done.
ZNF99
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: 6.275439e-03	ci left: 9.718541e-01	ci right 9.780650e-01	k: 9751	n:10000
KS ci ratio: 1.930639e-02	ci left: 7.968933e-01	ci right 8.125288e-01	k: 8048	n:10000
ZNF99   10000 perm   2 sec   (5439 perm/sec)   p_kst 8.048000e-01   p_cons 9.751000e-01   p_joint 1

Outputting figure to mutsig2_images.part000000000200/ZNF99.3_3141_10000_0.8048_0.9751_1.png
                gene_name: ZNF99
               theta_stop: 0.019 
                    nperm: 10000 
                     p_ks: 0.80 
        ci_ks_bounds_left: 0.80 
       ci_ks_bounds_right: 0.81 
                   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: 20 percent done.
ZZEF1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 5.221033e-02	ci left: 3.509817e-01	ci right 3.698997e-01	k: 3604	n:10000
Cons ci ratio: 7.331842e-02	ci left: 2.140838e-01	ci right 2.304783e-01	k: 2222	n:10000
KS ci ratio: 4.158686e-02	ci left: 4.605772e-01	ci right 4.802401e-01	k: 4704	n:10000
ZZEF1   10000 perm   2 sec   (4136 perm/sec)   p_kst 4.704000e-01   p_cons 2.222000e-01   p_joint 3.604000e-01

Outputting figure to mutsig2_images.part000000000200/ZZEF1.3_9106_10000_0.4704_0.2222_0.3604.png
                gene_name: ZZEF1
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.47 
        ci_ks_bounds_left: 0.46 
       ci_ks_bounds_right: 0.48 
                   p_cons: 0.22 
      ci_cons_bounds_left: 0.21 
     ci_cons_bounds_right: 0.23 
                  p_joint: 0.36 
     ci_joint_bounds_left: 0.35 
    ci_joint_bounds_right: 0.37 

Current progress: 30 percent done.
ZNF816A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.651132e-02	ci left: 5.255657e-01	ci right 5.452137e-01	k: 5354	n:10000
Cons ci ratio: 1.455778e-01	ci left: 6.265923e-02	ci right 7.259445e-02	k: 675	n:10000
KS ci ratio: 3.025773e-02	ci left: 6.170337e-01	ci right 6.360925e-01	k: 6266	n:10000
ZNF816A   10000 perm   2 sec   (6479 perm/sec)   p_kst 6.266000e-01   p_cons 6.750000e-02   p_joint 5.354000e-01

Joint ci ratio: 7.717746e-02	ci left: 1.098234e-01	ci right 1.186891e-01	k: 2284	n:20000
Cons ci ratio: 1.035173e-01	ci left: 6.342669e-02	ci right 7.039986e-02	k: 1337	n:20000
KS ci ratio: 2.150405e-02	ci left: 6.174952e-01	ci right 6.309687e-01	k: 12485	n:20000
ZNF816A   20000 perm   4 sec   (5573 perm/sec)   p_kst 6.242500e-01   p_cons 6.685000e-02   p_joint 1.142000e-01

Joint ci ratio: 6.340779e-02	ci left: 1.094055e-01	ci right 1.166029e-01	k: 3389	n:30000
Cons ci ratio: 8.571830e-02	ci left: 6.236657e-02	ci right 6.798467e-02	k: 1954	n:30000
KS ci ratio: 1.762132e-02	ci left: 6.170530e-01	ci right 6.280565e-01	k: 18677	n:30000
ZNF816A   30000 perm   6 sec   (5296 perm/sec)   p_kst 6.225667e-01   p_cons 6.513333e-02   p_joint 1.129667e-01

Outputting figure to mutsig2_images.part000000000200/ZNF816A.2_1968_30000_0.62257_0.065133_0.11297.png
                gene_name: ZNF816A
               theta_stop: 0.086 
                    nperm: 30000 
                     p_ks: 0.62 
        ci_ks_bounds_left: 0.62 
       ci_ks_bounds_right: 0.63 
                   p_cons: 0.065 
      ci_cons_bounds_left: 0.062 
     ci_cons_bounds_right: 0.068 
                  p_joint: 0.11 
     ci_joint_bounds_left: 0.11 
    ci_joint_bounds_right: 0.12 

Current progress: 40 percent done.
ZNF829
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.592994e-02	ci left: 8.513105e-01	ci right 8.650802e-01	k: 8583	n:10000
Cons ci ratio: 5.081322e-02	ci left: 3.635097e-01	ci right 3.825643e-01	k: 3730	n:10000
KS ci ratio: 4.653285e-02	ci left: 4.053188e-01	ci right 4.247308e-01	k: 4150	n:10000
ZNF829   10000 perm   2 sec   (5767 perm/sec)   p_kst 4.150000e-01   p_cons 3.730000e-01   p_joint 8.583000e-01

Outputting figure to mutsig2_images.part000000000200/ZNF829.2_1566_10000_0.415_0.373_0.8583.png
                gene_name: ZNF829
               theta_stop: 0.051 
                    nperm: 10000 
                     p_ks: 0.41 
        ci_ks_bounds_left: 0.41 
       ci_ks_bounds_right: 0.42 
                   p_cons: 0.37 
      ci_cons_bounds_left: 0.36 
     ci_cons_bounds_right: 0.38 
                  p_joint: 0.86 
     ci_joint_bounds_left: 0.85 
    ci_joint_bounds_right: 0.87 

Current progress: 50 percent done.
ZNF831
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 8.707717e-02	ci left: 1.611128e-01	ci right 1.758809e-01	k: 1684	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: 3.499718e-02	ci left: 5.465975e-01	ci right 5.661697e-01	k: 5564	n:10000
ZNF831   10000 perm   2 sec   (4991 perm/sec)   p_kst 5.564000e-01   p_cons 1.236000e-01   p_joint 1.684000e-01

Joint ci ratio: 6.705073e-02	ci left: 1.410344e-01	ci right 1.508688e-01	k: 2918	n:20000
Cons ci ratio: 7.409931e-02	ci left: 1.181830e-01	ci right 1.273270e-01	k: 2454	n:20000
KS ci ratio: 2.492173e-02	ci left: 5.460272e-01	ci right 5.598574e-01	k: 11059	n:20000
ZNF831   20000 perm   4 sec   (4485 perm/sec)   p_kst 5.529500e-01   p_cons 1.227000e-01   p_joint 1.459000e-01

Outputting figure to mutsig2_images.part000000000200/ZNF831.2_5054_20000_0.55295_0.1227_0.1459.png
                gene_name: ZNF831
               theta_stop: 0.074 
                    nperm: 20000 
                     p_ks: 0.55 
        ci_ks_bounds_left: 0.55 
       ci_ks_bounds_right: 0.56 
                   p_cons: 0.12 
      ci_cons_bounds_left: 0.12 
     ci_cons_bounds_right: 0.13 
                  p_joint: 0.15 
     ci_joint_bounds_left: 0.14 
    ci_joint_bounds_right: 0.15 

Current progress: 60 percent done.
ZNF845
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.241139e-02	ci left: 5.841983e-01	ci right 6.035469e-01	k: 5939	n:10000
Cons ci ratio: 2.778928e-02	ci left: 6.561554e-01	ci right 6.747481e-01	k: 6655	n:10000
KS ci ratio: 7.300181e-02	ci left: 2.155637e-01	ci right 2.319975e-01	k: 2237	n:10000
ZNF845   10000 perm   2 sec   (5366 perm/sec)   p_kst 2.237000e-01   p_cons 6.655000e-01   p_joint 5.939000e-01

Outputting figure to mutsig2_images.part000000000200/ZNF845.2_2925_10000_0.2237_0.6655_0.5939.png
                gene_name: ZNF845
               theta_stop: 0.073 
                    nperm: 10000 
                     p_ks: 0.22 
        ci_ks_bounds_left: 0.22 
       ci_ks_bounds_right: 0.23 
                   p_cons: 0.67 
      ci_cons_bounds_left: 0.66 
     ci_cons_bounds_right: 0.67 
                  p_joint: 0.59 
     ci_joint_bounds_left: 0.58 
    ci_joint_bounds_right: 0.60 

Current progress: 70 percent done.
ZSCAN1
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.684280e-02	ci left: 5.210611e-01	ci right 5.407209e-01	k: 5309	n:10000
Cons ci ratio: 5.036011e-02	ci left: 3.676872e-01	ci right 3.867843e-01	k: 3772	n:10000
KS ci ratio: 3.280928e-02	ci left: 5.782787e-01	ci right 5.976700e-01	k: 5880	n:10000
ZSCAN1   10000 perm   2 sec   (6640 perm/sec)   p_kst 5.880000e-01   p_cons 3.772000e-01   p_joint 5.309000e-01

Outputting figure to mutsig2_images.part000000000200/ZSCAN1.2_1243_10000_0.588_0.3772_0.5309.png
                gene_name: ZSCAN1
               theta_stop: 0.050 
                    nperm: 10000 
                     p_ks: 0.59 
        ci_ks_bounds_left: 0.58 
       ci_ks_bounds_right: 0.60 
                   p_cons: 0.38 
      ci_cons_bounds_left: 0.37 
     ci_cons_bounds_right: 0.39 
                  p_joint: 0.53 
     ci_joint_bounds_left: 0.52 
    ci_joint_bounds_right: 0.54 

Current progress: 80 percent done.
ZSCAN5A
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 3.516050e-02	ci left: 5.442931e-01	ci right 5.638753e-01	k: 5541	n:10000
Cons ci ratio: 6.924324e-02	ci left: 2.342244e-01	ci right 2.511257e-01	k: 2426	n:10000
KS ci ratio: 3.400154e-02	ci left: 5.608290e-01	ci right 5.803299e-01	k: 5706	n:10000
ZSCAN5A   10000 perm   2 sec   (6471 perm/sec)   p_kst 5.706000e-01   p_cons 2.426000e-01   p_joint 5.541000e-01

Outputting figure to mutsig2_images.part000000000200/ZSCAN5A.2_1507_10000_0.5706_0.2426_0.5541.png
                gene_name: ZSCAN5A
               theta_stop: 0.069 
                    nperm: 10000 
                     p_ks: 0.57 
        ci_ks_bounds_left: 0.56 
       ci_ks_bounds_right: 0.58 
                   p_cons: 0.24 
      ci_cons_bounds_left: 0.23 
     ci_cons_bounds_right: 0.25 
                  p_joint: 0.55 
     ci_joint_bounds_left: 0.54 
    ci_joint_bounds_right: 0.56 

Current progress: 90 percent done.
ZZZ3
Processing conservation and coverage...
Processing mutations... 
Generating list of throwable mutations...
Starting permutations...
Joint ci ratio: 1.931867e-02	ci left: 7.966903e-01	ci right 8.123319e-01	k: 8046	n:10000
Cons ci ratio: 2.355520e-02	ci left: 7.259294e-01	ci right 7.433338e-01	k: 7347	n:10000
KS ci ratio: 2.781424e-02	ci left: 6.557528e-01	ci right 6.743510e-01	k: 6651	n:10000
ZZZ3   10000 perm   2 sec   (5907 perm/sec)   p_kst 6.651000e-01   p_cons 7.347000e-01   p_joint 8.046000e-01

Outputting figure to mutsig2_images.part000000000200/ZZZ3.2_2756_10000_0.6651_0.7347_0.8046.png
                gene_name: ZZZ3
               theta_stop: 0.028 
                    nperm: 10000 
                     p_ks: 0.67 
        ci_ks_bounds_left: 0.66 
       ci_ks_bounds_right: 0.67 
                   p_cons: 0.73 
      ci_cons_bounds_left: 0.73 
     ci_cons_bounds_right: 0.74 
                  p_joint: 0.80 
     ci_joint_bounds_left: 0.80 
    ci_joint_bounds_right: 0.81 

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.165.3896/
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/181708/iteration1/scatter.0000000200
mFile: fh_MutSigRun
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/fh_MutSigRun /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigRun.165.3896/ -whichjob 200 -i BLCA -maf /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf -ppr /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt -cov /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat -cat /xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.mutcategs.txt -pat /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt -genes /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt -b hg19 -genesets /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt -cosmic /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv -refseq /xchip/cga1/annotation/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 10 10:41:37 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25375
 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 10 10:41:38 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25379
 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 10 10:41:39 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25382
 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 10 10:41:45 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25386
 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 10 10:41:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25389
 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 10 10:41:40 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25392
 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 10 10:41:44 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25395
 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 10 10:41:40 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25398
 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 10 10:41:39 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25400
 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 10 10:41:48 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25402
 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 10 10:41:48 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25405
 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 10 10:41:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25408
 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 10 10:41:52 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25411
 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 10 10:41:51 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25415
 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 10 10:41:51 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25418
 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 10 10:41:50 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25423
 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 10 10:41:57 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25428
 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 10 10:41:54 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25433
 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 10 10:42:13 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25438
 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 10 10:42:15 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25441
 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 10 10:42:16 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25443
 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 10 10:42:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25446
 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 10 10:42:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25449
 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 10 10:42:13 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25500
 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 10 10:42:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25509
 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 10 10:42:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25519
 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 10 10:42:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25525
 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 10 10:42:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25531
 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 10 10:42:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25539
 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 10 10:42:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25546
 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 10 10:42:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25552
 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 10 10:42:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25558
 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 10 10:42:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25562
 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 10 10:42:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25566
 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 10 10:42:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25569
 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 10 10:42:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25575
 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 10 10:42:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25579
 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 10 10:42:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25583
 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 10 10:42:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25589
 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 10 10:42:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25594
 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 10 10:42:40 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25599
 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 10 10:42:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25626
 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 10 10:42:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25632
 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 10 10:42:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25639
 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 10 10:42:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25648
 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 10 10:42:42 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25655
 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 10 10:42:47 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25661
 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 10 10:42:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25665
 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 10 10:42:42 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25671
 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 10 10:42:39 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25676
 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 10 10:42:42 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25681
 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 10 10:42:48 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25685
 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 10 10:42:43 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25691
 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 10 10:42:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25695
 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 10 10:42:50 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25700
 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 10 10:42:51 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25706
 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 10 10:42:53 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25712
 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 10 10:42:51 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25715
 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 10 10:42:51 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25719
 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 10 10:42:51 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25723
 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 10 10:42:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25733
 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 10 10:42:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25740
 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 10 10:43:03 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25747
 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 10 10:43:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25755
 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 10 10:43:06 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25762
 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 10 10:43:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25766
 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 10 10:43:02 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25773
 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 10 10:43:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25780
 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 10 10:43:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25788
 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 10 10:43:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25794
 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 10 10:43:05 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25803
 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 10 10:43:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25809
 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 10 10:43:05 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25816
 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 10 10:43:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25822
 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 10 10:43:05 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25828
 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 10 10:43:18 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25834
 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 10 10:43:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25842
 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 10 10:43:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25848
 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 10 10:43:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25853
 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 10 10:43:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25857
 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 10 10:43:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25861
 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 10 10:43:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25865
 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 10 10:43:36 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25870
 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 10 10:43:36 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25875
 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 10 10:43:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25878
 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 10 10:43:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 25881
 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 10 10:43:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15911
 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 10 10:43:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15914
 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 10 10:43:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15917
 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 10 10:43:39 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15921
 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 10 10:43:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15924
 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 10 10:43:36 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15927
 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 10 10:43:36 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15929
 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 10 10:43:37 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15933
 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 10 10:43:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15938
 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 10 10:43:36 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15941
 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 10 10:43:36 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15944
 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 10 10:43:37 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15947
 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 10 10:43:40 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15951
 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 10 10:43:40 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15954
 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 10 10:43:46 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15961
 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 10 10:43:39 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15964
 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 10 10:43:44 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15968
 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 10 10:43:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15971
 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 10 10:43:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15974
 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 10 10:43:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15978
 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 10 10:43:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15981
 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 10 10:43:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15984
 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 10 10:43:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15988
 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 10 10:43:53 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15990
 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 10 10:44:00 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 15995
 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 10 10:44:02 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16000
 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 10 10:44:01 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16002
 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 10 10:44:08 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16005
 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 10 10:44:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16009
 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 10 10:44:07 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16012
 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 10 10:44:08 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16016
 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 10 10:44:05 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16018
 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 10 10:44:08 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16022
 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 10 10:44:07 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16025
 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 10 10:44:32 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16028
 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 10 10:44:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16031
 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 10 10:44:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16035
 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 10 10:44:37 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16038
 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 10 10:44:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16042
 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 10 10:44:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16044
 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 10 10:44:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16048
 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 10 10:44:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16051
 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 10 10:44:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16054
 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 10 10:44:33 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16057
 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 10 10:44:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16060
 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 10 10:44:31 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16063
 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 10 10:44:30 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16066
 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 10 10:44:34 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16069
 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 10 10:44:34 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16072
 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 10 10:44:34 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16075
 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 10 10:44:46 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16079
 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 10 10:44:51 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16082
 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 10 10:44:44 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16084
 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 10 10:44:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16088
 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 10 10:44:43 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16092
 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 10 10:44:48 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16094
 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 10 10:44:52 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16098
 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 10 10:44:52 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16102
 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 10 10:44:53 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16106
 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 10 10:44:50 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16110
 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 10 10:44:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16113
 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 10 10:44:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16116
 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 10 10:44:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16119
 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 10 10:44:50 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16122
 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 10 10:44:50 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16125
 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 10 10:44:49 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16129
 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 10 10:45:03 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16132
 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 10 10:44:59 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16137
 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 10 10:45:01 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16139
 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 10 10:45:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16142
 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 10 10:45:10 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16146
 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 10 10:45:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16150
 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 10 10:45:12 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16152
 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 10 10:45:10 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16154
 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 10 10:45:11 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16158
 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 10 10:45:10 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16160
 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 10 10:45:10 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16163
 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 10 10:45:15 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16167
 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 10 10:45:38 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16171
 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 10 10:45:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16173
 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 10 10:45:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16177
 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 10 10:45:38 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16180
 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 10 10:45:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16183
 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 10 10:45:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16187
 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 10 10:45:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16190
 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 10 10:45:42 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16193
 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 10 10:45:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16196
 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 10 10:45:36 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16200
 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 10 10:45:37 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16203
 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 10 10:45:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16206
 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 10 10:45:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16209
 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 10 10:45:35 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16210
 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 10 10:45:36 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16213
 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 10 10:45:36 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16216
 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 10 10:45:37 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16220
 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 10 10:45:42 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16223
 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 10 10:45:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16228
 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 10 10:45:41 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16231
 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 10 10:45:46 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16235
 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 10 10:45:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16237
 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 10 10:45:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16240
 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 10 10:45:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16244
 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 10 10:45:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16247
 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 10 10:45:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16250
 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 10 10:45:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16254
 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 10 10:45:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16257
 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 10 10:45:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16260
 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 10 10:45:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16263
 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 10 10:45:55 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16266
 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 10 10:45:57 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16269
 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 10 10:46:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16273
 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 10 10:46:04 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16277
 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 10 10:46:05 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16280
 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 10 10:46:08 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16284
 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
==> scatter.0000000004.tries <==
1
==> scatter.0000000005.tries <==
1
==> scatter.0000000006.tries <==
1
==> scatter.0000000007.tries <==
1
==> scatter.0000000008.tries <==
1
==> scatter.0000000009.tries <==
1
==> scatter.0000000010.tries <==
1
==> scatter.0000000011.tries <==
1
==> scatter.0000000012.tries <==
1
==> scatter.0000000013.tries <==
1
==> scatter.0000000014.tries <==
1
==> scatter.0000000015.tries <==
1
==> scatter.0000000016.tries <==
1
==> scatter.0000000017.tries <==
1
==> scatter.0000000018.tries <==
1
==> scatter.0000000019.tries <==
1
==> scatter.0000000020.tries <==
1
==> scatter.0000000021.tries <==
1
==> scatter.0000000022.tries <==
1
==> scatter.0000000023.tries <==
1
==> scatter.0000000024.tries <==
1
==> scatter.0000000025.tries <==
1
==> scatter.0000000026.tries <==
1
==> scatter.0000000027.tries <==
1
==> scatter.0000000028.tries <==
1
==> scatter.0000000029.tries <==
1
==> scatter.0000000030.tries <==
1
==> scatter.0000000031.tries <==
1
==> scatter.0000000032.tries <==
1
==> scatter.0000000033.tries <==
1
==> scatter.0000000034.tries <==
1
==> scatter.0000000035.tries <==
1
==> scatter.0000000036.tries <==
1
==> scatter.0000000037.tries <==
1
==> scatter.0000000038.tries <==
1
==> scatter.0000000039.tries <==
1
==> scatter.0000000040.tries <==
1
==> scatter.0000000041.tries <==
1
==> scatter.0000000042.tries <==
1
==> scatter.0000000043.tries <==
1
==> scatter.0000000044.tries <==
1
==> scatter.0000000045.tries <==
1
==> scatter.0000000046.tries <==
1
==> scatter.0000000047.tries <==
1
==> scatter.0000000048.tries <==
1
==> scatter.0000000049.tries <==
1
==> scatter.0000000050.tries <==
1
==> scatter.0000000051.tries <==
1
==> scatter.0000000052.tries <==
1
==> scatter.0000000053.tries <==
1
==> scatter.0000000054.tries <==
1
==> scatter.0000000055.tries <==
1
==> scatter.0000000056.tries <==
1
==> scatter.0000000057.tries <==
1
==> scatter.0000000058.tries <==
1
==> scatter.0000000059.tries <==
1
==> scatter.0000000060.tries <==
1
==> scatter.0000000061.tries <==
1
==> scatter.0000000062.tries <==
1
==> scatter.0000000063.tries <==
1
==> scatter.0000000064.tries <==
1
==> scatter.0000000065.tries <==
1
==> scatter.0000000066.tries <==
1
==> scatter.0000000067.tries <==
1
==> scatter.0000000068.tries <==
1
==> scatter.0000000069.tries <==
1
==> scatter.0000000070.tries <==
1
==> scatter.0000000071.tries <==
1
==> scatter.0000000072.tries <==
1
==> scatter.0000000073.tries <==
1
==> scatter.0000000074.tries <==
1
==> scatter.0000000075.tries <==
1
==> scatter.0000000076.tries <==
1
==> scatter.0000000077.tries <==
1
==> scatter.0000000078.tries <==
1
==> scatter.0000000079.tries <==
1
==> scatter.0000000080.tries <==
1
==> scatter.0000000081.tries <==
1
==> scatter.0000000082.tries <==
1
==> scatter.0000000083.tries <==
1
==> scatter.0000000084.tries <==
1
==> scatter.0000000085.tries <==
1
==> scatter.0000000086.tries <==
1
==> scatter.0000000087.tries <==
1
==> scatter.0000000088.tries <==
1
==> scatter.0000000089.tries <==
1
==> scatter.0000000090.tries <==
1
==> scatter.0000000091.tries <==
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
==> scatter.0000000139.tries <==
1
==> scatter.0000000140.tries <==
1
==> scatter.0000000141.tries <==
1
==> scatter.0000000142.tries <==
1
==> scatter.0000000143.tries <==
1
==> scatter.0000000144.tries <==
1
==> scatter.0000000145.tries <==
1
==> scatter.0000000146.tries <==
1
==> scatter.0000000147.tries <==
1
==> scatter.0000000148.tries <==
1
==> scatter.0000000149.tries <==
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 <==
1
==> 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 10 14:11:14 2012
 vncext:      VNC extension running!
 vncext:      Listening for VNC connections on port 16288
 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.

